Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2600 (ff0e675117*) started at 2026-07-06T15:48:40.575 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.39s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.27.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.9 [f70d9fcc] + CommonWorldInvalidations v1.1.0 [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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[efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.96s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.4 s ✓ BGEN 7.6 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 24.0 s ✓ MendelIHT 3 dependencies successfully precompiled in 38 seconds. 173 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 71.72s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_vCFQw7/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 v0.25.129 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 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libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/XAng5/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.1s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 9.7s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** 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 = -1589.3465122898476, backtracks = 0, tol = 1.5137242139678555 Iteration 2: loglikelihood = -1422.7362596504822, backtracks = 0, tol = 0.15333145227928494 Iteration 3: loglikelihood = -1413.3722003530497, backtracks = 0, tol = 0.03706882804440865 Iteration 4: loglikelihood = -1413.1126426411583, backtracks = 0, tol = 0.005964561150576908 Iteration 5: loglikelihood = -1413.1045338121285, backtracks = 0, tol = 0.0011442203004944172 Iteration 6: loglikelihood = -1413.104267366633, backtracks = 0, tol = 0.00018253655606455786 Iteration 7: loglikelihood = -1413.1042585347357, backtracks = 0, tol = 3.729241021774614e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06640505790710449 Final loglikelihood: -1413.1042585347357 SNP PVE: 0.8903227983560009 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1004 -0.610377 2 │ 1409 0.749491 3 │ 4740 0.422286 4 │ 4933 -1.6631 5 │ 5620 -0.406496 6 │ 7605 0.644611 7 │ 7732 0.180092 8 │ 8555 0.397956 9 │ 8730 0.831302 10 │ 9233 -1.50772 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0178438Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.5s **** 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 logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.1s **** 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 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 = -1503.797662581288, backtracks = 0, tol = 0.24474860323047143 Iteration 2: loglikelihood = -1412.9996544475841, backtracks = 0, tol = 0.050291637019503364 Iteration 3: loglikelihood = -1384.3637890384157, backtracks = 0, tol = 0.0411807244482058 Iteration 4: loglikelihood = -1362.2479740804597, backtracks = 0, tol = 0.07424265156072657 Iteration 5: loglikelihood = -1355.8682613555907, backtracks = 0, tol = 0.09268721202512203 Iteration 6: loglikelihood = -1346.8408936065505, backtracks = 0, tol = 0.03185797277275027 Iteration 7: loglikelihood = -1345.414866130162, backtracks = 1, tol = 0.013979961902700384 Iteration 8: loglikelihood = -1344.6698525624822, backtracks = 2, tol = 0.008237737448970786 Iteration 9: loglikelihood = -1344.15731248894, backtracks = 2, tol = 0.007928172983674204 Iteration 10: loglikelihood = -1343.8523779847337, backtracks = 2, tol = 0.005967891249927863 Iteration 11: loglikelihood = -1343.6749777216974, backtracks = 2, tol = 0.004599954291389421 Iteration 12: loglikelihood = -1343.5727446952428, backtracks = 2, tol = 0.003555524962115574 Iteration 13: loglikelihood = -1343.5141861937866, backtracks = 2, tol = 0.0027451671602568917 Iteration 14: loglikelihood = -1343.4807909327162, backtracks = 2, tol = 0.0021157015854278054 Iteration 15: loglikelihood = -1343.4618101759893, backtracks = 2, tol = 0.0016162505710164104 Iteration 16: loglikelihood = -1343.4510496862886, backtracks = 2, tol = 0.0012327230123128096 Iteration 17: loglikelihood = -1343.4449613233778, backtracks = 2, tol = 0.000935071110337918 Iteration 18: loglikelihood = -1343.4415215463214, backtracks = 2, tol = 0.0007085550657307154 Iteration 19: loglikelihood = -1343.43958031443, backtracks = 2, tol = 0.0005350711225593577 Iteration 20: loglikelihood = -1343.438485692227, backtracks = 2, tol = 0.000403833164417367 Iteration 21: loglikelihood = -1343.4378688403872, backtracks = 2, tol = 0.00030412344768229846 Iteration 22: loglikelihood = -1343.4375213872174, backtracks = 2, tol = 0.0002289703160217885 Iteration 23: loglikelihood = -1343.4373257455925, backtracks = 2, tol = 0.00017215012596101637 Iteration 24: loglikelihood = -1343.4372156134027, backtracks = 2, tol = 0.000129416503621782 Iteration 25: loglikelihood = -1343.4371536288309, backtracks = 2, tol = 9.720424693822857e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1489.4301437320296, backtracks = 0, tol = 0.2724667073465844 Iteration 2: loglikelihood = -1472.5142059104028, backtracks = 0, tol = 0.13579347671542785 Iteration 3: loglikelihood = -1471.0695967875797, backtracks = 0, tol = 0.11293374636472492 Iteration 4: loglikelihood = -1468.0205664320197, backtracks = 0, tol = 0.1086060064525735 Iteration 5: loglikelihood = -1467.942565244867, backtracks = 1, tol = 0.005236467942412943 Iteration 6: loglikelihood = -1467.9212888663, backtracks = 1, tol = 0.0030608867701273535 Iteration 7: loglikelihood = -1467.9155849383808, backtracks = 1, tol = 0.0016936666133743638 Iteration 8: loglikelihood = -1467.9140600085923, backtracks = 1, tol = 0.000901317582804986 Iteration 9: loglikelihood = -1467.9136488823713, backtracks = 1, tol = 0.0004672918901196653 Iteration 10: loglikelihood = -1467.9135364464046, backtracks = 1, tol = 0.00023782283343213803 Iteration 11: loglikelihood = -1467.9135052181332, backtracks = 1, tol = 0.00011904347667284833 Iteration 12: loglikelihood = -1467.9134964362988, backtracks = 1, tol = 5.838962865172238e-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 = -1920.5321194859587, backtracks = 0, tol = 0.6915792831349489 Iteration 2: loglikelihood = -1500.8215483048173, backtracks = 0, tol = 0.12795254702354728 Iteration 3: loglikelihood = -1402.7123832182917, backtracks = 0, tol = 0.05815417630168832 Iteration 4: loglikelihood = -1394.1697842620135, backtracks = 0, tol = 0.02843319913454376 Iteration 5: loglikelihood = -1393.367543659953, backtracks = 0, tol = 0.0055604770141148546 Iteration 6: loglikelihood = -1393.3480505821283, backtracks = 0, tol = 0.0007815890827905601 Iteration 7: loglikelihood = -1393.3474959415523, backtracks = 0, tol = 0.0001582024950400376 Iteration 8: loglikelihood = -1393.3474795298407, backtracks = 0, tol = 2.2373208141943464e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1571.742835110355, backtracks = 0, tol = 0.47322137403645986 Iteration 2: loglikelihood = -1423.8554805739398, backtracks = 0, tol = 0.08387504070230675 Iteration 3: loglikelihood = -1402.9825927687612, backtracks = 0, tol = 0.03596220225361295 Iteration 4: loglikelihood = -1394.2645562600155, backtracks = 0, tol = 0.030072355803492535 Iteration 5: loglikelihood = -1393.5790954560448, backtracks = 0, tol = 0.004992431185908192 Iteration 6: loglikelihood = -1393.5707295051284, backtracks = 0, tol = 0.0005296252163273303 Iteration 7: loglikelihood = -1393.5705427019036, backtracks = 0, tol = 8.071137842538251e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.9s **** 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 linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1424.0523883862445, backtracks = 0, tol = 0.1521780633954804 Iteration 2: loglikelihood = -1381.8563199982607, backtracks = 0, tol = 0.09661244221359157 Iteration 3: loglikelihood = -1340.0020944594655, backtracks = 0, tol = 0.1366349912241305 Iteration 4: loglikelihood = -1323.8761625476814, backtracks = 0, tol = 0.10650770857719928 Iteration 5: loglikelihood = -1318.9562381829055, backtracks = 0, tol = 0.061230093985847035 Iteration 6: loglikelihood = -1317.9897486211212, backtracks = 0, tol = 0.025616549308342725 Iteration 7: loglikelihood = -1317.6877775260227, backtracks = 0, tol = 0.008074105024318422 Iteration 8: loglikelihood = -1317.5955849808704, backtracks = 0, tol = 0.00770846249310841 Iteration 9: loglikelihood = -1317.5666468280754, backtracks = 0, tol = 0.00249560472238697 Iteration 10: loglikelihood = -1317.5577473259516, backtracks = 0, tol = 0.0023945500647201143 Iteration 11: loglikelihood = -1317.5549579643907, backtracks = 0, tol = 0.0007676217904625842 Iteration 12: loglikelihood = -1317.5540925091855, backtracks = 0, tol = 0.0007509808472087736 Iteration 13: loglikelihood = -1317.5538196043385, backtracks = 0, tol = 0.00023887120830868964 Iteration 14: loglikelihood = -1317.5537340819074, backtracks = 0, tol = 0.00023791425585707935 Iteration 15: loglikelihood = -1317.5537068897343, backtracks = 0, tol = 7.50048615941526e-5 0.799839 seconds (1.45 M allocations: 32.399 MiB, 72.59% 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 = -1463.469527461367, backtracks = 0, tol = 0.1521780633954804 Iteration 2: loglikelihood = -1430.8619740465533, backtracks = 0, tol = 0.09661244221359157 Iteration 3: loglikelihood = -1401.6938822006605, backtracks = 0, tol = 0.13505523855845786 Iteration 4: loglikelihood = -1383.4003294588545, backtracks = 0, tol = 0.10859107965969424 Iteration 5: loglikelihood = -1373.456467705298, backtracks = 0, tol = 0.06314187823053599 Iteration 6: loglikelihood = -1366.0406340470363, backtracks = 0, tol = 0.015438108413279547 Iteration 7: loglikelihood = -1360.3654377482203, backtracks = 0, tol = 0.004550292305140141 Iteration 8: loglikelihood = -1355.597478488918, backtracks = 0, tol = 0.002263245043365736 Iteration 9: loglikelihood = -1351.6682464027933, backtracks = 0, tol = 0.0008784453062322307 Iteration 10: loglikelihood = -1348.3409580286313, backtracks = 0, tol = 0.0005466910032326524 Iteration 11: loglikelihood = -1345.516065802066, backtracks = 0, tol = 0.0004896258708226194 Iteration 12: loglikelihood = -1343.0842011520417, backtracks = 0, tol = 0.00047926925032725035 Iteration 13: loglikelihood = -1340.9771919244365, backtracks = 0, tol = 0.00043199120084314057 Iteration 14: loglikelihood = -1339.1351003167817, backtracks = 0, tol = 0.00040508599278185685 Iteration 15: loglikelihood = -1337.5144318068842, backtracks = 0, tol = 0.0003720140452521673 Iteration 16: loglikelihood = -1336.0790304981495, backtracks = 0, tol = 0.00034697283214505254 Iteration 17: loglikelihood = -1334.8007477335352, backtracks = 0, tol = 0.00032223954336349855 Iteration 18: loglikelihood = -1333.6563611855781, backtracks = 0, tol = 0.00030140842701225756 Iteration 19: loglikelihood = -1332.6270930086393, backtracks = 0, tol = 0.00028204746945168483 Iteration 20: loglikelihood = -1331.6973375987707, backtracks = 0, tol = 0.00026499817742786663 Iteration 21: loglikelihood = -1330.8541720455926, backtracks = 0, tol = 0.0002493904580479496 Iteration 22: loglikelihood = -1330.0867349871617, backtracks = 0, tol = 0.00023534931028025877 Iteration 23: loglikelihood = -1329.385877765158, backtracks = 0, tol = 0.00022250505389672705 Iteration 24: loglikelihood = -1328.74382202816, backtracks = 0, tol = 0.0002108090895456542 Iteration 25: loglikelihood = -1328.1539281445203, backtracks = 0, tol = 0.0002000714341301519 Iteration 26: loglikelihood = -1327.6104903848627, backtracks = 0, tol = 0.00019021418083513196 Iteration 27: loglikelihood = -1327.1085844177046, backtracks = 0, tol = 0.00018112235168924034 Iteration 28: loglikelihood = -1326.6439378170378, backtracks = 0, tol = 0.00017272456536314375 Iteration 29: loglikelihood = -1326.2128284542134, backtracks = 0, tol = 0.0001649429313452415 Iteration 30: loglikelihood = -1325.8119993240048, backtracks = 0, tol = 0.00015771907247579155 Iteration 31: loglikelihood = -1325.4385896158235, backtracks = 0, tol = 0.00015099647042883803 Iteration 32: loglikelihood = -1325.0900769686384, backtracks = 0, tol = 0.00014472880539945858 Iteration 33: loglikelihood = -1324.764229796508, backtracks = 0, tol = 0.00013887334646969999 Iteration 34: loglikelihood = -1324.4590671660992, backtracks = 0, tol = 0.00013339348906002497 Iteration 35: loglikelihood = -1324.1728251964776, backtracks = 0, tol = 0.00012825607158180422 Iteration 36: loglikelihood = -1323.903928595552, backtracks = 0, tol = 0.00012343201355022757 Iteration 37: loglikelihood = -1323.6509665592516, backtracks = 0, tol = 0.000118895105262735 Iteration 38: loglikelihood = -1323.4126722100225, backtracks = 0, tol = 0.00011462204663184331 Iteration 39: loglikelihood = -1323.1879050279742, backtracks = 0, tol = 0.00011059182972302387 Iteration 40: loglikelihood = -1322.9756357571246, backtracks = 0, tol = 0.00010678561142546523 Iteration 41: loglikelihood = -1322.7749334073085, backtracks = 0, tol = 0.00010318635728491167 Iteration 42: loglikelihood = -1322.584954013087, backtracks = 0, tol = 9.977868842133409e-5 0.394659 seconds (1.49 M allocations: 27.071 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 = -3634.5625, backtracks = 0, tol = 0.07796460293928677 Iteration 2: loglikelihood = -3589.5857, backtracks = 0, tol = 0.04494680980133618 Iteration 3: loglikelihood = -3583.7153, backtracks = 1, tol = 0.012391865224899122 Iteration 4: loglikelihood = -3571.4243, backtracks = 1, tol = 0.06303916340111114 Iteration 5: loglikelihood = -3569.0168, backtracks = 1, tol = 0.0076427429561517005 Iteration 6: loglikelihood = -3568.1414, backtracks = 1, tol = 0.0045559032984250816 Iteration 7: loglikelihood = -3567.8743, backtracks = 1, tol = 0.0032220270144862136 Iteration 8: loglikelihood = -3567.7974, backtracks = 1, tol = 0.001872251508657402 Iteration 9: loglikelihood = -3555.368, backtracks = 1, tol = 0.07164493603034645 Iteration 10: loglikelihood = -3553.672, backtracks = 1, tol = 0.007844160795627417 Iteration 11: loglikelihood = -3553.1072, backtracks = 1, tol = 0.00412517726013054 Iteration 12: loglikelihood = -3552.9238, backtracks = 1, tol = 0.0030169362951388123 Iteration 13: loglikelihood = -3548.049, backtracks = 1, tol = 0.07389482822638718 Iteration 14: loglikelihood = -3544.2754, backtracks = 0, tol = 0.08778444897847824 Iteration 15: loglikelihood = -3542.1084, backtracks = 0, tol = 0.012705111057122642 Iteration 16: loglikelihood = -3542.067, backtracks = 0, tol = 0.0016819000221667789 Iteration 17: loglikelihood = -3542.067, backtracks = 0, tol = 0.0002557890134838611 Iteration 18: loglikelihood = -3542.069, backtracks = 3, tol = 2.3589109625010052e-5 25.837864 seconds (16.34 M allocations: 691.721 MiB, 2.41% gc time, 95.73% 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 = -3526.5996, backtracks = 0, tol = 0.07796460293928677 Iteration 2: loglikelihood = -3409.4026, backtracks = 0, tol = 0.04612108337221028 Iteration 3: loglikelihood = -3198.9265, backtracks = 1, tol = 0.012109933775640144 Iteration 4: loglikelihood = -2956.6511, backtracks = 1, tol = 0.008052982712660252 Iteration 5: loglikelihood = -2945.4653, backtracks = 0, tol = 0.10407837700751046 Iteration 6: loglikelihood = -2737.0593, backtracks = 0, tol = 0.10451281766631726 Iteration 7: loglikelihood = -2586.851, backtracks = 0, tol = 0.09634007258369422 Iteration 8: loglikelihood = -2485.9417, backtracks = 0, tol = 0.09633713606274363 Iteration 9: loglikelihood = -2370.248, backtracks = 0, tol = 0.09517971884844541 Iteration 10: loglikelihood = -2322.3804, backtracks = 0, tol = 0.10707649292282408 Iteration 11: loglikelihood = -2238.9304, backtracks = 0, tol = 0.10703229036231417 Iteration 12: loglikelihood = -2212.462, backtracks = 0, tol = 0.11104392933923823 Iteration 13: loglikelihood = -2203.6233, backtracks = 0, tol = 0.11565536057760194 Iteration 14: loglikelihood = -2193.4639, backtracks = 0, tol = 0.11515063136421146 Iteration 15: loglikelihood = -2180.1653, backtracks = 0, tol = 0.11761754163453302 Iteration 16: loglikelihood = -2164.4604, backtracks = 1, tol = 0.03471097894810149 Iteration 17: loglikelihood = -2154.2078, backtracks = 1, tol = 0.06806408037503553 Iteration 18: loglikelihood = -2151.8813, backtracks = 1, tol = 0.029511314447137806 Iteration 19: loglikelihood = -2151.2637, backtracks = 1, tol = 0.015356345635833971 Iteration 20: loglikelihood = -2151.085, backtracks = 1, tol = 0.008041904692501175 Iteration 21: loglikelihood = -2151.0276, backtracks = 1, tol = 0.004196450538792673 Iteration 22: loglikelihood = -2151.0115, backtracks = 1, tol = 0.0021919488990604146 Iteration 23: loglikelihood = -2151.0056, backtracks = 1, tol = 0.0011488906696283444 Iteration 24: loglikelihood = -2151.004, backtracks = 1, tol = 0.0006040437361205448 Iteration 25: loglikelihood = -2151.0034, backtracks = 1, tol = 0.00031827031319699454 Iteration 26: loglikelihood = -2151.0032, backtracks = 1, tol = 0.00016800481758376854 Iteration 27: loglikelihood = -2150.9932, backtracks = 2, tol = 4.444590004965917e-5 0.238145 seconds (1.60 M allocations: 26.502 MiB, 9.56% gc time) 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.576688 seconds (1.03 M allocations: 133.661 MiB, 0.81% gc time, 91.47% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 6.0s 10.890245 seconds (4.00 M allocations: 82.396 MiB, 0.90% gc time, 0.72% compilation time) 5.326124 seconds (3.98 M allocations: 91.674 MiB, 0.14% gc time) 10.697040 seconds (20.38 M allocations: 438.626 MiB, 1.11% gc time, 16.37% compilation time: 77% of which was recompilation) 8.608269 seconds (20.18 M allocations: 434.186 MiB, 1.25% gc time) 37.076049 seconds (3.40 M allocations: 4.230 GiB, 6.41% gc time, 28.76% compilation time) 55.276761 seconds (72.53 k allocations: 183.668 MiB, 0.15% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m26.0s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 15.044 ms (78 allocations: 4.56 KiB) 4.499 μs (0 allocations: 0 bytes) 171.009 μs (4 allocations: 288 bytes) 6.840 μs (0 allocations: 0 bytes) 49.860 μs (2 allocations: 64 bytes) 31.060 μs (0 allocations: 0 bytes) 25.590 μs (0 allocations: 0 bytes) 30.129 μs (0 allocations: 0 bytes) 111.819 μs (0 allocations: 0 bytes) 39.772 ms (78 allocations: 4.56 KiB) 18.439 μs (0 allocations: 0 bytes) 196.568 μs (4 allocations: 288 bytes) 34.980 μs (0 allocations: 0 bytes) 262.868 μs (2 allocations: 64 bytes) 83.249 μs (0 allocations: 0 bytes) 126.409 μs (0 allocations: 0 bytes) 152.608 μs (0 allocations: 0 bytes) 214.148 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m11.3s **** 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 0.436079 seconds (44.31 k allocations: 5.347 MiB, 63.78% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.039111 seconds (258.63 k allocations: 167.866 MiB, 57.32% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:53 Cross validating... 13%|████▏ | ETA: 0:00:57 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:23 Cross validating... 32%|██████████▏ | ETA: 0:00:20 Cross validating... 35%|███████████▏ | ETA: 0:00:17 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:14 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross 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100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 3007.9088779034664 1 2003.9412229082313 2 1229.7998982978886 3 979.4317885703621 4 783.6840364737707 5 663.3199332413842 6 522.7723457105153 7 465.8941710168016 8 408.56641145733477 9 340.3761410269075 10 340.39822295570104 11 344.8998834829987 12 348.4758635129774 13 358.9888039240347 14 353.8950775888096 15 354.37589075531514 16 353.91079128710044 17 366.72627641248573 18 362.60407220528015 19 384.4531108837786 20 365.5226103544328 Best k = 9 12.668689 seconds (11.31 M allocations: 304.304 MiB, 0.87% gc time, 62.23% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 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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: 0:00:01 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: 0:00:04 Crossvalidation Results: k MSE 0 3007.9088779034664 1 2005.4122334174745 2 1231.3960409284277 3 984.1151300154149 4 791.250721220464 5 668.1775324279974 6 525.0335293217959 7 469.2629911341966 8 412.1003173283489 9 344.17005836443036 10 347.2804140173748 11 358.28469930865947 12 367.22721918411037 13 374.227341247601 14 383.03260301594094 15 384.73221203565697 16 391.82164916056763 17 398.0449983617372 18 406.60689502937123 19 400.923275403626 20 429.1638927415088 Best k = 9 4.989432 seconds (10.63 M allocations: 224.281 MiB, 1.07% gc time, 1.29% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:49 Cross validating... 8%|██▌ | ETA: 0:02:14 Cross validating... 13%|████▏ | ETA: 0:01:20 Cross validating... 17%|█████▋ | ETA: 0:00:56 Cross validating... 22%|███████▏ | ETA: 0:00:42 Cross validating... 27%|████████▋ | ETA: 0:00:33 Cross validating... 32%|██████████▏ | ETA: 0:00:26 Cross validating... 37%|███████████▋ | ETA: 0:00:21 Cross validating... 41%|█████████████▎ | ETA: 0:00:18 Cross validating... 46%|██████████████▊ | ETA: 0:00:15 Cross validating... 51%|████████████████▎ | ETA: 0:00:12 Cross validating... 56%|█████████████████▊ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 1661.0757749023437 1 1335.8947655029297 2 1117.5862526855467 3 864.2915620117187 4 673.4905548095703 5 531.8945846557617 6 455.88695220947267 7 391.5362918395996 8 356.8446892089844 9 337.7342290039063 10 340.1342070922851 11 340.0165564575195 12 346.60980319213866 13 346.6086923522949 14 356.9530812988281 15 362.3973127441406 16 354.25289968872073 17 364.49552416992185 18 353.6857726135254 19 356.2389190979004 20 374.5070723571777 Best k = 9 15.215532 seconds (12.27 M allocations: 307.861 MiB, 0.50% gc time, 82.92% 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... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross 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Results: k MSE 0 1661.0757749023437 1 1335.8997745361328 2 1117.9063514404297 3 865.1535421142578 4 673.8246612548828 5 531.8946071166993 6 458.0076543273926 7 392.7585544433594 8 361.20218029785156 9 343.6153556213379 10 350.0499942321777 11 358.64422933959963 12 365.4105089416504 13 366.780720123291 14 374.516338104248 15 381.93580767822266 16 386.5892923278809 17 389.7851381225586 18 393.50623727416996 19 403.39968301391605 20 429.2604931640625 Best k = 9 2.750615 seconds (10.74 M allocations: 197.155 MiB, 2.82% gc time, 1.74% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:31 Cross 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0 462.41426837688994 1 406.31621113875724 2 330.5590765811436 3 316.36428441397055 4 299.0083597288449 5 289.13024410428653 6 277.1589719445077 7 259.84092975033224 8 234.56221732431442 9 237.45372224346076 10 240.44179087839797 11 239.55928867692637 12 250.57509910661875 13 257.98010800107534 14 250.7991125470337 15 243.46326198953102 16 263.8403993312995 17 250.05527093968308 18 256.37787413405124 19 286.4822318952902 20 270.8542506870888 Best k = 8 8.451188 seconds (17.57 M allocations: 419.149 MiB, 1.02% gc time, 30.87% 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... 5%|█▌ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:05 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | 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... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.41426837688994 1 406.5310729810575 2 331.34935118286677 3 322.4784466222405 4 300.29139438201275 5 291.47815153407095 6 279.323670719756 7 262.4381892745705 8 239.69512554489484 9 248.50295742714596 10 250.52172759332387 11 257.87081301976633 12 268.80293765181204 13 270.82739502450863 14 262.6191855136969 15 283.84144449394034 16 286.60836787809603 17 302.24990782804315 18 293.0465178800366 19 315.847635973677 20 304.7245524528428 Best k = 8 6.083001 seconds (17.70 M allocations: 366.693 MiB, 1.71% gc time, 1.26% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.0s **** 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: 0:00:49 Cross validating... 6%|██ | ETA: 0:00:26 Cross validating... 10%|███ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:12 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.8396328756268 1 448.62591001303747 2 414.4948328935907 3 375.5159711335647 4 332.10661951494967 5 325.2610173523826 6 313.0050082021895 7 310.07447160421714 8 314.70765714492086 9 310.7996962491833 10 321.2951810911641 11 319.7875414358952 12 316.89923750104225 13 330.66646257749983 14 308.3283644600542 15 329.0923545628534 16 322.05655500638125 17 328.2276692967668 18 325.8270022871593 19 332.9907690154759 20 364.08309608207315 Best k = 14 7.304563 seconds (16.45 M allocations: 390.766 MiB, 7.64% gc time, 37.54% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 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: 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validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 464.8396328756268 1 451.5589862390693 2 409.25155170189726 3 378.859588554727 4 335.24941715900786 5 329.54032374761164 6 317.49312223338023 7 318.3547515725516 8 328.66753055235125 9 330.0549111558055 10 339.6492724863148 11 338.1508661528439 12 346.4036258102497 13 359.15486603086083 14 349.64990765778487 15 364.2599926977099 16 363.7205207172167 17 378.53329602368524 18 383.623592144127 19 392.44318486984116 20 403.5499663973899 Best k = 6 4.408673 seconds (17.48 M allocations: 360.766 MiB, 1.41% gc time, 1.14% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:11 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 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100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 607.9132296009284 1 559.4695407507439 2 485.4862310885743 3 453.62151246922735 4 416.2530729585039 5 406.0287421176926 6 414.1332132659578 7 409.7760729696015 8 401.8696786323891 9 404.29230267878734 10 404.22818865419606 11 406.75489105598547 12 410.742378367061 13 409.4687863932568 14 402.0095741446643 15 410.8974837519818 16 401.3052365812078 17 421.43422481742755 18 407.7968813614512 19 425.42415829745636 20 429.11619017006524 Best k = 16 8.449594 seconds (16.43 M allocations: 402.752 MiB, 1.48% gc time, 32.15% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 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... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 607.9132296009284 1 553.0027754281646 2 482.1861269273565 3 456.30047589423066 4 418.9035587206427 5 410.90502643642543 6 423.59738113904666 7 426.6230389820504 8 424.1786519495064 9 431.05176520044006 10 430.6606983066861 11 447.64167253603034 12 450.45590520722874 13 451.08589698392547 14 441.2210861668847 15 434.2255405262864 16 456.78188439621636 17 441.0766142439312 18 445.2067867642256 19 460.37016071266123 20 445.37884558396615 Best k = 5 5.836047 seconds (15.44 M allocations: 319.211 MiB, 1.08% gc time, 1.22% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 5%|█▌ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:01:01 Cross validating... 8%|██▌ | ETA: 0:00:49 Cross validating... 10%|███ | ETA: 0:00:50 Cross validating... 11%|███▌ | ETA: 0:00:51 Cross validating... 13%|████▏ | ETA: 0:00:50 Cross validating... 16%|█████▏ | ETA: 0:00:40 Cross validating... 17%|█████▋ | ETA: 0:00:36 Cross validating... 19%|██████▏ | ETA: 0:00:33 Cross validating... 21%|██████▋ | ETA: 0:00:31 Cross validating... 22%|███████▏ | ETA: 0:00:32 Cross validating... 24%|███████▋ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:31 Cross validating... 27%|████████▋ | ETA: 0:00:31 Cross validating... 29%|█████████▏ | ETA: 0:00:32 Cross validating... 30%|█████████▋ | ETA: 0:00:30 Cross validating... 32%|██████████▏ | ETA: 0:00:30 Cross validating... 33%|██████████▋ | ETA: 0:00:30 Cross validating... 37%|███████████▋ | ETA: 0:00:26 Cross validating... 40%|████████████▊ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:22 Cross validating... 43%|█████████████▊ | ETA: 0:00:21 Cross validating... 44%|██████████████▎ | ETA: 0:00:20 Cross validating... 46%|██████████████▊ | ETA: 0:00:19 Cross validating... 48%|███████████████▎ | ETA: 0:00:18 Cross 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78%|████████████████████████▉ | ETA: 0:00:08 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:08 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:07 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:05 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:38 Crossvalidation Results: k MSE 0 299.67444081677905 1 266.5777820858076 2 244.0148676201378 3 237.14592115504044 4 233.0366843568803 5 224.77206013320597 6 223.5430749927296 7 222.31145500492926 8 221.24555588118795 9 218.97537243095422 10 225.45952184039874 11 221.43393176107298 12 224.8051363251151 13 223.88562488293147 14 222.77952292614236 15 225.6759294747651 16 225.34512476340652 17 225.7568410714203 18 227.0029240844038 19 226.85465245943567 20 231.02163100068367 Best k = 9 38.873305 seconds (116.47 M allocations: 2.972 GiB, 1.27% gc time, 6.09% 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: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross 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validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 299.67444081677905 1 266.2999625240721 2 244.68260415859197 3 238.12903471670867 4 234.4265394512407 5 226.28583931050866 6 222.43362689631263 7 227.48752357584954 8 225.66270323802104 9 227.83579374783096 10 237.56920769600754 11 239.91783880774892 12 242.14782423633613 13 249.6760357754552 14 240.08441717678917 15 249.7718353815166 16 247.8330324403584 17 249.17843389428458 18 254.5072224424331 19 256.23367252496547 20 261.44278511559367 Best k = 6 11.425227 seconds (33.38 M allocations: 689.897 MiB, 1.38% gc time, 0.77% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 50.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:06 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 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211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 6.439159 seconds (17.22 M allocations: 343.618 MiB, 2.08% gc time, 43.61% 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... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 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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 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 3.398838 seconds (16.26 M allocations: 288.223 MiB, 1.66% gc time, 2.07% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:16 Cross validating... 3%|█ | ETA: 0:00:56 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: 0:00:27 Cross validating... 10%|███▎ | ETA: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:24 Cross validating... 12%|███▉ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:23 Cross validating... 14%|████▌ | ETA: 0:00:22 Cross validating... 15%|████▊ | ETA: 0:00:21 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▌ | ETA: 0:00:20 Cross validating... 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0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 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: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 4007.6961107086513 2 3630.0937009789372 3 3171.449265930104 4 2839.2622170243726 5 2327.307964940678 6 2149.865285923241 7 2081.002709395839 8 2096.4042109846523 9 2109.819532623031 10 2121.4140208046424 11 2119.8903004511253 12 2142.231739871137 13 2146.9470016143555 14 2164.2631966988197 15 2211.7860208840216 16 2206.997593601395 17 2211.9580162923994 18 2256.490667859762 19 2248.7523639906826 20 2236.566693671765 Best k = 7 18.740594 seconds (321.71 k allocations: 244.003 MiB, 0.35% gc time, 8.52% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m01.5s **** 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... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 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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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | 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2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross 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97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m27.4s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Core.TypeEgal{Float64}, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Core.TypeEgal{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:533 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.7s RNG of the outermost testset: Xoshiro(0x88a28afbd16eac95, 0x7361e0deb245a58d, 0xfa0fe958aeb8a01f, 0xeaaae767a43f159b, 0x2fc41028cf945514) 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 1099.35s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1224.4s: package tests unexpectedly errored