Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2407 (ce8c59448a*) started at 2026-06-19T00:36:35.703 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.35s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.6.1 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.7 [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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[b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.3+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.4+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.7+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.61s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 2.3 s ✓ CodecBzip2 4.2 s ✓ BGEN 7.8 s ✓ VCFTools 26.1 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 23.2 s ✓ MendelIHT 5 dependencies successfully precompiled in 66 seconds. 169 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 92.54s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_EQcALh/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.126 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 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nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:219 └ @ Distributions ~/.julia/packages/Distributions/nfRUl/src/multivariate/mvnormal.jl:219 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.3s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 2.3s **** 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 = -1635.5079040183239, backtracks = 0, tol = 1.7957646052778549 Iteration 2: loglikelihood = -1445.8173685776565, backtracks = 0, tol = 0.16893532764362304 Iteration 3: loglikelihood = -1426.0407658892104, backtracks = 0, tol = 0.055910575578397854 Iteration 4: loglikelihood = -1424.6578779830472, backtracks = 0, tol = 0.0442020828119111 Iteration 5: loglikelihood = -1424.4394027989522, backtracks = 0, tol = 0.004605602244589313 Iteration 6: loglikelihood = -1424.4371175240346, backtracks = 0, tol = 0.0003961869001338313 Iteration 7: loglikelihood = -1424.4370859640132, backtracks = 0, tol = 6.144091433208163e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06480693817138672 Final loglikelihood: -1424.4370859640132 SNP PVE: 0.876929460580801 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 394 -1.98741 2 │ 1738 -0.404713 3 │ 2461 -0.778787 4 │ 3222 0.248566 5 │ 6618 -0.404493 6 │ 7481 -0.504423 7 │ 7578 -0.560832 8 │ 7674 1.25329 9 │ 7708 0.370559 10 │ 8875 0.14285 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00790499Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1454.7596420003463, backtracks = 0, tol = 0.3880670228384457 Iteration 2: loglikelihood = -1359.8089950176493, backtracks = 0, tol = 0.06825190633996803 Iteration 3: loglikelihood = -1335.5272594856426, backtracks = 0, tol = 0.0750726303802966 Iteration 4: loglikelihood = -1322.5541002158645, backtracks = 0, tol = 0.058855508619731774 Iteration 5: loglikelihood = -1317.7144437060713, backtracks = 0, tol = 0.03261044199339968 Iteration 6: loglikelihood = -1316.0327733276931, backtracks = 1, tol = 0.012897071219693754 Iteration 7: loglikelihood = -1314.7539674562217, backtracks = 1, tol = 0.06298587519833758 Iteration 8: loglikelihood = -1313.0026240749626, backtracks = 0, tol = 0.016651845861255465 Iteration 9: loglikelihood = -1312.6986069266143, backtracks = 1, tol = 0.006880377424736484 Iteration 10: loglikelihood = -1311.94652720566, backtracks = 1, tol = 0.05500120125472005 Iteration 11: loglikelihood = -1311.7715075618548, backtracks = 1, tol = 0.003892025351031373 Iteration 12: loglikelihood = -1311.7298971219748, backtracks = 2, tol = 0.0015853822532195829 Iteration 13: loglikelihood = -1311.7035827190405, backtracks = 2, tol = 0.0014571210450733147 Iteration 14: loglikelihood = -1311.687495220159, backtracks = 2, tol = 0.001240530150789293 Iteration 15: loglikelihood = -1311.677979664245, backtracks = 2, tol = 0.0010024983323414852 Iteration 16: loglikelihood = -1311.6724797966033, backtracks = 2, tol = 0.0007812927323307768 Iteration 17: loglikelihood = -1311.6693419911983, backtracks = 2, tol = 0.0005974402253330033 Iteration 18: loglikelihood = -1311.6675636063655, backtracks = 2, tol = 0.00045246197148876577 Iteration 19: loglikelihood = -1311.6665590161654, backtracks = 2, tol = 0.00034113879022360443 Iteration 20: loglikelihood = -1311.665992500235, backtracks = 2, tol = 0.00025662428452089936 Iteration 21: loglikelihood = -1311.6656733227, backtracks = 2, tol = 0.00019283436901557528 Iteration 22: loglikelihood = -1311.6654935936035, backtracks = 2, tol = 0.0001448092139530308 Iteration 23: loglikelihood = -1311.6653924217228, backtracks = 2, tol = 0.00010870593102627869 Iteration 24: loglikelihood = -1311.6653354830871, backtracks = 2, tol = 8.158438699700738e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1483.1622350172913, backtracks = 0, tol = 0.3536082581517932 Iteration 2: loglikelihood = -1452.439108161352, backtracks = 0, tol = 0.13988706783903043 Iteration 3: loglikelihood = -1449.290004924108, backtracks = 0, tol = 0.0985005597042789 Iteration 4: loglikelihood = -1445.1741540497758, backtracks = 0, tol = 0.09087332276691805 Iteration 5: loglikelihood = -1443.198376980025, backtracks = 0, tol = 0.06766582362035403 Iteration 6: loglikelihood = -1443.0599279937635, backtracks = 1, tol = 0.004566682887119853 Iteration 7: loglikelihood = -1443.0219717247373, backtracks = 1, tol = 0.0023713310924675887 Iteration 8: loglikelihood = -1443.0111711311222, backtracks = 1, tol = 0.001279004487957992 Iteration 9: loglikelihood = -1443.0080785808543, backtracks = 1, tol = 0.0007350866335517622 Iteration 10: loglikelihood = -1443.0072108647732, backtracks = 1, tol = 0.0004292097745613635 Iteration 11: loglikelihood = -1443.0070734072588, backtracks = 2, tol = 0.000123266614484245 Iteration 12: loglikelihood = -1443.0069947688967, backtracks = 2, tol = 9.498878284833728e-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 = -1726.1390063447493, backtracks = 0, tol = 0.774971050014847 Iteration 2: loglikelihood = -1444.477891566791, backtracks = 0, tol = 0.12097756642085615 Iteration 3: loglikelihood = -1407.6298542083439, backtracks = 0, tol = 0.03962362306923937 Iteration 4: loglikelihood = -1405.78917693114, backtracks = 0, tol = 0.02820650150445906 Iteration 5: loglikelihood = -1405.5133051093685, backtracks = 0, tol = 0.028105108147707353 Iteration 6: loglikelihood = -1405.20162520989, backtracks = 0, tol = 0.0031737693056566522 Iteration 7: loglikelihood = -1405.1957898207238, backtracks = 1, tol = 0.0002897102344843247 Iteration 8: loglikelihood = -1405.1941771967427, backtracks = 1, tol = 0.00013336950065420092 Iteration 9: loglikelihood = -1405.193747701237, backtracks = 1, tol = 7.145129143002358e-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 = -1461.027021143695, backtracks = 0, tol = 0.24270637070872242 Iteration 2: loglikelihood = -1409.3757786482724, backtracks = 0, tol = 0.05934663163565607 Iteration 3: loglikelihood = -1406.231147773189, backtracks = 0, tol = 0.033354208477831174 Iteration 4: loglikelihood = -1406.0579264071243, backtracks = 0, tol = 0.02894251591026233 Iteration 5: loglikelihood = -1405.7394983853358, backtracks = 0, tol = 0.03127181515437282 Iteration 6: loglikelihood = -1405.3831055209694, backtracks = 0, tol = 0.0037210208068947197 Iteration 7: loglikelihood = -1405.3805907619026, backtracks = 1, tol = 0.00018779436931843851 Iteration 8: loglikelihood = -1405.3799307237132, backtracks = 1, tol = 0.00010868473055459665 Iteration 9: loglikelihood = -1405.3797608955172, backtracks = 1, tol = 5.8865414819073764e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1564.4648054812285, backtracks = 0, tol = 0.2257538879325429 Iteration 2: loglikelihood = -1472.4845225406946, backtracks = 0, tol = 0.12774016580795614 Iteration 3: loglikelihood = -1435.0239306999397, backtracks = 0, tol = 0.13256537206487964 Iteration 4: loglikelihood = -1388.8408875932612, backtracks = 0, tol = 0.0881063592844063 Iteration 5: loglikelihood = -1373.6280653610152, backtracks = 0, tol = 0.06296752420582646 Iteration 6: loglikelihood = -1359.501938885171, backtracks = 0, tol = 0.06665167060824093 Iteration 7: loglikelihood = -1351.590694120248, backtracks = 0, tol = 0.05045360724086156 Iteration 8: loglikelihood = -1348.7002512677534, backtracks = 0, tol = 0.022524024589333218 Iteration 9: loglikelihood = -1341.7660884490433, backtracks = 0, tol = 0.061009964943124946 Iteration 10: loglikelihood = -1340.17715457381, backtracks = 0, tol = 0.013907231735944377 Iteration 11: loglikelihood = -1339.8585967792808, backtracks = 0, tol = 0.005475388569795805 Iteration 12: loglikelihood = -1339.6982366009304, backtracks = 0, tol = 0.007502153212451625 Iteration 13: loglikelihood = -1339.610768519325, backtracks = 0, tol = 0.00305418814814146 Iteration 14: loglikelihood = -1339.5623626391975, backtracks = 0, tol = 0.004113359285778096 Iteration 15: loglikelihood = -1339.5355107286275, backtracks = 0, tol = 0.0016786861628105502 Iteration 16: loglikelihood = -1339.520536015147, backtracks = 0, tol = 0.0023013004043637114 Iteration 17: loglikelihood = -1339.5122081383086, backtracks = 0, tol = 0.0009366851507624925 Iteration 18: loglikelihood = -1339.5075515177716, backtracks = 0, tol = 0.0012967827112813901 Iteration 19: loglikelihood = -1339.504962394138, backtracks = 0, tol = 0.0005191920420698018 Iteration 20: loglikelihood = -1339.5035135159624, backtracks = 0, tol = 0.0007330784755126724 Iteration 21: loglikelihood = -1339.5027095311955, backtracks = 0, tol = 0.0002868559099892205 Iteration 22: loglikelihood = -1339.50225989535, backtracks = 0, tol = 0.00041466580253210906 Iteration 23: loglikelihood = -1339.5020112849306, backtracks = 0, tol = 0.00015798060626255814 Iteration 24: loglikelihood = -1339.5018725203477, backtracks = 0, tol = 0.00023422519283561045 Iteration 25: loglikelihood = -1339.5017961907877, backtracks = 0, tol = 8.663940532748823e-5 1.120678 seconds (2.34 M allocations: 46.206 MiB, 7.63% gc time, 59.13% 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 = -1588.7455736525017, backtracks = 0, tol = 0.2257538879325429 Iteration 2: loglikelihood = -1533.4539462466555, backtracks = 0, tol = 0.15064907012931897 Iteration 3: loglikelihood = -1501.624905117393, backtracks = 0, tol = 0.12258287916696929 Iteration 4: loglikelihood = -1475.303822541863, backtracks = 0, tol = 0.08138098328974494 Iteration 5: loglikelihood = -1451.8842628339657, backtracks = 0, tol = 0.08524379814499741 Iteration 6: loglikelihood = -1432.674810260277, backtracks = 0, tol = 0.08152515170272492 Iteration 7: loglikelihood = -1419.721058832331, backtracks = 0, tol = 0.08485576118349936 Iteration 8: loglikelihood = -1411.542668684766, backtracks = 0, tol = 0.08434414193764521 Iteration 9: loglikelihood = -1402.8098175612051, backtracks = 0, tol = 0.06940652846871002 Iteration 10: loglikelihood = -1396.9181369783855, backtracks = 0, tol = 0.007036832748150743 Iteration 11: loglikelihood = -1391.74419489187, backtracks = 0, tol = 0.0038555112348244184 Iteration 12: loglikelihood = -1387.4038971648492, backtracks = 0, tol = 0.0013691121735681863 Iteration 13: loglikelihood = -1383.5814622596781, backtracks = 0, tol = 0.0009731479152387408 Iteration 14: loglikelihood = -1381.7709938079706, backtracks = 0, tol = 0.06524959554655427 Iteration 15: loglikelihood = -1377.386877543739, backtracks = 0, tol = 0.0651160291989087 Iteration 16: loglikelihood = -1374.7944428571577, backtracks = 0, tol = 0.004864509163574357 Iteration 17: loglikelihood = -1372.45678851803, backtracks = 0, tol = 0.0015212943561310366 Iteration 18: loglikelihood = -1370.4132954827737, backtracks = 0, tol = 0.0006014327614868836 Iteration 19: loglikelihood = -1368.5556497755665, backtracks = 0, tol = 0.0004405959171034027 Iteration 20: loglikelihood = -1365.558724039143, backtracks = 1, tol = 0.0002019425611597565 Iteration 21: loglikelihood = -1363.0607361099283, backtracks = 1, tol = 0.0003815943401240538 Iteration 22: loglikelihood = -1360.9538324310302, backtracks = 1, tol = 0.0004248134695114663 Iteration 23: loglikelihood = -1359.1578053422859, backtracks = 1, tol = 0.0004187581977408126 Iteration 24: loglikelihood = -1357.6123561588365, backtracks = 1, tol = 0.00039347183514917865 Iteration 25: loglikelihood = -1356.271470965327, backtracks = 1, tol = 0.00036219645082335647 Iteration 26: loglikelihood = -1355.0994218613287, backtracks = 1, tol = 0.0003305738026257725 Iteration 27: loglikelihood = -1353.9947192308398, backtracks = 1, tol = 0.0003008886147894119 Iteration 28: loglikelihood = -1353.0172239919398, backtracks = 1, tol = 0.00028368006530308273 Iteration 29: loglikelihood = -1352.1483708627777, backtracks = 1, tol = 0.0002684058137334416 Iteration 30: loglikelihood = -1351.372054525167, backtracks = 1, tol = 0.0002522085241524067 Iteration 31: loglikelihood = -1350.6750459999978, backtracks = 1, tol = 0.00023649124831764243 Iteration 32: loglikelihood = -1350.0463520649976, backtracks = 1, tol = 0.00022177815520773626 Iteration 33: loglikelihood = -1349.4768180883161, backtracks = 1, tol = 0.00020826176301481206 Iteration 34: loglikelihood = -1348.9587875599682, backtracks = 1, tol = 0.0001959553562049735 Iteration 35: loglikelihood = -1348.4280017326098, backtracks = 1, tol = 0.00018479141823689335 Iteration 36: loglikelihood = -1347.9407256663628, backtracks = 1, tol = 0.00018456036368539808 Iteration 37: loglikelihood = -1347.4944175655846, backtracks = 1, tol = 0.00018145728083550448 Iteration 38: loglikelihood = -1347.0847280623707, backtracks = 1, tol = 0.0001755293850356918 Iteration 39: loglikelihood = -1346.707856314751, backtracks = 1, tol = 0.00016864605193057697 Iteration 40: loglikelihood = -1346.3603268072434, backtracks = 1, tol = 0.00016148636237809497 Iteration 41: loglikelihood = -1346.0390662220193, backtracks = 1, tol = 0.00015446066739518207 Iteration 42: loglikelihood = -1345.7413697443674, backtracks = 1, tol = 0.0001477574189479918 Iteration 43: loglikelihood = -1345.464867262321, backtracks = 1, tol = 0.00014145719637948122 Iteration 44: loglikelihood = -1345.207483588412, backtracks = 1, tol = 0.00013558000087032513 Iteration 45: loglikelihood = -1344.9674002627264, backtracks = 1, tol = 0.00013011485492005017 Iteration 46: loglikelihood = -1344.7430203924466, backtracks = 1, tol = 0.00012503580369097297 Iteration 47: loglikelihood = -1344.5259494554339, backtracks = 1, tol = 0.00012031098884858183 Iteration 48: loglikelihood = -1344.3226045206443, backtracks = 1, tol = 0.00011765724973709738 Iteration 49: loglikelihood = -1344.1320173441427, backtracks = 1, tol = 0.00011465302223267481 Iteration 50: loglikelihood = -1343.953132049696, backtracks = 1, tol = 0.00011114139152039778 Iteration 51: loglikelihood = -1343.7850145845784, backtracks = 1, tol = 0.00010786409071738294 Iteration 52: loglikelihood = -1343.6268092407865, backtracks = 1, tol = 0.00010475715334886206 Iteration 53: loglikelihood = -1343.477742827215, backtracks = 1, tol = 0.00010171601947960654 Iteration 54: loglikelihood = -1343.3371155596624, backtracks = 1, tol = 9.87756488968242e-5 0.633436 seconds (2.67 M allocations: 49.060 MiB, 3.89% 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 = -3834.2124, backtracks = 0, tol = 0.07277453068521703 Iteration 2: loglikelihood = -3807.6653, backtracks = 0, tol = 0.03730527038323034 Iteration 3: loglikelihood = -3804.6685, backtracks = 1, tol = 0.006777443596285104 Iteration 4: loglikelihood = -3787.089, backtracks = 1, tol = 0.05597277499118216 Iteration 5: loglikelihood = -3760.1602, backtracks = 0, tol = 0.08107205585102091 Iteration 6: loglikelihood = -3757.0442, backtracks = 1, tol = 0.008225885013514697 Iteration 7: loglikelihood = -3756.107, backtracks = 1, tol = 0.0043509503807547135 Iteration 8: loglikelihood = -3755.8086, backtracks = 1, tol = 0.0025393853540091366 Iteration 9: loglikelihood = -3755.722, backtracks = 1, tol = 0.0017282414875991648 Iteration 10: loglikelihood = -3755.699, backtracks = 1, tol = 0.0009516000979424662 Iteration 11: loglikelihood = -3755.6902, backtracks = 1, tol = 0.0004896326859252611 Iteration 12: loglikelihood = -3755.6948, backtracks = 3, tol = 6.163018392894608e-5 26.627240 seconds (13.92 M allocations: 650.506 MiB, 1.57% gc time, 97.42% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3727.7136, backtracks = 0, tol = 0.07277453068521703 Iteration 2: loglikelihood = -3622.0413, backtracks = 0, tol = 0.03807819612435514 Iteration 3: loglikelihood = -3395.4558, backtracks = 1, tol = 0.006814345746353492 Iteration 4: loglikelihood = -3111.0627, backtracks = 1, tol = 0.005621322977793799 Iteration 5: loglikelihood = -3099.0608, backtracks = 0, tol = 0.09550991168635925 Iteration 6: loglikelihood = -2866.3306, backtracks = 0, tol = 0.0991328371979431 Iteration 7: loglikelihood = -2747.8567, backtracks = 0, tol = 0.09936646426685311 Iteration 8: loglikelihood = -2565.4973, backtracks = 0, tol = 0.10839101455644903 Iteration 9: loglikelihood = -2457.5344, backtracks = 0, tol = 0.10773686159494389 Iteration 10: loglikelihood = -2383.2002, backtracks = 0, tol = 0.11681012777491154 Iteration 11: loglikelihood = -2320.6482, backtracks = 0, tol = 0.11583461940074169 Iteration 12: loglikelihood = -2283.0894, backtracks = 0, tol = 0.10636071970717467 Iteration 13: loglikelihood = -2260.4802, backtracks = 0, tol = 0.10600197667606354 Iteration 14: loglikelihood = -2241.3809, backtracks = 0, tol = 0.11041047191659667 Iteration 15: loglikelihood = -2240.1528, backtracks = 0, tol = 0.11055118664387387 Iteration 16: loglikelihood = -2233.0198, backtracks = 0, tol = 0.11392204330219337 Iteration 17: loglikelihood = -2217.1443, backtracks = 1, tol = 0.044357852028729154 Iteration 18: loglikelihood = -2211.2856, backtracks = 0, tol = 0.0922552923232838 Iteration 19: loglikelihood = -2207.5195, backtracks = 1, tol = 0.023066493740139887 Iteration 20: loglikelihood = -2202.9966, backtracks = 1, tol = 0.05209770249051973 Iteration 21: loglikelihood = -2199.6821, backtracks = 0, tol = 0.08790426716226475 Iteration 22: loglikelihood = -2199.001, backtracks = 1, tol = 0.008082569961613688 Iteration 23: loglikelihood = -2198.8206, backtracks = 1, tol = 0.004208254155468913 Iteration 24: loglikelihood = -2198.7727, backtracks = 1, tol = 0.0021721729727369513 Iteration 25: loglikelihood = -2198.762, backtracks = 1, tol = 0.0011204273671107873 Iteration 26: loglikelihood = -2198.7588, backtracks = 1, tol = 0.0006148657339641896 Iteration 27: loglikelihood = -2198.7578, backtracks = 1, tol = 0.00036174065757007634 Iteration 28: loglikelihood = -2198.7559, backtracks = 1, tol = 0.00020942797383959044 Iteration 29: loglikelihood = -2198.7551, backtracks = 2, tol = 6.0011080512817196e-5 0.215112 seconds (1.70 M allocations: 28.122 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.3s **** 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.014426 seconds (1.02 M allocations: 132.820 MiB, 0.89% gc time, 90.87% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.4s 10.008884 seconds (4.00 M allocations: 82.389 MiB, 0.39% gc time, 0.69% compilation time) 5.276220 seconds (3.98 M allocations: 91.679 MiB, 0.40% gc time) 10.601170 seconds (20.38 M allocations: 438.620 MiB, 0.68% gc time, 17.13% compilation time: 78% of which was recompilation) 8.568849 seconds (20.18 M allocations: 434.186 MiB, 1.07% gc time) 38.019809 seconds (3.35 M allocations: 4.228 GiB, 6.81% gc time, 30.18% compilation time) 55.992049 seconds (72.50 k allocations: 183.667 MiB, 0.24% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m27.6s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 15.433 ms (78 allocations: 4.56 KiB) 4.393 μs (0 allocations: 0 bytes) 151.660 μs (4 allocations: 288 bytes) 6.773 μs (0 allocations: 0 bytes) 47.910 μs (2 allocations: 64 bytes) 30.100 μs (0 allocations: 0 bytes) 32.470 μs (0 allocations: 0 bytes) 29.950 μs (0 allocations: 0 bytes) 106.599 μs (0 allocations: 0 bytes) 41.650 ms (78 allocations: 4.56 KiB) 18.020 μs (0 allocations: 0 bytes) 166.100 μs (4 allocations: 288 bytes) 33.970 μs (0 allocations: 0 bytes) 261.960 μs (2 allocations: 64 bytes) 83.390 μs (0 allocations: 0 bytes) 182.260 μs (0 allocations: 0 bytes) 172.040 μs (0 allocations: 0 bytes) 224.680 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m12.8s **** 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 0.455106 seconds (43.84 k allocations: 5.329 MiB, 63.89% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 2.035080 seconds (256.73 k allocations: 167.469 MiB, 55.72% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:55 Cross validating... 11%|███▌ | ETA: 0:01:06 Cross validating... 14%|████▋ | ETA: 0:00:50 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:19 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ 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validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 2743.559098566063 1 1445.894432783787 2 891.2512877151689 3 704.7051268571562 4 604.7047333461273 5 521.0927281809504 6 473.13971488387983 7 408.28769710854095 8 364.86165174559505 9 344.13183122065965 10 345.63393965665193 11 346.9649467646916 12 351.1550275506218 13 353.3471307710373 14 356.0095779848468 15 367.79000135640104 16 369.71826990505735 17 369.43601072780325 18 380.46958469403216 19 395.87041487275167 20 392.9058506611102 Best k = 9 12.835053 seconds (11.26 M allocations: 298.526 MiB, 1.05% gc time, 61.67% 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: 0:00:03 Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 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... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 2743.559098566063 1 1449.1880033300254 2 894.2738162463052 3 708.7215184615362 4 608.3243858425366 5 525.8140051780418 6 481.0526929064773 7 414.0382399773555 8 370.32778345111774 9 351.1825987177227 10 355.8188292106222 11 360.77983424993886 12 369.39527046818574 13 374.9579096327515 14 387.9978358360382 15 390.0144931288735 16 396.60846298524905 17 396.1710484999861 18 394.4994011134007 19 418.7937307348875 20 404.78793184429946 Best k = 9 5.148402 seconds (10.45 M allocations: 219.791 MiB, 2.06% gc time, 1.09% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:21 Cross validating... 10%|███ | ETA: 0:02:00 Cross validating... 16%|█████▏ | ETA: 0:01:08 Cross validating... 21%|██████▋ | ETA: 0:00:50 Cross validating... 25%|████████▏ | ETA: 0:00:39 Cross validating... 30%|█████████▋ | ETA: 0:00:31 Cross 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997.9806260986327 3 796.3598967285157 4 653.0125831298828 5 553.7540711669922 6 454.5304691772461 7 385.2932152709961 8 348.24323785400395 9 336.74355517578124 10 344.88825115966796 11 344.28650775146485 12 347.542530456543 13 348.95763018798834 14 352.262841003418 15 353.6341002197266 16 366.99301043701166 17 361.5490489501953 18 372.7004539184571 19 377.93246697998046 20 365.93806115722657 Best k = 9 16.326929 seconds (12.11 M allocations: 304.154 MiB, 1.01% gc time, 83.95% 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... 19%|██████▏ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross 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1302.9236037597657 2 1001.2940384521485 3 797.0523731689452 4 656.0729310302735 5 560.8029986572266 6 459.0963904418946 7 390.3264998779297 8 355.7096306762695 9 346.2537088623047 10 356.80901489257815 11 366.58829681396486 12 374.7049376220703 13 380.51362670898436 14 391.8535552978515 15 395.99784472656256 16 405.31749548339843 17 422.82843395996093 18 414.4791848144531 19 418.4653688354492 20 430.85138513183597 Best k = 9 2.605958 seconds (10.48 M allocations: 192.490 MiB, 2.20% gc time, 1.81% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.4s **** 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: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:23 Cross 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Crossvalidation Results: k MSE 0 464.5718009854164 1 360.02972775683384 2 318.6192361400015 3 297.5978054517032 4 293.92905664892635 5 288.35683742093 6 293.7737893175059 7 291.75960364213256 8 290.95010650994436 9 286.6332220106664 10 285.27464051762524 11 305.5928533330466 12 304.6485461826484 13 303.44120600490515 14 315.69925624268006 15 317.93740452425476 16 297.8047761877223 17 305.6841210230346 18 292.6588040545435 19 338.70659451578916 20 303.85368810532435 Best k = 10 8.551635 seconds (16.74 M allocations: 392.146 MiB, 1.06% gc time, 31.62% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 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97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.5718009854164 1 360.1629682724173 2 319.27424491425046 3 298.3519190922197 4 296.3980776071479 5 290.71384549268225 6 313.21309562079466 7 314.1451248460319 8 315.57143778388064 9 307.81950148291776 10 317.3584325503341 11 324.2651936550909 12 317.6532042812306 13 347.3159798888073 14 359.22519542576805 15 330.5198434036543 16 360.11832085462925 17 366.2627199255978 18 358.380443550639 19 361.4953325731679 20 375.1555178944772 Best k = 5 6.149460 seconds (17.14 M allocations: 353.582 MiB, 1.61% gc time, 1.15% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.2s **** 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: 0:00:46 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... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 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... 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: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 465.2240384874132 1 424.88087167223625 2 403.0396179366671 3 381.4235623495711 4 354.2345223960855 5 345.3126290473582 6 339.57412955521824 7 319.8933520302968 8 332.05912290117317 9 317.7145193338229 10 316.48537450650923 11 320.69115459920863 12 327.359915092615 13 340.13724225960635 14 325.11181183911515 15 327.90012938666143 16 329.5971573388216 17 343.3252816821224 18 335.600235723467 19 334.8999473781532 20 337.0868284688625 Best k = 10 7.134041 seconds (16.77 M allocations: 397.819 MiB, 7.21% gc time, 37.22% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 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 0 465.2240384874132 1 425.10805035535077 2 404.91491825822845 3 384.57522946611493 4 364.2896721125212 5 350.09442222152416 6 346.10930615376856 7 334.42814643206145 8 344.23108924700443 9 331.10142930375895 10 329.6289768737116 11 340.5273916791482 12 349.59283435438647 13 350.729939349878 14 361.96150632270616 15 369.3351733958995 16 378.2371754664896 17 384.0922903655342 18 387.1740349571144 19 393.62855364133463 20 404.46606483705466 Best k = 10 4.176671 seconds (17.06 M allocations: 350.522 MiB, 1.61% gc time, 1.13% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 8%|██▌ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 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Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 673.6011139541209 1 510.24213675110303 2 418.9439428889504 3 399.8726724414146 4 398.2866089763722 5 396.2407259479571 6 389.2009260187724 7 390.45202491815337 8 387.16764941186125 9 386.7181150402931 10 396.6545126989238 11 391.5740899088611 12 389.8764707730187 13 390.223543113803 14 398.8166697059628 15 404.41632941264197 16 395.26767861155804 17 408.0204221752151 18 397.40157959688474 19 409.67234134793597 20 410.221268702609 Best k = 9 8.587433 seconds (15.32 M allocations: 368.554 MiB, 0.91% gc time, 31.15% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | 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... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross 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100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 673.6011139541209 1 509.0980008370527 2 422.80551129429546 3 409.16941548938996 4 397.47139968453564 5 405.24611917701145 6 412.1700676391189 7 409.3102388701502 8 406.79939008238557 9 407.70583324156564 10 402.9142977793768 11 417.1283952433216 12 415.62989199020666 13 424.402538781821 14 422.4310148916644 15 420.7131965438169 16 439.7537912413344 17 436.5831179798265 18 441.0925585313987 19 433.8134615789938 20 445.7331924637603 Best k = 4 6.050325 seconds (14.51 M allocations: 293.370 MiB, 0.98% gc time, 1.09% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 15.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 8%|██▌ | ETA: 0:00:38 Cross validating... 10%|███ | ETA: 0:00:32 Cross validating... 11%|███▌ | ETA: 0:00:36 Cross validating... 13%|████▏ | ETA: 0:00:39 Cross validating... 14%|████▋ | ETA: 0:00:35 Cross validating... 16%|█████▏ | ETA: 0:00:32 Cross validating... 17%|█████▋ | ETA: 0:00:34 Cross validating... 19%|██████▏ | ETA: 0:00:32 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 25%|████████▏ | ETA: 0:00:26 Cross validating... 27%|████████▋ | ETA: 0:00:28 Cross validating... 29%|█████████▏ | ETA: 0:00:28 Cross validating... 30%|█████████▋ | ETA: 0:00:27 Cross validating... 32%|██████████▏ | ETA: 0:00:28 Cross validating... 33%|██████████▋ | ETA: 0:00:28 Cross validating... 37%|███████████▋ | ETA: 0:00:25 Cross validating... 40%|████████████▊ | ETA: 0:00:22 Cross validating... 43%|█████████████▊ | ETA: 0:00:21 Cross validating... 46%|██████████████▊ | ETA: 0:00:18 Cross validating... 49%|███████████████▊ | ETA: 0:00:16 Cross validating... 52%|████████████████▊ | ETA: 0:00:15 Cross validating... 54%|█████████████████▎ | ETA: 0:00:15 Cross validating... 56%|█████████████████▊ | ETA: 0:00:14 Cross validating... 57%|██████████████████▎ | ETA: 0:00:13 Cross validating... 59%|██████████████████▊ | ETA: 0:00:12 Cross validating... 60%|███████████████████▎ | ETA: 0:00:12 Cross validating... 62%|███████████████████▊ | ETA: 0:00:12 Cross validating... 63%|████████████████████▍ | ETA: 0:00:12 Cross validating... 65%|████████████████████▉ | ETA: 0:00:12 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:11 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:10 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:08 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:07 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:07 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:06 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:06 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:05 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:05 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:04 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:04 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:03 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:33 Crossvalidation Results: k MSE 0 327.37975108339134 1 265.7330335439903 2 232.98363064817937 3 223.12903118323143 4 225.36307120544512 5 224.96437965294234 6 226.07486117748442 7 224.0615768299483 8 224.5139651335304 9 226.1670299548369 10 225.72362580491838 11 226.53946736157087 12 225.50835718750056 13 226.14631802913323 14 226.19215802874197 15 228.34365084695034 16 229.66971917340658 17 228.72978682264005 18 233.56398115056962 19 232.3689107574691 20 233.98777606519417 Best k = 3 34.130195 seconds (96.74 M allocations: 2.425 GiB, 1.06% gc time, 6.76% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross 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100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 327.37975108339134 1 265.36568012175496 2 233.43943599623867 3 224.24112648368566 4 229.999505367515 5 232.58106884736776 6 233.7513875955957 7 232.52724143151306 8 231.3903240752096 9 239.6862099451062 10 235.38433962889735 11 250.09861366581418 12 243.58761987493318 13 242.74191135301146 14 241.96312782691768 15 267.6033999239574 16 254.72821774388382 17 262.56077003965527 18 272.6138195537562 19 264.6305815816785 20 269.1454948075973 Best k = 3 11.127755 seconds (31.04 M allocations: 633.498 MiB, 0.96% gc time, 0.62% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 45.7s **** 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 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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 6.231076 seconds (16.96 M allocations: 336.386 MiB, 1.59% gc time, 45.95% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 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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 3.286051 seconds (16.17 M allocations: 286.687 MiB, 1.78% gc time, 1.96% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.0s **** 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! **** **** 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validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:20 Crossvalidation Results: k MSE 1 2354.3264544745584 2 2007.676762586869 3 1803.3100882409053 4 1601.7234162365726 5 1524.2531540624987 6 1505.8395337537847 7 1511.9727695109602 8 1518.5520308436767 9 1526.170161245008 10 1539.2530610969086 11 1558.4552033010332 12 1561.4611595670174 13 1569.741617695406 14 1577.90162339457 15 1571.183890694027 16 1588.3779815585096 17 1598.8943197664962 18 1593.674597008357 19 1592.206280241583 20 1598.9484304318576 Best k = 6 20.478051 seconds (325.35 k allocations: 222.889 MiB, 0.66% gc time, 8.25% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 25.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m05.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 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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: 0:00:12 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: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 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validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 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: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 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 1m27.2s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:522 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.9s RNG of the outermost testset: Xoshiro(0xc363a649bdfd71c0, 0xabf88813d014223a, 0xc1ac43a54dd70d19, 0x5e2b0a818c088731, 0x22d7da4a87a8cc42) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 Testing failed after 1099.04s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1238.69s: package tests unexpectedly errored