Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1886 (984ad247db*) started at 2026-03-12T22:39:21.738 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.09s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.5.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.23.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [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 To see why use `status --outdated -m` Installation completed after 6.05s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4607.4 ms ✓ BGEN 7769.7 ms ✓ VCFTools 28098.3 ms ✓ 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`. 25375.7 ms ✓ MendelIHT 4 dependencies successfully precompiled in 70 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 91.08s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_wVaMr6/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.1 [2913bbd2] StatsBase v0.34.10 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v1.68.0+1 [3f19e933] p7zip_jll v17.8.0+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 22.3s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.3s 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 1.3s 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 = -1717.139409850963, backtracks = 0, tol = 1.348852065786079 Iteration 2: loglikelihood = -1470.658167890157, backtracks = 0, tol = 0.183066054657732 Iteration 3: loglikelihood = -1452.3931027459944, backtracks = 0, tol = 0.05541231946029764 Iteration 4: loglikelihood = -1452.0747941271643, backtracks = 0, tol = 0.007796301445816671 Iteration 5: loglikelihood = -1452.0667661293878, backtracks = 0, tol = 0.0011782837457879796 Iteration 6: loglikelihood = -1452.0665536899153, backtracks = 0, tol = 0.00017732611118201978 Iteration 7: loglikelihood = -1452.06654800222, backtracks = 0, tol = 3.0126873227216548e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.0637359619140625 Final loglikelihood: -1452.06654800222 SNP PVE: 0.8953608425166717 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 916 0.438739 2 │ 2195 -0.253587 3 │ 3349 -0.779469 4 │ 3461 1.18657 5 │ 6839 -0.963678 6 │ 7031 -1.54861 7 │ 7773 -0.261115 8 │ 8079 -1.42599 9 │ 8092 0.323667 10 │ 8160 1.14343 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0110296Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1481.7990725048237, backtracks = 0, tol = 0.2542464630667851 Iteration 2: loglikelihood = -1375.27972302846, backtracks = 0, tol = 0.06329438883331245 Iteration 3: loglikelihood = -1343.2772690010834, backtracks = 0, tol = 0.07391652183693138 Iteration 4: loglikelihood = -1338.831704570702, backtracks = 0, tol = 0.07570729597473853 Iteration 5: loglikelihood = -1320.054983486481, backtracks = 0, tol = 0.03599563853184222 Iteration 6: loglikelihood = -1311.7489588227804, backtracks = 1, tol = 0.06102170619933342 Iteration 7: loglikelihood = -1305.8288232481264, backtracks = 0, tol = 0.07739910967315697 Iteration 8: loglikelihood = -1301.7355107812518, backtracks = 0, tol = 0.0684806548187055 Iteration 9: loglikelihood = -1300.4878345363152, backtracks = 0, tol = 0.014136328008999043 Iteration 10: loglikelihood = -1299.8972669059374, backtracks = 0, tol = 0.013448123628967487 Iteration 11: loglikelihood = -1299.4950548051743, backtracks = 0, tol = 0.01177877595377329 Iteration 12: loglikelihood = -1299.217884207761, backtracks = 0, tol = 0.008308258403122371 Iteration 13: loglikelihood = -1299.0655726275718, backtracks = 1, tol = 0.004644794091672574 Iteration 14: loglikelihood = -1298.9515107948355, backtracks = 3, tol = 0.004181241618641764 Iteration 15: loglikelihood = -1298.8422426074007, backtracks = 3, tol = 0.004728886740078604 Iteration 16: loglikelihood = -1298.7534196554393, backtracks = 3, tol = 0.004332006124195264 Iteration 17: loglikelihood = -1298.682488319802, backtracks = 3, tol = 0.004006071185555147 Iteration 18: loglikelihood = -1298.6263667319993, backtracks = 3, tol = 0.003587019284928824 Iteration 19: loglikelihood = -1298.58221977914, backtracks = 3, tol = 0.0032500236296605267 Iteration 20: loglikelihood = -1298.5476432862317, backtracks = 3, tol = 0.002880397310097436 Iteration 21: loglikelihood = -1298.5206488620327, backtracks = 3, tol = 0.002585409266218561 Iteration 22: loglikelihood = -1298.4996308058257, backtracks = 3, tol = 0.0022757327914140297 Iteration 23: loglikelihood = -1298.4833008507426, backtracks = 3, tol = 0.0020328572773361015 Iteration 24: loglikelihood = -1298.4706382708478, backtracks = 3, tol = 0.001778960199157444 Iteration 25: loglikelihood = -1298.4608353895978, backtracks = 3, tol = 0.0015852456729768022 Iteration 26: loglikelihood = -1298.4532584388978, backtracks = 3, tol = 0.0013787273929277623 Iteration 27: loglikelihood = -1298.4474095223243, backtracks = 3, tol = 0.001227411173257757 Iteration 28: loglikelihood = -1298.4428998832952, backtracks = 3, tol = 0.0010598780198943524 Iteration 29: loglikelihood = -1298.4394249988782, backtracks = 3, tol = 0.0009439859607821806 Iteration 30: loglikelihood = -1298.4367475573974, backtracks = 3, tol = 0.0008092145983245799 Iteration 31: loglikelihood = -1298.4346821089073, backtracks = 3, tol = 0.0007230311204775039 Iteration 32: loglikelihood = -1298.4330851099637, backtracks = 3, tol = 0.0006172542409551118 Iteration 33: loglikelihood = -1298.431845890002, backtracks = 3, tol = 0.000555541962310754 Iteration 34: loglikelihood = -1298.4308804725779, backtracks = 3, tol = 0.00047476483550836597 Iteration 35: loglikelihood = -1298.4301253401914, backtracks = 3, tol = 0.0004310556278020187 Iteration 36: loglikelihood = -1298.429532781954, backtracks = 3, tol = 0.0003695199686846296 Iteration 37: loglikelihood = -1298.4290665902968, backtracks = 3, tol = 0.0003375890626016046 Iteration 38: loglikelihood = -1298.4286991788472, backtracks = 3, tol = 0.0002899994796465524 Iteration 39: loglikelihood = -1298.4284092308135, backtracks = 3, tol = 0.0002658091882288503 Iteration 40: loglikelihood = -1298.4281802211988, backtracks = 3, tol = 0.0002285494490296841 Iteration 41: loglikelihood = -1298.4279992139432, backtracks = 3, tol = 0.00020983576265691452 Iteration 42: loglikelihood = -1298.4278560824418, backtracks = 3, tol = 0.00018048923058881517 Iteration 43: loglikelihood = -1298.4277428514163, backtracks = 3, tol = 0.00016587199191237507 Iteration 44: loglikelihood = -1298.4276532488752, backtracks = 3, tol = 0.00014269785601135772 Iteration 45: loglikelihood = -1298.4275823222647, backtracks = 3, tol = 0.0001312268856906164 Iteration 46: loglikelihood = -1298.4275261674966, backtracks = 3, tol = 0.00011290351031120149 Iteration 47: loglikelihood = -1298.4274816977559, backtracks = 3, tol = 0.00010387729309602217 Iteration 48: loglikelihood = -1298.427446476155, backtracks = 3, tol = 8.93782552122183e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1516.2137723466951, backtracks = 0, tol = 0.28012403218291154 Iteration 2: loglikelihood = -1475.6737075264593, backtracks = 0, tol = 0.1623163222519217 Iteration 3: loglikelihood = -1464.500215496699, backtracks = 0, tol = 0.12101426301594473 Iteration 4: loglikelihood = -1460.8065452168603, backtracks = 0, tol = 0.1064768274092872 Iteration 5: loglikelihood = -1460.5278894555736, backtracks = 1, tol = 0.009126122911932195 Iteration 6: loglikelihood = -1460.3895679490854, backtracks = 1, tol = 0.010083586581448794 Iteration 7: loglikelihood = -1460.3529175623198, backtracks = 2, tol = 0.00434604107524135 Iteration 8: loglikelihood = -1460.3311347944932, backtracks = 2, tol = 0.0035075192229853214 Iteration 9: loglikelihood = -1460.3185729388276, backtracks = 2, tol = 0.0027119891357688867 Iteration 10: loglikelihood = -1460.3114064519457, backtracks = 2, tol = 0.002068484015153559 Iteration 11: loglikelihood = -1460.3073469538926, backtracks = 2, tol = 0.0015676219925329286 Iteration 12: loglikelihood = -1460.305058880229, backtracks = 2, tol = 0.001182988845579334 Iteration 13: loglikelihood = -1460.3037739055649, backtracks = 2, tol = 0.0008899965880944052 Iteration 14: loglikelihood = -1460.3030541986195, backtracks = 2, tol = 0.0006680473293195798 Iteration 15: loglikelihood = -1460.3026518997435, backtracks = 2, tol = 0.0005005912768084969 Iteration 16: loglikelihood = -1460.3024273604829, backtracks = 2, tol = 0.00037462715414427454 Iteration 17: loglikelihood = -1460.302302176395, backtracks = 2, tol = 0.0002800868715003917 Iteration 18: loglikelihood = -1460.3022324428896, backtracks = 2, tol = 0.00020925108616260635 Iteration 19: loglikelihood = -1460.3021936223954, backtracks = 2, tol = 0.00015624376199823497 Iteration 20: loglikelihood = -1460.3021720212698, backtracks = 2, tol = 0.00011661567267081951 Iteration 21: loglikelihood = -1460.3021600058537, backtracks = 2, tol = 8.701119081609931e-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 = -1864.72116739123, backtracks = 0, tol = 0.7707649458218436 Iteration 2: loglikelihood = -1518.7893335350097, backtracks = 0, tol = 0.11644420020658132 Iteration 3: loglikelihood = -1436.6760313689488, backtracks = 0, tol = 0.04722854863539535 Iteration 4: loglikelihood = -1435.238768396918, backtracks = 0, tol = 0.006768944458926678 Iteration 5: loglikelihood = -1434.9765816255638, backtracks = 0, tol = 0.03056437014908455 Iteration 6: loglikelihood = -1434.815007434965, backtracks = 0, tol = 0.00273057311083191 Iteration 7: loglikelihood = -1434.8123959087425, backtracks = 0, tol = 0.0003380203420607402 Iteration 8: loglikelihood = -1434.812325341534, backtracks = 0, tol = 5.088099200450762e-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 = -1647.7145903505611, backtracks = 0, tol = 0.40034024369648424 Iteration 2: loglikelihood = -1456.9225867713328, backtracks = 0, tol = 0.09537356521985 Iteration 3: loglikelihood = -1438.2313299789375, backtracks = 0, tol = 0.040788766786337104 Iteration 4: loglikelihood = -1436.08467643751, backtracks = 0, tol = 0.033685036759399045 Iteration 5: loglikelihood = -1435.88674423666, backtracks = 0, tol = 0.0020536616068039496 Iteration 6: loglikelihood = -1435.239702417235, backtracks = 0, tol = 0.033563454620939494 Iteration 7: loglikelihood = -1435.1702035707342, backtracks = 1, tol = 0.0012051297297082457 Iteration 8: loglikelihood = -1435.1516841780422, backtracks = 1, tol = 0.000624989824794841 Iteration 9: loglikelihood = -1435.1468057493419, backtracks = 1, tol = 0.00031814543408863855 Iteration 10: loglikelihood = -1435.145540561263, backtracks = 1, tol = 0.0001594598656910236 Iteration 11: loglikelihood = -1435.1452169898564, backtracks = 1, tol = 7.925823865855756e-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 10.7s **** 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 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 = -1464.0807925113106, backtracks = 0, tol = 0.2080075275073403 Iteration 2: loglikelihood = -1417.5923291330794, backtracks = 0, tol = 0.12289455022074795 Iteration 3: loglikelihood = -1383.880614782477, backtracks = 0, tol = 0.1175163277906479 Iteration 4: loglikelihood = -1373.9563924452616, backtracks = 0, tol = 0.1036403193696849 Iteration 5: loglikelihood = -1372.6250989372525, backtracks = 0, tol = 0.014933157367936012 Iteration 6: loglikelihood = -1372.2770883321978, backtracks = 0, tol = 0.016029045215169256 Iteration 7: loglikelihood = -1372.1620570571527, backtracks = 0, tol = 0.0048656631920076035 Iteration 8: loglikelihood = -1372.1228886665244, backtracks = 0, tol = 0.005455197205801719 Iteration 9: loglikelihood = -1372.109399905348, backtracks = 0, tol = 0.001660186111065348 Iteration 10: loglikelihood = -1372.104736967351, backtracks = 0, tol = 0.0018951262368294842 Iteration 11: loglikelihood = -1372.1031214971863, backtracks = 0, tol = 0.0005700309201888673 Iteration 12: loglikelihood = -1372.1025607446345, backtracks = 0, tol = 0.0006625335056589153 Iteration 13: loglikelihood = -1372.1023662715943, backtracks = 0, tol = 0.00019629256530938623 Iteration 14: loglikelihood = -1372.1022986963515, backtracks = 0, tol = 0.00023204991233611672 Iteration 15: loglikelihood = -1372.1022752849472, backtracks = 0, tol = 6.760057203119086e-5 0.833054 seconds (1.25 M allocations: 29.205 MiB, 73.34% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1506.560913615843, backtracks = 0, tol = 0.2080075275073403 Iteration 2: loglikelihood = -1468.2397707026214, backtracks = 0, tol = 0.15441938058985022 Iteration 3: loglikelihood = -1440.6345151960566, backtracks = 0, tol = 0.11443454416823656 Iteration 4: loglikelihood = -1429.1949528666535, backtracks = 0, tol = 0.10828295524977141 Iteration 5: loglikelihood = -1418.709424962744, backtracks = 0, tol = 0.09401754575832888 Iteration 6: loglikelihood = -1411.8751926032046, backtracks = 0, tol = 0.011390657277520488 Iteration 7: loglikelihood = -1406.7209020020557, backtracks = 0, tol = 0.0022398869240428743 Iteration 8: loglikelihood = -1402.469280784567, backtracks = 0, tol = 0.0007734941348989789 Iteration 9: loglikelihood = -1398.7002188079214, backtracks = 0, tol = 0.08222506689517182 Iteration 10: loglikelihood = -1395.7721350632455, backtracks = 0, tol = 0.005811238181143365 Iteration 11: loglikelihood = -1393.2856331612716, backtracks = 0, tol = 0.0013792872462197326 Iteration 12: loglikelihood = -1391.323763536269, backtracks = 0, tol = 0.08104319107603926 Iteration 13: loglikelihood = -1389.394758584732, backtracks = 0, tol = 0.006428161190600682 Iteration 14: loglikelihood = -1387.8299957031081, backtracks = 0, tol = 0.0008159744711197103 Iteration 15: loglikelihood = -1386.449417843752, backtracks = 0, tol = 0.0003595976835826518 Iteration 16: loglikelihood = -1384.3535286852823, backtracks = 1, tol = 0.00020938803219608076 Iteration 17: loglikelihood = -1383.284503770643, backtracks = 0, tol = 0.0788198702728196 Iteration 18: loglikelihood = -1382.3162809758878, backtracks = 0, tol = 0.005124672173547027 Iteration 19: loglikelihood = -1380.8985705635557, backtracks = 1, tol = 0.0005067019072470041 Iteration 20: loglikelihood = -1379.733124245698, backtracks = 1, tol = 0.0004940548506463558 Iteration 21: loglikelihood = -1378.7662176675224, backtracks = 1, tol = 0.00045694051369727425 Iteration 22: loglikelihood = -1377.956495824994, backtracks = 1, tol = 0.00041566284115009935 Iteration 23: loglikelihood = -1377.2724675085722, backtracks = 1, tol = 0.0003755895534126076 Iteration 24: loglikelihood = -1376.6899171228308, backtracks = 1, tol = 0.00033860848887932283 Iteration 25: loglikelihood = -1376.2238022436218, backtracks = 1, tol = 0.0003053438531846298 Iteration 26: loglikelihood = -1375.822460108369, backtracks = 1, tol = 0.00026917509833292467 Iteration 27: loglikelihood = -1375.4732536958634, backtracks = 1, tol = 0.00023866494689791948 Iteration 28: loglikelihood = -1375.1670639903937, backtracks = 1, tol = 0.00021358267693146168 Iteration 29: loglikelihood = -1374.8968821559197, backtracks = 1, tol = 0.00019282753171156019 Iteration 30: loglikelihood = -1374.6571924246705, backtracks = 1, tol = 0.00017541192114821453 Iteration 31: loglikelihood = -1374.4435774131086, backtracks = 1, tol = 0.0001605653414189337 Iteration 32: loglikelihood = -1374.2524417558768, backtracks = 1, tol = 0.00014771141740369586 Iteration 33: loglikelihood = -1374.0808163559832, backtracks = 1, tol = 0.0001364272673064077 Iteration 34: loglikelihood = -1373.926218846242, backtracks = 1, tol = 0.0001264048876171463 Iteration 35: loglikelihood = -1373.7865527542122, backtracks = 1, tol = 0.00011741927931164197 Iteration 36: loglikelihood = -1373.6600331364714, backtracks = 1, tol = 0.00010930400724043695 Iteration 37: loglikelihood = -1373.5451304066723, backtracks = 1, tol = 0.0001019333817289091 Iteration 38: loglikelihood = -1373.4405268696235, backtracks = 1, tol = 9.520994728171829e-5 0.455660 seconds (1.74 M allocations: 32.391 MiB, 5.55% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3786.723, backtracks = 0, tol = 0.08634101354072016 Iteration 2: loglikelihood = -3749.2056, backtracks = 0, tol = 0.039067632014787655 Iteration 3: loglikelihood = -3746.5518, backtracks = 1, tol = 0.009817850294839333 Iteration 4: loglikelihood = -3745.8472, backtracks = 1, tol = 0.005348514729749399 Iteration 5: loglikelihood = -3745.6672, backtracks = 1, tol = 0.0027812659406542873 Iteration 6: loglikelihood = -3745.623, backtracks = 1, tol = 0.0014118778503832217 Iteration 7: loglikelihood = -3745.6145, backtracks = 1, tol = 0.0007092521493641921 Iteration 8: loglikelihood = -3745.6116, backtracks = 1, tol = 0.0003542985828553134 Iteration 9: loglikelihood = -3745.6084, backtracks = 1, tol = 0.00017657750201767385 Iteration 10: loglikelihood = -3745.6135, backtracks = 3, tol = 2.196570546284887e-5 23.939040 seconds (14.42 M allocations: 658.762 MiB, 2.18% gc time, 96.63% 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 = -3678.7402, backtracks = 0, tol = 0.08634101354072016 Iteration 2: loglikelihood = -3565.4783, backtracks = 0, tol = 0.03990635217924642 Iteration 3: loglikelihood = -3348.9385, backtracks = 1, tol = 0.0093501640326021 Iteration 4: loglikelihood = -3092.0684, backtracks = 1, tol = 0.004524817677042511 Iteration 5: loglikelihood = -3004.4978, backtracks = 0, tol = 0.08275716102610922 Iteration 6: loglikelihood = -2820.9924, backtracks = 0, tol = 0.09175791167483577 Iteration 7: loglikelihood = -2672.241, backtracks = 0, tol = 0.08759670030872757 Iteration 8: loglikelihood = -2534.74, backtracks = 0, tol = 0.08010672327368505 Iteration 9: loglikelihood = -2419.576, backtracks = 0, tol = 0.07825199151670595 Iteration 10: loglikelihood = -2327.385, backtracks = 0, tol = 0.08013919879886451 Iteration 11: loglikelihood = -2260.8552, backtracks = 0, tol = 0.0873036754293546 Iteration 12: loglikelihood = -2217.6812, backtracks = 0, tol = 0.08283389285860521 Iteration 13: loglikelihood = -2194.9417, backtracks = 0, tol = 0.08944157666682825 Iteration 14: loglikelihood = -2175.8984, backtracks = 0, tol = 0.0970571421031625 Iteration 15: loglikelihood = -2170.6067, backtracks = 0, tol = 0.09661270407596355 Iteration 16: loglikelihood = -2163.4995, backtracks = 0, tol = 0.10059992336330573 Iteration 17: loglikelihood = -2158.4734, backtracks = 1, tol = 0.019303006505531156 Iteration 18: loglikelihood = -2157.4182, backtracks = 1, tol = 0.009513951241635257 Iteration 19: loglikelihood = -2157.003, backtracks = 0, tol = 0.08772607142030256 Iteration 20: loglikelihood = -2156.1438, backtracks = 0, tol = 0.09187156511936401 Iteration 21: loglikelihood = -2154.3723, backtracks = 0, tol = 0.09629347431376933 Iteration 22: loglikelihood = -2153.7637, backtracks = 1, tol = 0.009119065479011607 Iteration 23: loglikelihood = -2153.6426, backtracks = 1, tol = 0.004269510962389766 Iteration 24: loglikelihood = -2153.6177, backtracks = 1, tol = 0.0020650313943489447 Iteration 25: loglikelihood = -2153.6133, backtracks = 1, tol = 0.00102045916683063 Iteration 26: loglikelihood = -2153.6099, backtracks = 2, tol = 0.00025498747472981587 Iteration 27: loglikelihood = -2153.609, backtracks = 3, tol = 9.623627864797442e-5 0.214521 seconds (1.56 M allocations: 25.919 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 28.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 5.517727 seconds (1.18 M allocations: 138.709 MiB, 15.79% gc time, 92.19% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 6.0s 9.532047 seconds (4.00 M allocations: 82.491 MiB, 0.34% gc time, 0.64% compilation time) 5.299120 seconds (3.98 M allocations: 91.679 MiB, 0.41% gc time) 10.267681 seconds (20.41 M allocations: 439.552 MiB, 0.83% gc time, 17.57% compilation time: 79% of which was recompilation) 8.177018 seconds (20.18 M allocations: 434.191 MiB, 0.92% gc time) 55.496275 seconds (3.76 M allocations: 4.239 GiB, 8.14% gc time, 21.50% compilation time) 52.409177 seconds (71.97 k allocations: 183.460 MiB, 0.27% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m39.6s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.168 ms (78 allocations: 4.56 KiB) 4.954 μs (0 allocations: 0 bytes) 152.458 μs (4 allocations: 288 bytes) 6.695 μs (0 allocations: 0 bytes) 53.749 μs (2 allocations: 64 bytes) 40.739 μs (0 allocations: 0 bytes) 24.959 μs (0 allocations: 0 bytes) 24.249 μs (0 allocations: 0 bytes) 85.259 μs (0 allocations: 0 bytes) 33.562 ms (78 allocations: 4.56 KiB) 22.070 μs (0 allocations: 0 bytes) 157.948 μs (4 allocations: 288 bytes) 32.679 μs (0 allocations: 0 bytes) 223.118 μs (2 allocations: 64 bytes) 75.529 μs (0 allocations: 0 bytes) 125.259 μs (0 allocations: 0 bytes) 142.299 μs (0 allocations: 0 bytes) 201.808 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m31.2s **** 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 **** **** 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 0.428214 seconds (49.19 k allocations: 5.483 MiB, 62.72% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.7s **** 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 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 2.140450 seconds (312.10 k allocations: 169.913 MiB, 60.68% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.9s **** 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: 0:03:35 Cross validating... 16%|█████▏ | ETA: 0:00:41 Cross validating... 21%|██████▋ | ETA: 0:00:30 Cross validating... 24%|███████▋ | ETA: 0:00:26 Cross validating... 27%|████████▋ | ETA: 0:00:22 Cross validating... 30%|█████████▋ | ETA: 0:00:19 Cross validating... 33%|██████████▋ | ETA: 0:00:17 Cross validating... 37%|███████████▋ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:13 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:08 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 62%|███████████████████▊ | ETA: 0:00:06 Cross validating... 65%|████████████████████▉ | ETA: 0:00:05 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 3402.3984674845196 1 2694.677747261321 2 1789.3163416049022 3 1446.0246131331046 4 1021.9649238467543 5 672.8745513047896 6 495.7255512252203 7 438.9687690860011 8 423.745598531287 9 387.7825495292448 10 360.1047635994174 11 364.47942087910644 12 364.9091973749232 13 366.85317932215224 14 371.1742146957191 15 375.3912821410531 16 377.3033031127798 17 376.6741152712291 18 391.60973514445504 19 395.7438610689837 20 435.9147260002688 Best k = 10 11.503949 seconds (11.44 M allocations: 302.245 MiB, 0.89% gc time, 62.84% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | 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... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 3402.3984674845196 1 2696.4768208325477 2 1795.9602576041723 3 1470.6519394826398 4 1038.578640466518 5 682.1091894718681 6 504.2217540602016 7 450.1927958518347 8 436.67077464331294 9 398.50419784992596 10 370.6511761201794 11 383.5733423234269 12 385.8264204309688 13 392.66199593560566 14 404.12115676704934 15 414.4645378805795 16 420.65656120031565 17 428.20671417977815 18 423.0898638579522 19 434.97007808764226 20 428.34006751110445 Best k = 10 4.569455 seconds (10.81 M allocations: 228.034 MiB, 1.06% gc time, 0.95% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 16.9s **** 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: 0:06:33 Cross validating... 8%|██▌ | ETA: 0:02:31 Cross validating... 13%|████▏ | ETA: 0:01:30 Cross validating... 17%|█████▋ | ETA: 0:01:03 Cross validating... 22%|███████▏ | ETA: 0:00:47 Cross validating... 27%|████████▋ | ETA: 0:00:37 Cross validating... 30%|█████████▋ | ETA: 0:00:32 Cross validating... 33%|██████████▋ | ETA: 0:00:28 Cross validating... 38%|████████████▎ | ETA: 0:00:23 Cross validating... 43%|█████████████▊ | ETA: 0:00:19 Cross validating... 48%|███████████████▎ | ETA: 0:00:16 Cross validating... 52%|████████████████▊ | ETA: 0:00:13 Cross validating... 56%|█████████████████▊ | ETA: 0:00:12 Cross validating... 59%|██████████████████▊ | ETA: 0:00:10 Cross validating... 62%|███████████████████▊ | ETA: 0:00:09 Cross validating... 65%|████████████████████▉ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1552.4433142089845 1 1313.5479619140626 2 998.0231959228515 3 794.4585264892578 4 645.6955900878907 5 515.8894360961915 6 411.887051940918 7 365.54554467773437 8 342.5133753051758 9 330.03705364990236 10 333.84624371337895 11 333.4833843383789 12 339.33444097900394 13 340.9994603881836 14 339.6070771484375 15 346.0563224487305 16 351.94307696533207 17 366.4801988525391 18 345.7145684814453 19 343.79417413330077 20 377.7503499145508 Best k = 9 16.981617 seconds (12.40 M allocations: 307.186 MiB, 0.44% gc time, 82.08% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 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Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1552.4433142089845 1 1319.8456401367189 2 1004.1656080322266 3 796.0788399658204 4 661.3240054931641 5 518.138108581543 6 416.4754155883789 7 368.9532592773438 8 348.0610850219727 9 335.31492022705083 10 346.78789184570314 11 347.6100537109375 12 361.0156814575196 13 363.8901690673828 14 365.4673316040039 15 381.80606335449215 16 380.51397045898443 17 388.4408435058594 18 384.13101086425786 19 383.4296005859375 20 406.1177070922852 Best k = 9 3.117005 seconds (10.67 M allocations: 195.483 MiB, 1.74% gc time, 1.19% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 21.9s **** 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: 0:00:51 Cross validating... 6%|██ | ETA: 0:00:27 Cross validating... 10%|███ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:12 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: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross 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100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.7845211142245 1 407.42637735149594 2 373.80555856792745 3 336.1225599132061 4 304.605116826978 5 276.0864378668445 6 256.88796083733075 7 258.7667335732205 8 248.18892065599317 9 249.41188336037467 10 253.10097312802355 11 260.0681736417293 12 261.2308023500087 13 268.20044131214195 14 288.0057316978728 15 278.6431972128644 16 279.4311755326627 17 279.3437208895674 18 286.6264276906932 19 273.4213444860874 20 296.5038160594219 Best k = 8 7.504615 seconds (17.42 M allocations: 411.851 MiB, 1.08% gc time, 30.08% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 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: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 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 0 464.7845211142245 1 407.4507954886219 2 374.103491917748 3 337.0200587068576 4 305.54555768074056 5 276.5790505194502 6 258.5029555382771 7 261.2733532897337 8 252.44456491213344 9 261.17596336317825 10 268.8623295202274 11 272.67634614506534 12 286.177210813172 13 290.12320882816755 14 286.2392706611195 15 310.9472896320441 16 308.3946514435248 17 330.14596825987957 18 323.5362069057761 19 314.6702135053598 20 332.044139504416 Best k = 8 5.332427 seconds (17.53 M allocations: 363.844 MiB, 1.24% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:47 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:13 Cross validating... 17%|█████▋ | ETA: 0:00:11 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 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... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | 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 0 462.08096033477716 1 429.0191955875604 2 416.2803511771399 3 377.1359598944016 4 357.5370321675556 5 348.33988510255614 6 335.13151731348245 7 332.3035708874836 8 323.00777884733816 9 328.06995270200986 10 330.3086423032092 11 344.1778146451465 12 332.7265502414117 13 330.3827041321869 14 331.7281559528182 15 356.3406240524851 16 329.3568497854752 17 356.3305743034681 18 343.8293372151602 19 365.7560132678579 20 335.0958850179245 Best k = 8 8.654117 seconds (16.46 M allocations: 386.922 MiB, 9.65% gc time, 28.42% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 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: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.08096033477716 1 429.9100286660266 2 419.62561101834933 3 381.7623599543797 4 367.18783750632616 5 352.80448141226384 6 340.29736571088574 7 339.3762752202693 8 333.2195024642495 9 338.86470220378084 10 362.6325020470242 11 352.8264530984267 12 365.53389184763057 13 363.74995647215616 14 377.54031288253157 15 381.37407993447056 16 375.6506187964096 17 378.6980372332466 18 394.72865426772535 19 395.33497392700815 20 384.99383976537 Best k = 8 5.636326 seconds (16.69 M allocations: 340.427 MiB, 1.01% gc time, 0.77% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 16.4s **** 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... 3%|█ | ETA: 0:00:55 Cross validating... 6%|██ | ETA: 0:00:29 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 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... 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 0 677.5776303880646 1 611.1321234003526 2 534.021281253825 3 468.47539505090174 4 408.0431841135539 5 374.35351230774415 6 351.12288276133313 7 355.049605121833 8 359.31496866950056 9 356.810500704973 10 363.0117687927378 11 362.43548785938344 12 363.82996568727276 13 363.42340712544217 14 386.9407538016062 15 400.58734240824947 16 407.16756341376066 17 389.6313866724918 18 388.51818974578396 19 379.3027613307926 20 386.13514071097376 Best k = 6 7.478602 seconds (16.49 M allocations: 399.851 MiB, 1.06% gc time, 31.89% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 677.5776303880646 1 602.9107669783023 2 526.9322054805355 3 464.8705207148022 4 410.1146606318337 5 380.1587927272874 6 358.83204366227744 7 369.6727176549241 8 379.85123720464213 9 375.4037981072478 10 392.0108457968676 11 387.69916882072937 12 399.13048988543983 13 410.2373560244167 14 413.30117586766005 15 404.48790502452255 16 423.2553633112922 17 433.1633235892249 18 432.1385350051098 19 430.9719556508193 20 418.6010527467803 Best k = 6 5.235462 seconds (16.01 M allocations: 334.528 MiB, 1.10% gc time, 1.09% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.2s **** 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: 0:00:52 Cross validating... 5%|█▌ | ETA: 0:00:54 Cross validating... 6%|██ | ETA: 0:00:53 Cross validating... 10%|███ | ETA: 0:00:44 Cross validating... 11%|███▌ | ETA: 0:00:38 Cross validating... 13%|████▏ | ETA: 0:00:33 Cross validating... 14%|████▋ | ETA: 0:00:30 Cross validating... 16%|█████▏ | ETA: 0:00:27 Cross validating... 17%|█████▋ | ETA: 0:00:25 Cross validating... 19%|██████▏ | ETA: 0:00:23 Cross validating... 21%|██████▋ | ETA: 0:00:24 Cross validating... 22%|███████▏ | ETA: 0:00:26 Cross validating... 24%|███████▋ | ETA: 0:00:27 Cross validating... 25%|████████▏ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:27 Cross validating... 30%|█████████▋ | ETA: 0:00:27 Cross validating... 32%|██████████▏ | ETA: 0:00:27 Cross validating... 33%|██████████▋ | ETA: 0:00:26 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 40%|████████████▊ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:23 Cross validating... 43%|█████████████▊ | ETA: 0:00:23 Cross validating... 44%|██████████████▎ | ETA: 0:00:23 Cross validating... 46%|██████████████▊ | ETA: 0:00:21 Cross validating... 48%|███████████████▎ | ETA: 0:00:20 Cross validating... 49%|███████████████▊ | ETA: 0:00:20 Cross validating... 51%|████████████████▎ | ETA: 0:00:19 Cross validating... 52%|████████████████▊ | ETA: 0:00:18 Cross validating... 54%|█████████████████▎ | ETA: 0:00:17 Cross validating... 56%|█████████████████▊ | ETA: 0:00:16 Cross validating... 57%|██████████████████▎ | ETA: 0:00:16 Cross validating... 59%|██████████████████▊ | ETA: 0:00:16 Cross validating... 60%|███████████████████▎ | ETA: 0:00:15 Cross validating... 62%|███████████████████▊ | ETA: 0:00:14 Cross validating... 63%|████████████████████▍ | ETA: 0:00:14 Cross validating... 65%|████████████████████▉ | ETA: 0:00:13 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:13 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:11 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:11 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:10 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:09 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:08 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:08 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:07 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:07 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:43 Crossvalidation Results: k MSE 0 348.21215442004143 1 320.0870662816325 2 284.42192117103275 3 262.49005106452955 4 241.58812871438698 5 220.51661655389384 6 213.68908072248206 7 215.58917169930695 8 216.3165480096308 9 215.65464466048115 10 218.06278724922856 11 218.61369755041795 12 220.7009155871534 13 221.059919705634 14 220.63048953418496 15 223.3655349443227 16 224.23387930318387 17 226.03627961212337 18 223.87735444425334 19 227.76575702797592 20 223.8769722122214 Best k = 6 44.247515 seconds (146.97 M allocations: 3.752 GiB, 1.32% gc time, 4.47% 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: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:08 Cross validating... 14%|████▋ | ETA: 0:00:09 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 17%|█████▋ | ETA: 0:00:09 Cross 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83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 348.21215442004143 1 319.3129120796807 2 284.0089426463927 3 262.6653190832703 4 242.35395721406036 5 221.66446271510122 6 215.1595341900777 7 219.024025452546 8 222.45798632424658 9 221.5321918107312 10 226.91282060915387 11 229.9184252440331 12 235.73307158869574 13 240.1661803030476 14 238.651869041856 15 244.59567534221975 16 242.80260339551197 17 255.52957320136795 18 250.7777174243493 19 257.4585281504621 20 258.69026697992626 Best k = 6 14.267349 seconds (51.62 M allocations: 1.075 GiB, 1.23% gc time, 0.44% 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: 0:01:06 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | 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78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 7.095476 seconds (17.00 M allocations: 338.869 MiB, 2.29% gc time, 37.05% 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: 0:00:03 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: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 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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 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 4.125751 seconds (16.18 M allocations: 286.711 MiB, 1.29% gc time, 1.24% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 11.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:25 Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 4%|█▎ | ETA: 0:00:49 Cross validating... 5%|█▋ | ETA: 0:00:41 Cross validating... 6%|█▉ | ETA: 0:00:35 Cross validating... 7%|██▎ | ETA: 0:00:32 Cross validating... 8%|██▌ | ETA: 0:00:29 Cross validating... 9%|██▉ | ETA: 0:00:27 Cross validating... 10%|███▎ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:25 Cross validating... 12%|███▉ | ETA: 0:00:23 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... 18%|█████▊ | ETA: 0:00:20 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross 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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: 0:00:17 Crossvalidation Results: k MSE 1 2674.1862312617222 2 2291.345979175988 3 1863.4365047401361 4 1623.7067916332753 5 1336.7413978832699 6 1220.990909955011 7 1205.7613569023033 8 1207.7025774500999 9 1225.8893732844458 10 1228.4527066007138 11 1226.0584446332405 12 1237.9775184651585 13 1244.657053545926 14 1245.158492883646 15 1260.7076707533417 16 1266.9647148230097 17 1286.289067685198 18 1301.0714809061067 19 1285.7171796032987 20 1291.5885307424016 Best k = 7 18.022960 seconds (334.10 k allocations: 218.404 MiB, 0.35% gc time, 9.72% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m51.8s **** 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: 0:00:10 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 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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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:12 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%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 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validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 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: 0:00:10 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: 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ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 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... 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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 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:2243 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.0s RNG of the outermost testset: Xoshiro(0xfd42079c2644e095, 0xcf3a4586b7a12e5b, 0x946abc4cbcf1240e, 0xa8be9f2b131fb131, 0xee3cdfdd83bbf843) 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 1171.14s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1307.15s: package tests unexpectedly errored