Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2232 (ecceaba1c5*) started at 2026-05-27T10:34:42.008 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.09s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.6.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [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 v0.2.7 [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] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.4 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.125 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [38e38edf] + GLM v1.9.4 [c27321d9] + Glob v1.5.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.7 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 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[b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [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 v1.5.1+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.3+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 v3.5.6+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 5.59s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.4 s ✓ BGEN 6.8 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 21.7 s ✓ MendelIHT 3 dependencies successfully precompiled in 35 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 58.6s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_n7DnxF/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 v0.25.125 [38e38edf] GLM v1.9.4 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.2 [2913bbd2] StatsBase v0.34.10 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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: `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 = cholesky!(A::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}, ::Val{true}; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:216 └ @ LinearAlgebra ./deprecated.jl:216 Test Summary: | Pass Total Time loglikelihood | 4 4 14.8s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 10.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.4s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 1.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 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 = -1587.5196529619066, backtracks = 0, tol = 1.5113736302325036 Iteration 2: loglikelihood = -1407.0232724590694, backtracks = 0, tol = 0.169787531799438 Iteration 3: loglikelihood = -1393.3132504221321, backtracks = 0, tol = 0.058107545806150414 Iteration 4: loglikelihood = -1392.6575334477943, backtracks = 0, tol = 0.04512714572367041 Iteration 5: loglikelihood = -1392.5881876822943, backtracks = 0, tol = 0.002497462805422913 Iteration 6: loglikelihood = -1392.5877341081318, backtracks = 0, tol = 0.00018720458650526753 Iteration 7: loglikelihood = -1392.5877282843398, backtracks = 0, tol = 3.105142757035706e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06290006637573242 Final loglikelihood: -1392.5877282843398 SNP PVE: 0.9263490305615162 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 309 0.859904 2 │ 2162 -1.20568 3 │ 2902 1.01358 4 │ 3368 -0.118846 5 │ 3794 1.64079 6 │ 3947 -0.663558 7 │ 4497 -1.39845 8 │ 6661 -0.245377 9 │ 7665 -1.36758 10 │ 8921 1.48292 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00755188Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 21.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2510.5975224562862, backtracks = 0, tol = 0.3062292847771867 Iteration 2: loglikelihood = -1799.078256992229, backtracks = 0, tol = 0.06073627224027887 Iteration 3: loglikelihood = -1473.0797790877518, backtracks = 0, tol = 0.06691554626300882 Iteration 4: loglikelihood = -1415.6799707513655, backtracks = 0, tol = 0.052317281625347954 Iteration 5: loglikelihood = -1414.529887813536, backtracks = 0, tol = 0.12802060731098508 Iteration 6: loglikelihood = -1380.126549767567, backtracks = 0, tol = 0.041522338995449076 Iteration 7: loglikelihood = -1373.872172287628, backtracks = 0, tol = 0.046021119206155855 Iteration 8: loglikelihood = -1369.3283908854328, backtracks = 1, tol = 0.025808616374515703 Iteration 9: loglikelihood = -1363.5930483962359, backtracks = 0, tol = 0.03786771359828714 Iteration 10: loglikelihood = -1361.3624422112048, backtracks = 0, tol = 0.03996297067295434 Iteration 11: loglikelihood = -1359.192564688054, backtracks = 0, tol = 0.01966722017990357 Iteration 12: loglikelihood = -1358.2188563693562, backtracks = 0, tol = 0.010897921919201158 Iteration 13: loglikelihood = -1357.6109026706697, backtracks = 0, tol = 0.009522315431669507 Iteration 14: loglikelihood = -1357.215855344219, backtracks = 0, tol = 0.0068010256908488526 Iteration 15: loglikelihood = -1356.938790469671, backtracks = 0, tol = 0.006096729635004969 Iteration 16: loglikelihood = -1356.7468264311356, backtracks = 0, tol = 0.0045957755723198025 Iteration 17: loglikelihood = -1356.6082827591406, backtracks = 0, tol = 0.004929813055161489 Iteration 18: loglikelihood = -1356.5099972236587, backtracks = 0, tol = 0.0031246947221951565 Iteration 19: loglikelihood = -1356.4559052494378, backtracks = 1, tol = 0.0019559468859728186 Iteration 20: loglikelihood = -1356.3942917807797, backtracks = 2, tol = 0.00285426176953783 Iteration 21: loglikelihood = -1356.360328757141, backtracks = 2, tol = 0.0019593685070600645 Iteration 22: loglikelihood = -1356.3288589183398, backtracks = 2, tol = 0.002048320545161783 Iteration 23: loglikelihood = -1356.3097065491356, backtracks = 2, tol = 0.0015290776954907106 Iteration 24: loglikelihood = -1356.2922808991245, backtracks = 2, tol = 0.00155373039249134 Iteration 25: loglikelihood = -1356.2814091665987, backtracks = 2, tol = 0.0011773776839422772 Iteration 26: loglikelihood = -1356.2714426505886, backtracks = 2, tol = 0.0011988813881978384 Iteration 27: loglikelihood = -1356.2652406700395, backtracks = 2, tol = 0.000899114141547207 Iteration 28: loglikelihood = -1356.259424160213, backtracks = 2, tol = 0.0009346489268269966 Iteration 29: loglikelihood = -1356.2558798630273, backtracks = 2, tol = 0.0006817980096333812 Iteration 30: loglikelihood = -1356.25243576382, backtracks = 2, tol = 0.0007347661460871224 Iteration 31: loglikelihood = -1356.2504129611918, backtracks = 2, tol = 0.0005134253915703613 Iteration 32: loglikelihood = -1356.2483514498836, backtracks = 2, tol = 0.0005819645674184952 Iteration 33: loglikelihood = -1356.2472013639683, backtracks = 2, tol = 0.00038399448005341344 Iteration 34: loglikelihood = -1356.2459586611833, backtracks = 2, tol = 0.00046368560396178014 Iteration 35: loglikelihood = -1356.2453081014517, backtracks = 2, tol = 0.00028552812978471033 Iteration 36: loglikelihood = -1356.2445577595515, backtracks = 2, tol = 0.0003702798108875391 Iteration 37: loglikelihood = -1356.2441914988476, backtracks = 2, tol = 0.00021164217419689294 Iteration 38: loglikelihood = -1356.2437412614272, backtracks = 2, tol = 0.00029439435625544817 Iteration 39: loglikelihood = -1356.243535609092, backtracks = 2, tol = 0.00015698681078660522 Iteration 40: loglikelihood = -1356.243392979904, backtracks = 3, tol = 0.00011560774712602754 Iteration 41: loglikelihood = -1356.2432262919385, backtracks = 3, tol = 0.0001561454924156179 Iteration 42: loglikelihood = -1356.2430963157988, backtracks = 3, tol = 0.00013677652098792513 Iteration 43: loglikelihood = -1356.2429952181985, backtracks = 3, tol = 0.0001222810242907779 Iteration 44: loglikelihood = -1356.2429167185205, backtracks = 3, tol = 0.00010682647247368014 Iteration 45: loglikelihood = -1356.2428558388006, backtracks = 3, tol = 9.521036130901574e-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 = -1593.9558107992907, backtracks = 0, tol = 0.32831019359320246 Iteration 2: loglikelihood = -1532.254757161396, backtracks = 0, tol = 0.16482061020688024 Iteration 3: loglikelihood = -1503.5983290061345, backtracks = 0, tol = 0.09499991542363517 Iteration 4: loglikelihood = -1494.6826328666796, backtracks = 0, tol = 0.10723893844116297 Iteration 5: loglikelihood = -1492.7820243567562, backtracks = 0, tol = 0.10406619890452978 Iteration 6: loglikelihood = -1492.5729036506177, backtracks = 1, tol = 0.006503315840446463 Iteration 7: loglikelihood = -1492.4821684120782, backtracks = 1, tol = 0.004861129517274606 Iteration 8: loglikelihood = -1492.4649118421246, backtracks = 2, tol = 0.0016562046105491092 Iteration 9: loglikelihood = -1492.4549082069634, backtracks = 2, tol = 0.001241311253442226 Iteration 10: loglikelihood = -1492.4491333900385, backtracks = 2, tol = 0.000954210615814237 Iteration 11: loglikelihood = -1492.445807991681, backtracks = 2, tol = 0.0007324451651352174 Iteration 12: loglikelihood = -1492.4438963840619, backtracks = 2, tol = 0.0005607441702192461 Iteration 13: loglikelihood = -1492.4427989022245, backtracks = 2, tol = 0.00042846563908670017 Iteration 14: loglikelihood = -1492.4421694298323, backtracks = 2, tol = 0.00032690348484032037 Iteration 15: loglikelihood = -1492.4418086523656, backtracks = 2, tol = 0.00024911925841966957 Iteration 16: loglikelihood = -1492.4416019891553, backtracks = 2, tol = 0.0001896599559656243 Iteration 17: loglikelihood = -1492.4414836559033, backtracks = 2, tol = 0.0001442771427277945 Iteration 18: loglikelihood = -1492.4414159206601, backtracks = 2, tol = 0.00010968052169586734 Iteration 19: loglikelihood = -1492.4413771573945, backtracks = 2, tol = 8.333283609368203e-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 = -1751.1209251735681, backtracks = 0, tol = 0.8568184015553525 Iteration 2: loglikelihood = -1431.904017434774, backtracks = 0, tol = 0.11084203361127185 Iteration 3: loglikelihood = -1387.8479452553472, backtracks = 0, tol = 0.041900964111130125 Iteration 4: loglikelihood = -1387.5347977881563, backtracks = 1, tol = 0.0016836753068519017 Iteration 5: loglikelihood = -1387.454625481903, backtracks = 1, tol = 0.000923099568711359 Iteration 6: loglikelihood = -1387.4341524656222, backtracks = 1, tol = 0.0004967273986530325 Iteration 7: loglikelihood = -1387.4289402800973, backtracks = 1, tol = 0.00026274276583160993 Iteration 8: loglikelihood = -1387.427617533735, backtracks = 1, tol = 0.00013691104554529448 Iteration 9: loglikelihood = -1387.4272828393816, backtracks = 1, tol = 7.046230810479823e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1593.2646818524804, backtracks = 0, tol = 0.5073210233715154 Iteration 2: loglikelihood = -1418.1527399428041, backtracks = 0, tol = 0.0774281851396457 Iteration 3: loglikelihood = -1390.6218776973726, backtracks = 0, tol = 0.03857180056928392 Iteration 4: loglikelihood = -1388.1377989443297, backtracks = 0, tol = 0.028058923747412003 Iteration 5: loglikelihood = -1387.9139457734266, backtracks = 0, tol = 0.0024746734712143567 Iteration 6: loglikelihood = -1387.907981543522, backtracks = 0, tol = 0.0005123478479564989 Iteration 7: loglikelihood = -1387.907781231295, backtracks = 0, tol = 9.935200098691853e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** 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) = 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 = -1373.7263486630354, backtracks = 0, tol = 0.12626396758181507 Iteration 2: loglikelihood = -1347.0909538652038, backtracks = 0, tol = 0.0836930140321958 Iteration 3: loglikelihood = -1327.0215780250999, backtracks = 0, tol = 0.08427182274931189 Iteration 4: loglikelihood = -1319.6333485507241, backtracks = 0, tol = 0.10060403529664375 Iteration 5: loglikelihood = -1313.9519504140576, backtracks = 0, tol = 0.07875693847708838 Iteration 6: loglikelihood = -1313.403012322806, backtracks = 1, tol = 0.010582143220408149 Iteration 7: loglikelihood = -1313.148932626408, backtracks = 1, tol = 0.007613464760808875 Iteration 8: loglikelihood = -1313.0705011910022, backtracks = 1, tol = 0.004519159388623891 Iteration 9: loglikelihood = -1313.0497017252892, backtracks = 1, tol = 0.0026602911063254176 Iteration 10: loglikelihood = -1313.0443857721727, backtracks = 1, tol = 0.001269959431868516 Iteration 11: loglikelihood = -1313.0430372942155, backtracks = 1, tol = 0.0006958841613424852 Iteration 12: loglikelihood = -1313.0426957170464, backtracks = 1, tol = 0.0003223091098777898 Iteration 13: loglikelihood = -1313.0426091538764, backtracks = 1, tol = 0.00017776897269541724 Iteration 14: loglikelihood = -1313.0425871869197, backtracks = 1, tol = 8.107645597109928e-5 3.703015 seconds (2.69 M allocations: 51.870 MiB, 1.65% gc time, 17.04% 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 = -1430.454336333715, backtracks = 0, tol = 0.12626396758181507 Iteration 2: loglikelihood = -1408.076991849325, backtracks = 0, tol = 0.0836930140321958 Iteration 3: loglikelihood = -1394.5388958229519, backtracks = 0, tol = 0.08989012750853176 Iteration 4: loglikelihood = -1380.9780975459373, backtracks = 0, tol = 0.0772682786439821 Iteration 5: loglikelihood = -1369.4796535949667, backtracks = 0, tol = 0.08280763199474823 Iteration 6: loglikelihood = -1362.6810576374423, backtracks = 0, tol = 0.08632069193995237 Iteration 7: loglikelihood = -1357.40810459515, backtracks = 0, tol = 0.09513563047323693 Iteration 8: loglikelihood = -1351.5788860446626, backtracks = 0, tol = 0.08134579126107713 Iteration 9: loglikelihood = -1347.9807463284913, backtracks = 0, tol = 0.009258233737315392 Iteration 10: loglikelihood = -1344.876268152183, backtracks = 0, tol = 0.002159968808837808 Iteration 11: loglikelihood = -1342.2217176340441, backtracks = 0, tol = 0.00040476291058383736 Iteration 12: loglikelihood = -1339.9092788760463, backtracks = 0, tol = 0.00022823863099141864 Iteration 13: loglikelihood = -1337.8837156518864, backtracks = 0, tol = 0.0002885502675615829 Iteration 14: loglikelihood = -1336.0975487855012, backtracks = 0, tol = 0.0002785950083987761 Iteration 15: loglikelihood = -1335.5329933827052, backtracks = 0, tol = 0.087169450636231 Iteration 16: loglikelihood = -1333.164602641666, backtracks = 0, tol = 0.08719155352656328 Iteration 17: loglikelihood = -1331.8266069248557, backtracks = 0, tol = 0.004897549243551912 Iteration 18: loglikelihood = -1330.68715452456, backtracks = 0, tol = 0.000735685342435011 Iteration 19: loglikelihood = -1329.648792070612, backtracks = 0, tol = 0.00014681873183898392 Iteration 20: loglikelihood = -1328.7026573108703, backtracks = 0, tol = 0.0001468031743629836 Iteration 21: loglikelihood = -1327.8376126857513, backtracks = 0, tol = 0.00015242199202564365 Iteration 22: loglikelihood = -1327.0443227020223, backtracks = 0, tol = 0.00014727448897824066 Iteration 23: loglikelihood = -1326.314517816293, backtracks = 0, tol = 0.0001374171463786731 Iteration 24: loglikelihood = -1325.6410999953555, backtracks = 0, tol = 0.00012859051967473888 Iteration 25: loglikelihood = -1325.0179495529835, backtracks = 0, tol = 0.000120940049982761 Iteration 26: loglikelihood = -1324.439796511655, backtracks = 0, tol = 0.00011412805964128424 Iteration 27: loglikelihood = -1323.9020708222379, backtracks = 0, tol = 0.00010789874173956204 Iteration 28: loglikelihood = -1323.4007934322224, backtracks = 0, tol = 0.00010218910011160399 Iteration 29: loglikelihood = -1322.9324830631776, backtracks = 0, tol = 9.694020500872289e-5 0.284208 seconds (1.02 M allocations: 18.747 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3584.9275, backtracks = 0, tol = 0.0863182355283885 Iteration 2: loglikelihood = -3557.9578, backtracks = 0, tol = 0.03550120472864148 Iteration 3: loglikelihood = -3555.622, backtracks = 1, tol = 0.008457949029867174 Iteration 4: loglikelihood = -3540.237, backtracks = 1, tol = 0.05777834356436731 Iteration 5: loglikelihood = -3525.4568, backtracks = 0, tol = 0.07980742162029887 Iteration 6: loglikelihood = -3519.7788, backtracks = 0, tol = 0.08345952883541538 Iteration 7: loglikelihood = -3514.4814, backtracks = 0, tol = 0.014093065501827168 Iteration 8: loglikelihood = -3501.529, backtracks = 0, tol = 0.07739416447422229 Iteration 9: loglikelihood = -3499.2268, backtracks = 0, tol = 0.008647726463826767 Iteration 10: loglikelihood = -3499.0674, backtracks = 0, tol = 0.0036545997832991848 Iteration 11: loglikelihood = -3499.0547, backtracks = 1, tol = 0.00038865232988528995 Iteration 12: loglikelihood = -3499.048, backtracks = 1, tol = 0.0002969900598284486 Iteration 13: loglikelihood = -3499.0452, backtracks = 1, tol = 0.00025979633738742325 Iteration 14: loglikelihood = -3499.0515, backtracks = 3, tol = 3.2693272335799725e-5 24.045495 seconds (15.17 M allocations: 680.724 MiB, 2.66% gc time, 98.02% 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 = -3495.7454, backtracks = 0, tol = 0.0863182355283885 Iteration 2: loglikelihood = -3405.4885, backtracks = 0, tol = 0.03628133263990988 Iteration 3: loglikelihood = -3210.4937, backtracks = 1, tol = 0.008132078734138485 Iteration 4: loglikelihood = -2980.4688, backtracks = 1, tol = 0.004773096035518082 Iteration 5: loglikelihood = -2940.9272, backtracks = 0, tol = 0.09386934760379624 Iteration 6: loglikelihood = -2726.054, backtracks = 0, tol = 0.09430267938002623 Iteration 7: loglikelihood = -2656.7668, backtracks = 0, tol = 0.09363336084013801 Iteration 8: loglikelihood = -2526.0686, backtracks = 0, tol = 0.0933010497828962 Iteration 9: loglikelihood = -2440.532, backtracks = 0, tol = 0.09356615229868262 Iteration 10: loglikelihood = -2358.0693, backtracks = 0, tol = 0.09399387453775504 Iteration 11: loglikelihood = -2297.8354, backtracks = 0, tol = 0.09922334173907799 Iteration 12: loglikelihood = -2249.0583, backtracks = 0, tol = 0.100316722851566 Iteration 13: loglikelihood = -2223.013, backtracks = 0, tol = 0.10091342790978224 Iteration 14: loglikelihood = -2200.6035, backtracks = 0, tol = 0.10470121489415973 Iteration 15: loglikelihood = -2192.3896, backtracks = 0, tol = 0.10339895412010733 Iteration 16: loglikelihood = -2183.7256, backtracks = 0, tol = 0.106237732628313 Iteration 17: loglikelihood = -2182.6243, backtracks = 0, tol = 0.10492874569724478 Iteration 18: loglikelihood = -2179.015, backtracks = 0, tol = 0.1067293032540678 Iteration 19: loglikelihood = -2170.8872, backtracks = 1, tol = 0.03814567587554915 Iteration 20: loglikelihood = -2169.4387, backtracks = 1, tol = 0.016714371930006643 Iteration 21: loglikelihood = -2165.379, backtracks = 1, tol = 0.05124223080907744 Iteration 22: loglikelihood = -2164.4749, backtracks = 1, tol = 0.017605903055088832 Iteration 23: loglikelihood = -2164.255, backtracks = 1, tol = 0.008452217475691389 Iteration 24: loglikelihood = -2164.206, backtracks = 1, tol = 0.003999552322226755 Iteration 25: loglikelihood = -2164.195, backtracks = 1, tol = 0.001847352037967537 Iteration 26: loglikelihood = -2164.186, backtracks = 1, tol = 0.0008272528637032244 Iteration 27: loglikelihood = -2164.1882, backtracks = 3, tol = 8.993687486964644e-5 0.213489 seconds (1.54 M allocations: 25.520 MiB, 7.51% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 30.8s **** 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 4.145766 seconds (1.08 M allocations: 135.704 MiB, 0.96% gc time, 89.93% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.6s 9.892454 seconds (4.00 M allocations: 82.492 MiB, 0.39% gc time, 0.54% compilation time) 5.140604 seconds (3.98 M allocations: 91.674 MiB, 0.47% gc time) 9.340820 seconds (20.41 M allocations: 439.364 MiB, 1.03% gc time, 17.76% compilation time: 79% of which was recompilation) 6.983626 seconds (20.18 M allocations: 434.191 MiB, 1.03% gc time) 42.709851 seconds (3.77 M allocations: 4.239 GiB, 5.70% gc time, 24.96% compilation time) 52.917125 seconds (70.38 k allocations: 183.438 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m25.0s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 15.008 ms (78 allocations: 4.56 KiB) 4.424 μs (0 allocations: 0 bytes) 129.359 μs (4 allocations: 288 bytes) 6.748 μs (0 allocations: 0 bytes) 45.489 μs (2 allocations: 64 bytes) 29.030 μs (0 allocations: 0 bytes) 26.340 μs (0 allocations: 0 bytes) 28.360 μs (0 allocations: 0 bytes) 99.399 μs (0 allocations: 0 bytes) 38.459 ms (78 allocations: 4.56 KiB) 18.510 μs (0 allocations: 0 bytes) 168.468 μs (4 allocations: 288 bytes) 34.310 μs (0 allocations: 0 bytes) 254.858 μs (2 allocations: 64 bytes) 85.419 μs (0 allocations: 0 bytes) 124.659 μs (0 allocations: 0 bytes) 144.168 μs (0 allocations: 0 bytes) 208.418 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m10.1s **** 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 **** **** 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 0.410930 seconds (49.33 k allocations: 5.493 MiB, 62.27% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.789785 seconds (281.91 k allocations: 168.118 MiB, 55.90% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 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 **** Cross validating... 3%|█ | ETA: 0:03:26 Cross validating... 11%|███▌ | ETA: 0:00:58 Cross validating... 14%|████▋ | ETA: 0:00:44 Cross 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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... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 4312.339468443527 1 3476.431774065541 2 2734.766084007716 3 2152.1117920901547 4 1568.4969076962848 5 1090.3332309022744 6 751.918700674769 7 494.73001490114666 8 341.95214820147487 9 321.54951883190034 10 326.0750084111532 11 328.36802457478876 12 331.9748621546953 13 332.27346907735415 14 336.79961877158894 15 338.5639653947374 16 338.4803500294636 17 339.09855715799694 18 338.6544310908275 19 358.3994911396091 20 387.3380943423673 Best k = 9 11.272505 seconds (11.52 M allocations: 304.862 MiB, 1.43% gc time, 61.51% 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... 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94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 4312.339468443527 1 3483.890330489781 2 2739.9250963586182 3 2155.8582495982737 4 1571.9911708914499 5 1095.6332350280813 6 757.7326722528353 7 500.7092797657559 8 346.74764747905266 9 326.5303523557634 10 338.20891894965064 11 343.2272952551857 12 356.06456821485 13 355.8147214296451 14 365.2544133985408 15 370.52525212160117 16 374.60912727660383 17 382.18187163232 18 371.59248310681267 19 391.59788992109196 20 399.93675505697286 Best k = 9 4.382278 seconds (10.48 M allocations: 221.302 MiB, 1.32% gc time, 0.95% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 16.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:40 Cross validating... 6%|██ | ETA: 0:02:46 Cross validating... 10%|███ | ETA: 0:01:48 Cross validating... 14%|████▋ | ETA: 0:01:09 Cross validating... 19%|██████▏ | ETA: 0:00:49 Cross validating... 22%|███████▏ | ETA: 0:00:41 Cross validating... 25%|████████▏ | ETA: 0:00:35 Cross validating... 29%|█████████▏ | ETA: 0:00:30 Cross validating... 32%|██████████▏ | ETA: 0:00:26 Cross validating... 37%|███████████▋ | ETA: 0:00:21 Cross validating... 41%|█████████████▎ | ETA: 0:00:18 Cross validating... 46%|██████████████▊ | ETA: 0:00:15 Cross validating... 51%|████████████████▎ | ETA: 0:00:12 Cross validating... 56%|█████████████████▊ | ETA: 0:00:10 Cross validating... 59%|██████████████████▊ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1595.1720427246094 1 1296.941243408203 2 1072.4958173828127 3 883.9498161621094 4 707.119142944336 5 533.4279986572266 6 436.3282504272461 7 369.5486194458008 8 336.8523899536133 9 322.6066126098633 10 320.79615142822263 11 323.53758752441405 12 325.5314188842773 13 323.770332824707 14 331.103955078125 15 355.83697149658207 16 331.12563409423825 17 332.87365057373046 18 367.1837319335938 19 339.4272069091797 20 347.09899920654294 Best k = 10 15.438572 seconds (12.72 M allocations: 316.154 MiB, 0.50% gc time, 78.80% 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... 10%|███ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 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0:00:03 Crossvalidation Results: k MSE 0 1595.1720427246094 1 1296.941243408203 2 1078.5732268066406 3 895.482036743164 4 714.2270166015626 5 540.7026884765625 6 443.14855334472657 7 376.63584887695316 8 344.96965100097657 9 327.65195892333986 10 336.30173828125 11 343.1072428588867 12 351.19298699951173 13 352.9713244628906 14 361.91492425537115 15 380.0715133056641 16 371.4592077636719 17 376.1035811767578 18 390.97900756835935 19 383.7240400390625 20 394.10654992675785 Best k = 9 3.355471 seconds (10.79 M allocations: 198.544 MiB, 1.52% gc time, 1.22% 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: 0:00:55 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 59%|██████████████████▊ | ETA: 0:00:05 Cross validating... 62%|███████████████████▊ | ETA: 0:00:05 Cross validating... 65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:04 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 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: 0:00:09 Crossvalidation Results: k MSE 0 463.74505801105295 1 423.2629345447474 2 394.6443508949099 3 364.8690000488232 4 331.0898811899992 5 288.100512359536 6 269.10530217342995 7 240.3018885220878 8 238.9264661391082 9 227.7335796447252 10 235.23466869197875 11 241.05755851180464 12 241.92743504194988 13 237.30002259111203 14 234.42274927559697 15 240.14488898496637 16 257.6950633666352 17 237.80684959081674 18 257.806853837706 19 256.8419499261239 20 275.22442112084263 Best k = 9 10.588841 seconds (17.56 M allocations: 419.926 MiB, 1.00% gc time, 22.71% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 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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 0 463.74505801105295 1 423.3043508875918 2 395.59852645725795 3 367.49173225444895 4 335.3162205833299 5 291.9716480387779 6 271.95888843496294 7 245.76627466419677 8 243.32345601386777 9 238.76641428818556 10 243.57917872386764 11 247.7160914096947 12 247.87044157701575 13 253.9607837009163 14 266.1508668529688 15 271.7567866246731 16 283.0717205587014 17 283.868015752453 18 303.63870220043134 19 287.9050228392627 20 296.57774126660365 Best k = 9 5.427169 seconds (18.26 M allocations: 382.529 MiB, 1.11% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 16.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:44 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 10%|███ | ETA: 0:00:16 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: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 464.60514173028565 1 427.48506189450455 2 403.90824645898135 3 396.2622157957814 4 383.6769993948515 5 353.02532799359324 6 351.4343469989313 7 349.9510483563653 8 348.22218629277006 9 347.9049442200599 10 350.34043055563455 11 369.6737490944112 12 352.3699827889953 13 356.6268788407259 14 356.25918543850025 15 354.54237815968787 16 361.19490758717836 17 375.2131816511385 18 377.5564840881889 19 363.30955254863187 20 390.91916856428855 Best k = 9 8.236734 seconds (16.35 M allocations: 390.436 MiB, 6.28% gc time, 29.29% 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: 0:00:05 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: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 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100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 464.60514173028565 1 427.7028405757383 2 405.7242973430248 3 400.20325747943804 4 388.8479966561544 5 359.9889388666438 6 357.71164650252877 7 359.9291847755625 8 360.7748328465727 9 368.3338862325726 10 379.09066501426844 11 380.76920886711 12 394.6043630159241 13 392.15974537742113 14 402.15834867865243 15 408.28322986104433 16 407.1620303045403 17 411.11259878626925 18 424.2879336492024 19 423.2085690639381 20 441.8269921760658 Best k = 6 5.674973 seconds (17.04 M allocations: 350.753 MiB, 1.70% gc time, 0.69% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 15.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 948.7135351411142 1 897.1395866598392 2 770.6080972564582 3 663.9888598960013 4 544.3049752575464 5 490.0443305086852 6 438.15143196976703 7 414.57204168218345 8 375.9596178083265 9 386.15346978305286 10 385.05703580492445 11 377.6394565183315 12 392.92747829913856 13 397.405583007696 14 384.27668624305176 15 394.1926380016352 16 397.2142665047246 17 380.0393165592003 18 382.70821353914863 19 408.68407116863773 20 417.27181455370476 Best k = 8 7.692353 seconds (15.73 M allocations: 371.083 MiB, 1.12% gc time, 32.20% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 948.7135351411142 1 874.8721259718386 2 749.7117004235166 3 652.9749183084175 4 547.6940986300078 5 494.4874146203136 6 448.87730750218344 7 415.76362951526283 8 380.18526219238873 9 393.3972144549937 10 396.946026617953 11 401.18842725322725 12 396.063551332589 13 414.44645436563906 14 404.5902760680077 15 405.79941908793234 16 411.8130708237631 17 415.62814558668947 18 420.93845251423113 19 436.2045751524033 20 441.1430861850314 Best k = 8 5.228010 seconds (14.31 M allocations: 287.981 MiB, 0.91% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 5%|█▌ | ETA: 0:00:40 Cross validating... 6%|██ | ETA: 0:00:44 Cross validating... 8%|██▌ | ETA: 0:00:45 Cross validating... 10%|███ | ETA: 0:00:46 Cross validating... 11%|███▌ | ETA: 0:00:46 Cross validating... 13%|████▏ | ETA: 0:00:47 Cross validating... 14%|████▋ | ETA: 0:00:47 Cross validating... 17%|█████▋ | ETA: 0:00:42 Cross validating... 19%|██████▏ | ETA: 0:00:38 Cross validating... 21%|██████▋ | ETA: 0:00:35 Cross validating... 24%|███████▋ | ETA: 0:00:33 Cross validating... 25%|████████▏ | ETA: 0:00:31 Cross 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ETA: 0:00:04 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: 0:00:41 Crossvalidation Results: k MSE 0 392.0185988986847 1 343.90256211097125 2 304.625437994449 3 285.0429937391919 4 262.2751705789022 5 230.01096445803535 6 217.25717253931336 7 207.3616351357226 8 200.92307815761592 9 201.62994515030135 10 202.47007671652955 11 203.31503923087965 12 203.69194827835167 13 205.52164459880964 14 205.90017153355916 15 206.965015286276 16 208.27321370867782 17 208.95018537835404 18 208.0904955391947 19 205.38387623661328 20 206.40024884421308 Best k = 8 41.980762 seconds (138.92 M allocations: 3.587 GiB, 1.20% gc time, 4.94% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross validating... 22%|███████▏ | ETA: 0:00:06 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 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0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 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: 0:00:01 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: 0:00:10 Crossvalidation Results: k MSE 0 392.0185988986847 1 343.82485823783406 2 305.0692207436251 3 285.46633364243223 4 261.9012750825152 5 230.93805653487527 6 219.52722259288538 7 212.4877443230328 8 203.4467214221969 9 206.42215917310324 10 208.90594467732726 11 213.38382801511958 12 215.68804338817176 13 217.27825596687683 14 217.57884375059263 15 229.1301426206147 16 234.7617779879526 17 227.87340102427044 18 238.8371855098543 19 225.9470846378744 20 237.1300067332479 Best k = 8 10.667785 seconds (34.69 M allocations: 719.365 MiB, 1.23% gc time, 0.53% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 53.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 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validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 5.775770 seconds (17.00 M allocations: 337.705 MiB, 1.47% gc time, 44.02% 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... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | 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... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | 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... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.257186 seconds (16.17 M allocations: 286.699 MiB, 2.61% gc time, 1.58% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.6s **** 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: 0:01:17 Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 4%|█▎ | ETA: 0:00:46 Cross validating... 5%|█▋ | ETA: 0:00:40 Cross validating... 6%|█▉ | ETA: 0:00:36 Cross validating... 7%|██▎ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:30 Cross validating... 9%|██▉ | ETA: 0:00:29 Cross validating... 10%|███▎ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:26 Cross validating... 12%|███▉ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 0:00:24 Cross validating... 14%|████▌ | ETA: 0:00:23 Cross validating... 15%|████▊ | ETA: 0:00:22 Cross validating... 16%|█████▏ | ETA: 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100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 2381.599079730827 2 2289.958709582342 3 2219.596159187491 4 2198.6383607007856 5 2250.689020628776 6 2295.164377176224 7 2327.6810377914435 8 2332.5866296546897 9 2363.037621473411 10 2384.2398148822904 11 2402.8107684947754 12 2420.575130496931 13 2440.4336522770636 14 2430.2624817324845 15 2449.1248420438815 16 2468.748059227376 17 2469.703309726433 18 2464.4176257152058 19 2467.7417068047566 20 2468.467179646559 Best k = 4 19.360814 seconds (341.90 k allocations: 217.967 MiB, 0.63% gc time, 7.80% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.7s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m56.0s **** 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... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:18 Cross validating... 21%|██████▊ | ETA: 0:00:17 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 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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: 0:00:12 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: 0:00:16 Cross 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 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94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m25.7s 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] collect(itr::Base.Generator{UnitRange{Int64}, MendelIHT.var"#convert_bgen_gt##0#convert_bgen_gt##1"}) @ Base ~/.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:741 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [18] _start() @ Base ./client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.8s RNG of the outermost testset: Xoshiro(0xf686223b5958d1bf, 0x3c6ede34df78a7ad, 0x19ce4beeb2328384, 0x0aff054534be0063, 0x79d35d67e3f15d0f) 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 1051.59s 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] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [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:587 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:355 [12] _start() @ Base ./client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1158.56s: package tests unexpectedly errored