Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1741 (f7ebeb5678*) started at 2026-02-19T22:51:01.904 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.88s ################################################################################ # 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 v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [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 v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.92s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4351.6 ms ✓ BGEN 6508.5 ms ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 24289.5 ms ✓ MendelIHT 3 dependencies successfully precompiled in 38 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 59.94s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_mLa5t9/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 v17.7.0+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 15.4s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 9.3s 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 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.4s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1670.6677261460798, backtracks = 0, tol = 1.993805981751331 Iteration 2: loglikelihood = -1439.1332272285176, backtracks = 0, tol = 0.13738791419057134 Iteration 3: loglikelihood = -1424.2912903255528, backtracks = 0, tol = 0.033250578191262904 Iteration 4: loglikelihood = -1424.2052366378678, backtracks = 0, tol = 0.0027237332016974555 Iteration 5: loglikelihood = -1424.2038132195078, backtracks = 0, tol = 0.0002158139174058976 Iteration 6: loglikelihood = -1424.2037773428092, backtracks = 0, tol = 6.358945020046014e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05827188491821289 Final loglikelihood: -1424.2037773428092 SNP PVE: 0.9012386406104477 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 120 -0.567089 2 │ 213 0.24634 3 │ 537 -0.334881 4 │ 1702 -0.55765 5 │ 2338 -1.06402 6 │ 2851 0.950777 7 │ 5816 0.310803 8 │ 8181 -0.961738 9 │ 8557 0.29057 10 │ 8872 2.28042 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0186329Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.3s **** 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 logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -10394.336216423464, backtracks = 0, tol = 0.701053177716818 Iteration 2: loglikelihood = -4749.641065444793, backtracks = 0, tol = 0.05668283109622939 Iteration 3: loglikelihood = -2179.6124297184065, backtracks = 0, tol = 0.07102191290442574 Iteration 4: loglikelihood = -1573.802466649245, backtracks = 0, tol = 0.07818603981181597 Iteration 5: loglikelihood = -1446.8371837356, backtracks = 0, tol = 0.05674501057979111 Iteration 6: loglikelihood = -1392.9657821126752, backtracks = 0, tol = 0.06756366029631328 Iteration 7: loglikelihood = -1354.7087729244126, backtracks = 0, tol = 0.05003376743820579 Iteration 8: loglikelihood = -1347.6437794694762, backtracks = 0, tol = 0.021887844137158954 Iteration 9: loglikelihood = -1342.8850616813152, backtracks = 0, tol = 0.02301356511651068 Iteration 10: loglikelihood = -1339.9827445859999, backtracks = 0, tol = 0.012782808936418 Iteration 11: loglikelihood = -1337.9077775307662, backtracks = 0, tol = 0.0161938520502407 Iteration 12: loglikelihood = -1336.6866925159818, backtracks = 0, tol = 0.00829110330213066 Iteration 13: loglikelihood = -1332.0771341347568, backtracks = 0, tol = 0.05904029442986195 Iteration 14: loglikelihood = -1331.2482696763007, backtracks = 0, tol = 0.01119478005879904 Iteration 15: loglikelihood = -1330.881054397114, backtracks = 0, tol = 0.005760393526784175 Iteration 16: loglikelihood = -1330.7038923699924, backtracks = 0, tol = 0.006113504726202751 Iteration 17: loglikelihood = -1330.6031642681844, backtracks = 0, tol = 0.002968681265740444 Iteration 18: loglikelihood = -1330.5452369813886, backtracks = 0, tol = 0.0035667603273877597 Iteration 19: loglikelihood = -1330.5097875074216, backtracks = 0, tol = 0.0017743012786757028 Iteration 20: loglikelihood = -1330.4881064749266, backtracks = 0, tol = 0.0021990862542140472 Iteration 21: loglikelihood = -1330.474421440785, backtracks = 0, tol = 0.0010990967541170346 Iteration 22: loglikelihood = -1330.4658065712356, backtracks = 0, tol = 0.0013832496396195906 Iteration 23: loglikelihood = -1330.4602857217014, backtracks = 0, tol = 0.0006982973129526169 Iteration 24: loglikelihood = -1330.456756426911, backtracks = 0, tol = 0.0008833971648112783 Iteration 25: loglikelihood = -1330.4544759262758, backtracks = 0, tol = 0.0004485161633395399 Iteration 26: loglikelihood = -1330.4530051276838, backtracks = 0, tol = 0.0005689077572153243 Iteration 27: loglikelihood = -1330.4520502106127, backtracks = 0, tol = 0.0002901494338066746 Iteration 28: loglikelihood = -1330.4514310607447, backtracks = 0, tol = 0.0003684309007683665 Iteration 29: loglikelihood = -1330.451027923935, backtracks = 0, tol = 0.00018847336112898268 Iteration 30: loglikelihood = -1330.4507656782332, backtracks = 0, tol = 0.0002394420176167922 Iteration 31: loglikelihood = -1330.4505946243864, backtracks = 0, tol = 0.00012274721777340134 Iteration 32: loglikelihood = -1330.4504831214356, backtracks = 0, tol = 0.00015597162423814997 Iteration 33: loglikelihood = -1330.4504103110623, backtracks = 0, tol = 8.007273011903649e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1647.2992168617027, backtracks = 0, tol = 0.698093382623617 Iteration 2: loglikelihood = -1525.4719450141279, backtracks = 0, tol = 0.10193760433857366 Iteration 3: loglikelihood = -1463.2536671141963, backtracks = 0, tol = 0.08424328279556383 Iteration 4: loglikelihood = -1444.8919612515926, backtracks = 0, tol = 0.06268967415228469 Iteration 5: loglikelihood = -1442.6576298761936, backtracks = 0, tol = 0.08816208788123885 Iteration 6: loglikelihood = -1439.4674942549866, backtracks = 0, tol = 0.07027834686525325 Iteration 7: loglikelihood = -1438.6644339585973, backtracks = 0, tol = 0.06655266288420049 Iteration 8: loglikelihood = -1438.56473769825, backtracks = 1, tol = 0.0032473752149534945 Iteration 9: loglikelihood = -1438.5349930018933, backtracks = 1, tol = 0.0018625078318854416 Iteration 10: loglikelihood = -1438.526118787074, backtracks = 1, tol = 0.0013190260064057362 Iteration 11: loglikelihood = -1438.5234309970172, backtracks = 1, tol = 0.0008749708881721849 Iteration 12: loglikelihood = -1438.5226408756596, backtracks = 1, tol = 0.0005163265496474093 Iteration 13: loglikelihood = -1438.5224250301032, backtracks = 1, tol = 0.00026777925956972986 Iteration 14: loglikelihood = -1438.52236857147, backtracks = 1, tol = 0.00013119779006436102 Iteration 15: loglikelihood = -1438.522353976288, backtracks = 1, tol = 6.753948406973284e-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 = -1768.8762919841763, backtracks = 0, tol = 0.8023892643083852 Iteration 2: loglikelihood = -1460.9066237168972, backtracks = 0, tol = 0.1243481707928858 Iteration 3: loglikelihood = -1409.7767423240273, backtracks = 0, tol = 0.04118674062880106 Iteration 4: loglikelihood = -1406.0008404199134, backtracks = 0, tol = 0.027151708441346498 Iteration 5: loglikelihood = -1405.5518729590933, backtracks = 0, tol = 0.026654215952691327 Iteration 6: loglikelihood = -1405.2934694802334, backtracks = 0, tol = 0.003502050871370007 Iteration 7: loglikelihood = -1405.2875470219572, backtracks = 0, tol = 0.0005486583749135941 Iteration 8: loglikelihood = -1405.2873837347927, backtracks = 0, tol = 5.898383129771848e-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 = -1645.2341422498307, backtracks = 0, tol = 0.4814496577244835 Iteration 2: loglikelihood = -1437.7536822733043, backtracks = 0, tol = 0.10160671433049175 Iteration 3: loglikelihood = -1414.3089515628265, backtracks = 0, tol = 0.040917650647578574 Iteration 4: loglikelihood = -1407.3160708827431, backtracks = 0, tol = 0.029966535632208684 Iteration 5: loglikelihood = -1406.6374403124757, backtracks = 0, tol = 0.03129177377992218 Iteration 6: loglikelihood = -1406.3900968136065, backtracks = 0, tol = 0.004217898755651977 Iteration 7: loglikelihood = -1406.3857540942076, backtracks = 0, tol = 0.0005951562938726824 Iteration 8: loglikelihood = -1406.3856560772656, backtracks = 0, tol = 5.6718418109777216e-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 10.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1434.9138665186472, backtracks = 0, tol = 0.19801248353285297 Iteration 2: loglikelihood = -1394.4123858721837, backtracks = 0, tol = 0.08192375227326705 Iteration 3: loglikelihood = -1356.0949902102961, backtracks = 0, tol = 0.11883636344908058 Iteration 4: loglikelihood = -1344.768619901833, backtracks = 0, tol = 0.1000254894999079 Iteration 5: loglikelihood = -1342.2562696572859, backtracks = 0, tol = 0.08108155446201698 Iteration 6: loglikelihood = -1335.8039159210784, backtracks = 0, tol = 0.06471204146257294 Iteration 7: loglikelihood = -1332.3785394799534, backtracks = 0, tol = 0.07862792529219485 Iteration 8: loglikelihood = -1331.5522840060744, backtracks = 0, tol = 0.08653153536121624 Iteration 9: loglikelihood = -1331.2410892818439, backtracks = 0, tol = 0.00954000364634679 Iteration 10: loglikelihood = -1331.1995329257395, backtracks = 0, tol = 0.0024013391136508367 Iteration 11: loglikelihood = -1331.189709985257, backtracks = 0, tol = 0.0022393280899259114 Iteration 12: loglikelihood = -1331.1863470229862, backtracks = 0, tol = 0.0007481981045799632 Iteration 13: loglikelihood = -1331.1850367599118, backtracks = 0, tol = 0.0008888142447308587 Iteration 14: loglikelihood = -1331.1845148440766, backtracks = 0, tol = 0.00031787148345691367 Iteration 15: loglikelihood = -1331.1843061656168, backtracks = 0, tol = 0.00035445748981901626 Iteration 16: loglikelihood = -1331.1842225367695, backtracks = 0, tol = 0.00012949946716071638 Iteration 17: loglikelihood = -1331.1841890220892, backtracks = 0, tol = 0.00014165304377278335 Iteration 18: loglikelihood = -1331.1841755810892, backtracks = 0, tol = 5.218369379297925e-5 0.807369 seconds (1.68 M allocations: 36.127 MiB, 63.68% 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 = -1493.1684190111653, backtracks = 0, tol = 0.19801248353285297 Iteration 2: loglikelihood = -1458.2312323603787, backtracks = 0, tol = 0.10625733134759378 Iteration 3: loglikelihood = -1433.984977525023, backtracks = 0, tol = 0.12472205083795117 Iteration 4: loglikelihood = -1413.5128869854423, backtracks = 0, tol = 0.08970521712917542 Iteration 5: loglikelihood = -1402.0163403778022, backtracks = 0, tol = 0.08121979510446058 Iteration 6: loglikelihood = -1393.7124862791545, backtracks = 0, tol = 0.07978584267168518 Iteration 7: loglikelihood = -1386.585345813486, backtracks = 0, tol = 0.07844079747274425 Iteration 8: loglikelihood = -1380.707893551309, backtracks = 0, tol = 0.006183960620604297 Iteration 9: loglikelihood = -1376.0843789010087, backtracks = 0, tol = 0.0016801551755502133 Iteration 10: loglikelihood = -1372.1548461025645, backtracks = 0, tol = 0.0005262146370235131 Iteration 11: loglikelihood = -1369.964685822688, backtracks = 0, tol = 0.08109855411911165 Iteration 12: loglikelihood = -1366.2307816722573, backtracks = 0, tol = 0.0785909348321837 Iteration 13: loglikelihood = -1363.4949363272044, backtracks = 0, tol = 0.006089655273544408 Iteration 14: loglikelihood = -1361.2833154148252, backtracks = 0, tol = 0.001357689006099546 Iteration 15: loglikelihood = -1359.3081017801876, backtracks = 0, tol = 0.0005433730302351499 Iteration 16: loglikelihood = -1356.0995968622385, backtracks = 1, tol = 0.00018052195100384496 Iteration 17: loglikelihood = -1353.5118075354562, backtracks = 1, tol = 0.0002473928492967964 Iteration 18: loglikelihood = -1351.382048766385, backtracks = 1, tol = 0.00027250670728531863 Iteration 19: loglikelihood = -1349.607145906907, backtracks = 1, tol = 0.0002739259609786899 Iteration 20: loglikelihood = -1348.0717642605118, backtracks = 1, tol = 0.00026055535684864405 Iteration 21: loglikelihood = -1346.7628332452925, backtracks = 1, tol = 0.00024224330071397087 Iteration 22: loglikelihood = -1345.6355845209566, backtracks = 1, tol = 0.00022118425393076962 Iteration 23: loglikelihood = -1344.655800648888, backtracks = 1, tol = 0.0002001736709673503 Iteration 24: loglikelihood = -1343.797100696383, backtracks = 1, tol = 0.0001806606347293481 Iteration 25: loglikelihood = -1343.038930422762, backtracks = 1, tol = 0.00016539863654125818 Iteration 26: loglikelihood = -1342.3650958811543, backtracks = 1, tol = 0.00015254199175400505 Iteration 27: loglikelihood = -1341.7626915457186, backtracks = 1, tol = 0.0001413062679019489 Iteration 28: loglikelihood = -1341.2213143014524, backtracks = 1, tol = 0.00013144533534196006 Iteration 29: loglikelihood = -1340.7324849391694, backtracks = 1, tol = 0.0001227346324418292 Iteration 30: loglikelihood = -1340.28922011927, backtracks = 1, tol = 0.00011498498251202754 Iteration 31: loglikelihood = -1339.8857132619319, backtracks = 1, tol = 0.00010804265121666776 Iteration 32: loglikelihood = -1339.5170943118605, backtracks = 1, tol = 0.00010178442686452086 Iteration 33: loglikelihood = -1339.1792468207775, backtracks = 1, tol = 9.611166159318971e-5 0.446744 seconds (1.50 M allocations: 28.003 MiB, 12.64% 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 = -3480.6028, backtracks = 0, tol = 0.08781255157622245 Iteration 2: loglikelihood = -3436.186, backtracks = 0, tol = 0.07150957095380193 Iteration 3: loglikelihood = -3427.2192, backtracks = 1, tol = 0.01583680802731089 Iteration 4: loglikelihood = -3424.228, backtracks = 1, tol = 0.009204876442781071 Iteration 5: loglikelihood = -3423.2722, backtracks = 1, tol = 0.005145236516232178 Iteration 6: loglikelihood = -3422.9973, backtracks = 1, tol = 0.0032456963056604012 Iteration 7: loglikelihood = -3422.9204, backtracks = 1, tol = 0.0018132593097483682 Iteration 8: loglikelihood = -3422.9, backtracks = 1, tol = 0.000961035678039356 Iteration 9: loglikelihood = -3422.8965, backtracks = 1, tol = 0.0004970637165800113 Iteration 10: loglikelihood = -3422.8965, backtracks = 1, tol = 0.0002546331591186973 Iteration 11: loglikelihood = -3422.8972, backtracks = 3, tol = 3.247484687089548e-5 23.609856 seconds (14.85 M allocations: 665.897 MiB, 1.66% gc time, 96.99% 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 = -3396.41, backtracks = 0, tol = 0.08781255157622245 Iteration 2: loglikelihood = -3298.7405, backtracks = 0, tol = 0.07150957095380193 Iteration 3: loglikelihood = -3236.3867, backtracks = 0, tol = 0.09819786445921337 Iteration 4: loglikelihood = -3148.4824, backtracks = 0, tol = 0.09040315196850292 Iteration 5: loglikelihood = -3088.235, backtracks = 0, tol = 0.09456457738915271 Iteration 6: loglikelihood = -2998.8086, backtracks = 0, tol = 0.09507639365570618 Iteration 7: loglikelihood = -2913.5557, backtracks = 0, tol = 0.08490075294911428 Iteration 8: loglikelihood = -2820.481, backtracks = 0, tol = 0.08912291405549022 Iteration 9: loglikelihood = -2726.158, backtracks = 0, tol = 0.011627995345232569 Iteration 10: loglikelihood = -2635.0867, backtracks = 0, tol = 0.08494066969477833 Iteration 11: loglikelihood = -2541.4116, backtracks = 0, tol = 0.08871267942814813 Iteration 12: loglikelihood = -2455.6794, backtracks = 0, tol = 0.011087335480895147 Iteration 13: loglikelihood = -2383.5347, backtracks = 0, tol = 0.08419129676269578 Iteration 14: loglikelihood = -2319.1055, backtracks = 0, tol = 0.09184648783883416 Iteration 15: loglikelihood = -2269.2622, backtracks = 0, tol = 0.014370447174379858 Iteration 16: loglikelihood = -2235.2454, backtracks = 0, tol = 0.07989096091481783 Iteration 17: loglikelihood = -2212.6362, backtracks = 0, tol = 0.09575673293041549 Iteration 18: loglikelihood = -2193.3362, backtracks = 0, tol = 0.09549667706408486 Iteration 19: loglikelihood = -2181.8, backtracks = 0, tol = 0.08909815374565773 Iteration 20: loglikelihood = -2176.8247, backtracks = 0, tol = 0.08950270959651857 Iteration 21: loglikelihood = -2174.9563, backtracks = 0, tol = 0.09531660570059429 Iteration 22: loglikelihood = -2170.655, backtracks = 1, tol = 0.0129516074943534 Iteration 23: loglikelihood = -2170.012, backtracks = 0, tol = 0.08625390594269845 Iteration 24: loglikelihood = -2169.215, backtracks = 1, tol = 0.006122011352823926 Iteration 25: loglikelihood = -2169.0183, backtracks = 1, tol = 0.0031494799979758996 Iteration 26: loglikelihood = -2168.9688, backtracks = 1, tol = 0.0016312326642818524 Iteration 27: loglikelihood = -2168.9524, backtracks = 1, tol = 0.0008523813849930183 Iteration 28: loglikelihood = -2168.9465, backtracks = 1, tol = 0.0004467948805204751 Iteration 29: loglikelihood = -2168.9473, backtracks = 3, tol = 5.9489379668638534e-5 0.234620 seconds (1.52 M allocations: 25.173 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 27.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 5.459961 seconds (1.17 M allocations: 138.586 MiB, 15.08% gc time, 76.91% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.9s 10.393388 seconds (4.00 M allocations: 82.478 MiB, 0.68% gc time, 0.55% compilation time) 5.920240 seconds (3.98 M allocations: 91.675 MiB, 0.09% gc time) 11.654848 seconds (20.40 M allocations: 439.294 MiB, 0.91% gc time, 14.89% compilation time: 78% of which was recompilation) 9.565123 seconds (20.18 M allocations: 434.188 MiB, 0.95% gc time) 41.313444 seconds (3.71 M allocations: 4.237 GiB, 10.67% gc time, 28.06% compilation time) 52.251473 seconds (71.97 k allocations: 183.459 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m29.7s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.602 ms (78 allocations: 4.56 KiB) 4.978 μs (0 allocations: 0 bytes) 150.009 μs (4 allocations: 288 bytes) 8.848 μs (0 allocations: 0 bytes) 55.739 μs (2 allocations: 64 bytes) 45.700 μs (0 allocations: 0 bytes) 26.889 μs (0 allocations: 0 bytes) 36.260 μs (0 allocations: 0 bytes) 90.739 μs (0 allocations: 0 bytes) 40.342 ms (78 allocations: 4.56 KiB) 27.990 μs (0 allocations: 0 bytes) 192.258 μs (4 allocations: 288 bytes) 34.030 μs (0 allocations: 0 bytes) 231.168 μs (2 allocations: 64 bytes) 123.839 μs (0 allocations: 0 bytes) 146.058 μs (0 allocations: 0 bytes) 220.208 μs (0 allocations: 0 bytes) 359.197 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m35.8s **** 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 **** **** 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 0.413751 seconds (49.12 k allocations: 5.471 MiB, 60.84% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 2.115873 seconds (312.45 k allocations: 169.958 MiB, 58.64% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:35 Cross validating... 11%|███▌ | ETA: 0:01:00 Cross validating... 14%|████▋ | ETA: 0:00:46 Cross validating... 17%|█████▋ | ETA: 0:00:37 Cross validating... 21%|██████▋ | ETA: 0:00:31 Cross validating... 24%|███████▋ | ETA: 0:00:26 Cross validating... 27%|████████▋ | ETA: 0:00:23 Cross validating... 30%|█████████▋ | ETA: 0:00:20 Cross validating... 33%|██████████▋ | ETA: 0:00:17 Cross validating... 37%|███████████▋ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 3444.4811668012253 1 1679.7664499963885 2 1358.1942116170337 3 1021.5869624384547 4 674.868438706816 5 577.7944324390922 6 450.4545546192744 7 420.65215455162246 8 384.01367577538053 9 367.64887360274463 10 339.92994075202733 11 343.8333705954274 12 345.02708153695863 13 348.28214616097546 14 348.6526293374113 15 355.2550679677838 16 354.16001214533117 17 351.80595379743386 18 368.20111880961446 19 358.32480992416777 20 358.54466846314847 Best k = 10 12.168708 seconds (11.19 M allocations: 298.852 MiB, 0.85% gc time, 59.11% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:03 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: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 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... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 3444.4811668012253 1 1679.7664499963885 2 1364.6811185796375 3 1030.5219621862234 4 682.5868346329132 5 584.9361484835591 6 456.33478247473863 7 428.28392087096734 8 392.5457938055073 9 376.60337371464107 10 349.9816007451562 11 362.05977449204727 12 365.43538955728104 13 373.9238196771497 14 377.9229569281433 15 390.57599806768155 16 389.9844355072388 17 382.72519538996414 18 395.34372657397495 19 399.73240082544396 20 404.3904055486663 Best k = 10 5.176006 seconds (10.34 M allocations: 218.959 MiB, 0.85% gc time, 1.01% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.2s **** 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: 0:06:45 Cross validating... 8%|██▌ | ETA: 0:02:35 Cross validating... 13%|████▏ | ETA: 0:01:33 Cross validating... 17%|█████▋ | ETA: 0:01:05 Cross validating... 22%|███████▏ | ETA: 0:00:48 Cross validating... 27%|████████▋ | ETA: 0:00:38 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... 57%|██████████████████▎ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 65%|████████████████████▉ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 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... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1638.5486730957032 1 1377.6508592529296 2 1041.4466263427735 3 830.9933671264649 4 655.9747141113281 5 539.6352691650391 6 450.99423956298835 7 391.7745785217286 8 364.5580795898437 9 346.78227124023437 10 350.2716904907227 11 350.2202794799805 12 352.61332666015625 13 355.138103515625 14 355.4723954772949 15 369.59735375976567 16 360.16960751342776 17 365.72512551879885 18 361.64779431152346 19 376.97445565795897 20 370.8087105712891 Best k = 9 16.949607 seconds (12.20 M allocations: 303.746 MiB, 0.87% gc time, 84.33% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:00 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1638.5486730957032 1 1377.6583275146484 2 1041.5827452392577 3 831.8309326782228 4 658.3462542114257 5 540.4622127685547 6 451.60983349609376 7 395.7720277709961 8 370.4974467163086 9 352.1670115356445 10 361.64410235595705 11 363.72976098632813 12 368.1696428222656 13 378.36448294067384 14 382.7121344299316 15 386.3189297180176 16 391.6808811035156 17 403.4293891296387 18 399.56993640136716 19 414.9398788146973 20 424.9486935119629 Best k = 9 2.478720 seconds (10.32 M allocations: 189.266 MiB, 2.10% gc time, 1.57% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:56 Cross validating... 5%|█▌ | ETA: 0:00:39 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross 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79%|█████████████████████████▍ | 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... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:08 Crossvalidation Results: k MSE 0 460.6188422479093 1 384.26992154355725 2 365.88015980514274 3 329.8722204555248 4 290.76637352607145 5 284.15721474409133 6 275.41910828777253 7 274.52702851392155 8 274.0721255801701 9 279.9177809373247 10 271.54701608719995 11 276.4662676660856 12 270.5226233760763 13 291.65842766963556 14 268.32350606426917 15 300.54491506156774 16 280.8217806620013 17 296.35081487185 18 294.50635612992016 19 304.04022979018515 20 298.2171091396 Best k = 14 8.813792 seconds (18.02 M allocations: 420.242 MiB, 0.99% gc time, 26.73% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 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: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | 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81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 460.6188422479093 1 384.8867811548126 2 367.7622989973645 3 332.02015787556286 4 293.4868239318997 5 287.48460396850743 6 282.08050208408423 7 284.0202533972976 8 278.9200927127302 9 290.203022571125 10 277.60838969820463 11 292.85751676860923 12 284.6618808089023 13 317.8237866798336 14 301.4962767254706 15 315.7582919555781 16 330.6923146202083 17 342.95414906214324 18 341.6075133348744 19 367.76822664604276 20 327.2031002855966 Best k = 10 6.710623 seconds (18.63 M allocations: 391.732 MiB, 1.36% gc time, 0.84% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 16.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:46 Cross validating... 6%|██ | ETA: 0:00:24 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.2574616241667 1 425.3704211123344 2 409.3162443753322 3 373.90789924727 4 360.99707358604934 5 341.24076877291276 6 340.56055318151374 7 334.50543401907805 8 338.0759385111183 9 337.6696692059388 10 339.15225634050813 11 342.73565514179705 12 339.62107055761226 13 353.45266378391943 14 357.298597694452 15 363.68853889963907 16 348.1145431539803 17 352.9988433101929 18 394.9293600061534 19 361.011249600365 20 356.25723616818846 Best k = 7 7.806266 seconds (17.09 M allocations: 404.539 MiB, 12.75% gc time, 31.86% 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: 0:00:04 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: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 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... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 464.2574616241667 1 427.36109928210624 2 413.0294621886915 3 378.63805455028574 4 365.1072173599741 5 345.8036285463605 6 348.8021676595565 7 344.5501913544821 8 351.73496409805773 9 360.26584924663035 10 362.39684882762083 11 373.0811118894628 12 366.3225493141663 13 394.1051379380981 14 384.26631127501093 15 397.01774693467934 16 400.0387599663411 17 416.45807632750973 18 419.9273759408636 19 420.2251401893206 20 439.3196396473571 Best k = 7 4.467253 seconds (17.10 M allocations: 350.452 MiB, 2.09% gc time, 0.90% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic 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: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 8%|██▌ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | 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... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1068.2604257050477 1 586.5224663922039 2 525.0966182035634 3 491.5028804289861 4 454.72494967476484 5 444.0324027783422 6 457.19779856229894 7 452.53235735529194 8 456.2857415829699 9 484.518270223919 10 469.67141005378824 11 476.96897890823857 12 462.32259885344064 13 474.76733939268024 14 455.54968123540823 15 458.591570022091 16 464.432407966695 17 466.84290607732834 18 484.05678477874335 19 494.48477709688245 20 497.64694562594497 Best k = 5 8.641219 seconds (14.55 M allocations: 330.259 MiB, 0.78% gc time, 28.41% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:05 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 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87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 1068.2604257050477 1 576.6084603801677 2 517.89584754475 3 491.34711842708737 4 456.0241606813645 5 470.51332680117787 6 471.5748148029967 7 489.55718465265784 8 478.5378997959398 9 484.74454795670096 10 479.7529313937123 11 488.98811133235466 12 482.671052925283 13 496.8958000689711 14 499.0723047240648 15 515.9402989381281 16 530.323903858823 17 538.2360095857716 18 529.2902224916857 19 537.4799940191988 20 545.405470023347 Best k = 4 6.314933 seconds (13.78 M allocations: 273.587 MiB, 0.79% gc time, 0.85% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 15.4s **** 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: 0:01:30 Cross validating... 5%|█▌ | ETA: 0:01:21 Cross validating... 6%|██ | ETA: 0:01:02 Cross validating... 8%|██▌ | ETA: 0:00:50 Cross validating... 10%|███ | ETA: 0:00:52 Cross validating... 11%|███▌ | ETA: 0:00:45 Cross validating... 13%|████▏ | ETA: 0:00:46 Cross validating... 14%|████▋ | ETA: 0:00:47 Cross validating... 16%|█████▏ | ETA: 0:00:47 Cross validating... 17%|█████▋ | ETA: 0:00:48 Cross validating... 19%|██████▏ | ETA: 0:00:47 Cross validating... 21%|██████▋ | ETA: 0:00:47 Cross 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Cross validating... 56%|█████████████████▊ | ETA: 0:00:22 Cross validating... 57%|██████████████████▎ | ETA: 0:00:21 Cross validating... 59%|██████████████████▊ | ETA: 0:00:21 Cross validating... 60%|███████████████████▎ | ETA: 0:00:20 Cross validating... 62%|███████████████████▊ | ETA: 0:00:20 Cross validating... 63%|████████████████████▍ | ETA: 0:00:19 Cross validating... 65%|████████████████████▉ | ETA: 0:00:18 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:17 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:15 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:13 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:12 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:11 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:09 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:09 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:07 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:45 Crossvalidation Results: k MSE 0 440.631728418787 1 287.0111935575496 2 268.4903253112671 3 242.49640975891884 4 235.0891392622637 5 226.74179493070733 6 228.71547048340693 7 229.41909378949413 8 231.53880256784126 9 233.58885341100336 10 235.07354401394514 11 236.39899930661664 12 238.46227562477952 13 240.41841511180462 14 240.4432233433409 15 242.0608132952685 16 242.72254490331898 17 241.8176510205401 18 244.051413451273 19 244.50228427825888 20 244.00677635064216 Best k = 5 45.852778 seconds (125.62 M allocations: 3.147 GiB, 1.03% gc time, 4.67% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:07 Cross validating... 10%|███ | ETA: 0:00:07 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:08 Cross validating... 14%|████▋ | ETA: 0:00:08 Cross validating... 16%|█████▏ | ETA: 0:00:08 Cross validating... 17%|█████▋ | ETA: 0:00:08 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 21%|██████▋ | ETA: 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Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 440.631728418787 1 286.8811370657047 2 269.0529420839194 3 243.4217936459311 4 236.76684277900264 5 228.53767082594246 6 233.53398318831233 7 238.2034285980486 8 240.15861642354417 9 245.38153625462866 10 250.2677984658377 11 255.21963062894957 12 257.03049337306646 13 260.39610282480965 14 264.450767413969 15 269.9109544689748 16 267.7250159054543 17 274.8960153510433 18 285.8725788133495 19 277.36761204918025 20 298.71388013098493 Best k = 5 11.596291 seconds (30.48 M allocations: 614.267 MiB, 0.85% gc time, 0.47% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 57.9s **** 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: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.130810 seconds (17.00 M allocations: 337.764 MiB, 1.18% gc time, 42.18% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.515151 seconds (16.17 M allocations: 286.700 MiB, 1.47% gc time, 1.53% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:20 Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 4%|█▎ | ETA: 0:00:46 Cross validating... 5%|█▋ | ETA: 0:00:39 Cross validating... 6%|█▉ | ETA: 0:00:34 Cross validating... 7%|██▎ | ETA: 0:00:30 Cross validating... 8%|██▌ | ETA: 0:00:27 Cross validating... 9%|██▉ | ETA: 0:00:25 Cross validating... 10%|███▎ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:22 Cross validating... 12%|███▉ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:21 Cross validating... 14%|████▌ | ETA: 0:00:20 Cross validating... 15%|████▊ | ETA: 0:00:20 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:18 Cross validating... 21%|██████▊ | ETA: 0:00:17 Cross validating... 22%|███████ | ETA: 0:00:17 Cross 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1924.6534574909556 14 1980.740148878419 15 1996.3982606647462 16 1990.0125396127912 17 2027.7440403662772 18 2042.8911594288681 19 2068.2894992702227 20 2056.9769559714587 Best k = 9 17.105597 seconds (318.01 k allocations: 199.529 MiB, 0.38% gc time, 9.63% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 22.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m56.7s **** 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | 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| 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:20 Cross validating... 20%|██████▍ | ETA: 0:00:20 Cross validating... 21%|██████▊ | ETA: 0:00:19 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 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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: 0:00:13 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: 0:00:17 Cross 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m28.5s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [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:489 [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 4.2s RNG of the outermost testset: Xoshiro(0xb072531bcf2f3f40, 0xf7b2fb92b9e7b498, 0x20ed5ef8971a8da9, 0xf3d1e76e3ef51b51, 0xe6eb74b2a91ee08c) 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 1154.02s 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 1254.69s: package tests unexpectedly errored