Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2212 (062a90bc8c*) started at 2026-05-22T09:11:35.301 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.36s ################################################################################ # 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 v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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 6.26s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.1 s ✓ BGEN 7.8 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`. 23.6 s ✓ MendelIHT 3 dependencies successfully precompiled in 41 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 66.12s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_1RtGi9/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 17.9s 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 9.7s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 2.0s 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 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1742.95498746905, backtracks = 0, tol = 2.2462498960084436 Iteration 2: loglikelihood = -1481.5759468260424, backtracks = 0, tol = 0.1768201262415194 Iteration 3: loglikelihood = -1448.35286144487, backtracks = 0, tol = 0.04908992569861502 Iteration 4: loglikelihood = -1447.0009105699112, backtracks = 0, tol = 0.009821249748714457 Iteration 5: loglikelihood = -1446.9770529362313, backtracks = 0, tol = 0.0017347577234587996 Iteration 6: loglikelihood = -1446.976579572392, backtracks = 0, tol = 0.00015593508937026073 Iteration 7: loglikelihood = -1446.976569783061, backtracks = 0, tol = 3.6616688495084956e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06954598426818848 Final loglikelihood: -1446.976569783061 SNP PVE: 0.9444691795924696 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 834 -1.61269 2 │ 2337 1.93208 3 │ 3495 2.40774 4 │ 5539 0.180484 5 │ 6602 1.53754 6 │ 7790 -0.448659 7 │ 8496 -0.599588 8 │ 8683 -0.652388 9 │ 9857 -1.36023 10 │ 9930 0.60471 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0258991Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.2s **** 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 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 5.2s **** 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 = -4.864185615855135e6, backtracks = 0, tol = 0.7733567161797983 Iteration 2: loglikelihood = -1.824157964731594e6, backtracks = 0, tol = 0.036596664435490714 Iteration 3: loglikelihood = -692260.5335023231, backtracks = 0, tol = 0.038326869627595656 Iteration 4: loglikelihood = -267281.4855529499, backtracks = 0, tol = 0.04045445169130614 Iteration 5: loglikelihood = -105554.43224613796, backtracks = 0, tol = 0.04320000964782767 Iteration 6: loglikelihood = -42764.37846404853, backtracks = 0, tol = 0.046883834947044414 Iteration 7: loglikelihood = -17780.35420732439, backtracks = 0, tol = 0.05185011661927835 Iteration 8: loglikelihood = -7667.120094264121, backtracks = 0, tol = 0.058110298752050475 Iteration 9: loglikelihood = -3646.987016003561, backtracks = 0, tol = 0.06448639440957675 Iteration 10: loglikelihood = -2200.209482889302, backtracks = 0, tol = 0.0653338929192337 Iteration 11: loglikelihood = -1798.4367195362963, backtracks = 0, tol = 0.05368736866629795 Iteration 12: loglikelihood = -1727.3391039644116, backtracks = 0, tol = 0.02963186593381114 Iteration 13: loglikelihood = -1620.5156940309903, backtracks = 0, tol = 0.07098257008262522 Iteration 14: loglikelihood = -1587.4088867591827, backtracks = 0, tol = 0.04708618128604241 Iteration 15: loglikelihood = -1574.2165079779074, backtracks = 0, tol = 0.016041713694359572 Iteration 16: loglikelihood = -1560.001175285244, backtracks = 0, tol = 0.027218346145004155 Iteration 17: loglikelihood = -1549.6775824791239, backtracks = 0, tol = 0.016028286932560188 Iteration 18: loglikelihood = -1535.4191763567746, backtracks = 1, tol = 0.03547723767525637 Iteration 19: loglikelihood = -1533.025854306856, backtracks = 0, tol = 0.007950701257305457 Iteration 20: loglikelihood = -1530.8078295675266, backtracks = 0, tol = 0.01081282759340973 Iteration 21: loglikelihood = -1528.9689670236803, backtracks = 0, tol = 0.007253064110960819 Iteration 22: loglikelihood = -1527.1802735402034, backtracks = 0, tol = 0.010893380147647333 Iteration 23: loglikelihood = -1525.7395538688402, backtracks = 0, tol = 0.006581250519913841 Iteration 24: loglikelihood = -1517.6203203929417, backtracks = 0, tol = 0.050161649714303695 Iteration 25: loglikelihood = -1516.436256782373, backtracks = 0, tol = 0.005273392978648368 Iteration 26: loglikelihood = -1515.5401069220227, backtracks = 0, tol = 0.006291189436404818 Iteration 27: loglikelihood = -1514.8549929173917, backtracks = 0, tol = 0.004391404691584977 Iteration 28: loglikelihood = -1514.2870743973924, backtracks = 0, tol = 0.004968723425779859 Iteration 29: loglikelihood = -1513.8287679540772, backtracks = 0, tol = 0.0036879488105878125 Iteration 30: loglikelihood = -1513.435634262896, backtracks = 0, tol = 0.004135800267508932 Iteration 31: loglikelihood = -1513.110759437234, backtracks = 0, tol = 0.0031417072271546784 Iteration 32: loglikelihood = -1512.827184633955, backtracks = 0, tol = 0.0035226748471466358 Iteration 33: loglikelihood = -1512.5904082548336, backtracks = 0, tol = 0.0027031471997785994 Iteration 34: loglikelihood = -1512.382079926025, backtracks = 0, tol = 0.0030261782203908822 Iteration 35: loglikelihood = -1512.207728255751, backtracks = 0, tol = 0.0023348726782167948 Iteration 36: loglikelihood = -1512.0541028149828, backtracks = 0, tol = 0.002600606751900747 Iteration 37: loglikelihood = -1511.9258853673143, backtracks = 0, tol = 0.002014120617059232 Iteration 38: loglikelihood = -1511.8132599117653, backtracks = 0, tol = 0.002225729872926615 Iteration 39: loglikelihood = -1511.7197991214405, backtracks = 0, tol = 0.0017288039053525938 Iteration 40: loglikelihood = -1511.6382099895511, backtracks = 0, tol = 0.002014805267362026 Iteration 41: loglikelihood = -1511.5709894785357, backtracks = 0, tol = 0.0014732594704131912 Iteration 42: loglikelihood = -1511.5127822780357, backtracks = 0, tol = 0.0017841774007740562 Iteration 43: loglikelihood = -1511.4651844498064, backtracks = 0, tol = 0.0012451627743423849 Iteration 44: loglikelihood = -1511.4344599180704, backtracks = 1, tol = 0.0007723880013398819 Iteration 45: loglikelihood = -1511.4115132662012, backtracks = 0, tol = 0.0009642816280079721 Iteration 46: loglikelihood = -1511.3914364132866, backtracks = 0, tol = 0.000897187370898587 Iteration 47: loglikelihood = -1511.3739809899268, backtracks = 0, tol = 0.0008166371477470016 Iteration 48: loglikelihood = -1511.3586437391361, backtracks = 0, tol = 0.0007831850956348425 Iteration 49: loglikelihood = -1511.3452370957596, backtracks = 0, tol = 0.0006953797330662805 Iteration 50: loglikelihood = -1511.3334132216642, backtracks = 0, tol = 0.000686806570988754 Iteration 51: loglikelihood = -1511.323029675334, backtracks = 0, tol = 0.0005948572588825658 Iteration 52: loglikelihood = -1511.3138412767667, backtracks = 0, tol = 0.0006046939175982923 Iteration 53: loglikelihood = -1511.3057392870162, backtracks = 0, tol = 0.0005108708931039044 Iteration 54: loglikelihood = -1511.2985480169336, backtracks = 0, tol = 0.0005342836660893323 Iteration 55: loglikelihood = -1511.2921840421654, backtracks = 0, tol = 0.00044024295705595763 Iteration 56: loglikelihood = -1511.2865196864675, backtracks = 0, tol = 0.00047357404872472205 Iteration 57: loglikelihood = -1511.281490638858, backtracks = 0, tol = 0.000382147889950167 Iteration 58: loglikelihood = -1511.2770029764283, backtracks = 0, tol = 0.0004209746453999182 Iteration 59: loglikelihood = -1511.2730068902383, backtracks = 0, tol = 0.0003419686602099856 Iteration 60: loglikelihood = -1511.2694325415089, backtracks = 0, tol = 0.0003752043575085049 Iteration 61: loglikelihood = -1511.2662411761046, backtracks = 0, tol = 0.0003086230931835206 Iteration 62: loglikelihood = -1511.2633803634403, backtracks = 0, tol = 0.00033521968228991634 Iteration 63: loglikelihood = -1511.2608198145965, backtracks = 0, tol = 0.00028074990999786385 Iteration 64: loglikelihood = -1511.2585198256068, backtracks = 0, tol = 0.0003001628301833957 Iteration 65: loglikelihood = -1511.2564566185356, backtracks = 0, tol = 0.00025566131033228625 Iteration 66: loglikelihood = -1511.2545998882533, backtracks = 0, tol = 0.0002693232779216543 Iteration 67: loglikelihood = -1511.2529308865942, backtracks = 0, tol = 0.00023302315593184186 Iteration 68: loglikelihood = -1511.2514263134249, backtracks = 0, tol = 0.00024210867962927218 Iteration 69: loglikelihood = -1511.250071322977, backtracks = 0, tol = 0.00021255266630741833 Iteration 70: loglikelihood = -1511.2488478796843, backtracks = 0, tol = 0.00021802246138136595 Iteration 71: loglikelihood = -1511.2477441785654, backtracks = 0, tol = 0.00019400842289367387 Iteration 72: loglikelihood = -1511.246746171163, backtracks = 0, tol = 0.00019664629855848528 Iteration 73: loglikelihood = -1511.245844432095, backtracks = 0, tol = 0.00017718269244025123 Iteration 74: loglikelihood = -1511.245027954188, backtracks = 0, tol = 0.00017762623437235666 Iteration 75: loglikelihood = -1511.2442891822202, backtracks = 0, tol = 0.0001618954586089745 Iteration 76: loglikelihood = -1511.2436194443756, backtracks = 0, tol = 0.00016066156399836126 Iteration 77: loglikelihood = -1511.2430126614709, backtracks = 0, tol = 0.0001479897292346595 Iteration 78: loglikelihood = -1511.2424619663116, backtracks = 0, tol = 0.0001454958536217239 Iteration 79: loglikelihood = -1511.241962449546, backtracks = 0, tol = 0.00013532780810571117 Iteration 80: loglikelihood = -1511.2415086467834, backtracks = 0, tol = 0.00013190963086905978 Iteration 81: loglikelihood = -1511.2410965796755, backtracks = 0, tol = 0.00012378830419742842 Iteration 82: loglikelihood = -1511.240721880404, backtracks = 0, tol = 0.00011971439949764755 Iteration 83: loglikelihood = -1511.240381314534, backtracks = 0, tol = 0.00011326371050264685 Iteration 84: loglikelihood = -1511.2400713760262, backtracks = 0, tol = 0.00010874771387272783 Iteration 85: loglikelihood = -1511.2397894271662, backtracks = 0, tol = 0.00010365842693197804 Iteration 86: loglikelihood = -1511.2395326426097, backtracks = 0, tol = 9.886910860563365e-5 Test Summary: | Pass Total Time fit Poisson 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 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 = -1745.0915365449805, backtracks = 0, tol = 0.795478718333863 Iteration 2: loglikelihood = -1638.2703729202137, backtracks = 0, tol = 0.08515991162047498 Iteration 3: loglikelihood = -1567.7097745821445, backtracks = 0, tol = 0.08095032523852519 Iteration 4: loglikelihood = -1517.5654887527305, backtracks = 0, tol = 0.08508269740214593 Iteration 5: loglikelihood = -1490.7568435967846, backtracks = 0, tol = 0.08138382393562868 Iteration 6: loglikelihood = -1483.4713269780357, backtracks = 0, tol = 0.05363392378020518 Iteration 7: loglikelihood = -1479.057388052007, backtracks = 0, tol = 0.11510245191514917 Iteration 8: loglikelihood = -1478.2013509283568, backtracks = 0, tol = 0.0940629492810384 Iteration 9: loglikelihood = -1476.5763795084738, backtracks = 0, tol = 0.024858278907808864 Iteration 10: loglikelihood = -1475.1777986909951, backtracks = 0, tol = 0.07757966317042375 Iteration 11: loglikelihood = -1474.982628795733, backtracks = 1, tol = 0.005632711114791252 Iteration 12: loglikelihood = -1473.8690026237136, backtracks = 1, tol = 0.07791932799205198 Iteration 13: loglikelihood = -1473.7994972329282, backtracks = 0, tol = 0.006329678084190512 Iteration 14: loglikelihood = -1473.782737296983, backtracks = 1, tol = 0.002532620411522066 Iteration 15: loglikelihood = -1473.7749224061326, backtracks = 2, tol = 0.0018490028650937852 Iteration 16: loglikelihood = -1473.7689928887, backtracks = 2, tol = 0.0018825431230494946 Iteration 17: loglikelihood = -1473.7655023995383, backtracks = 2, tol = 0.0014998507798234435 Iteration 18: loglikelihood = -1473.7634547322602, backtracks = 2, tol = 0.0011858060616797862 Iteration 19: loglikelihood = -1473.7622836571343, backtracks = 2, tol = 0.0009125306807708845 Iteration 20: loglikelihood = -1473.7616168215773, backtracks = 2, tol = 0.000698274077874631 Iteration 21: loglikelihood = -1473.7612412468204, backtracks = 2, tol = 0.0005282222408958168 Iteration 22: loglikelihood = -1473.7610302703406, backtracks = 2, tol = 0.00039843175398632464 Iteration 23: loglikelihood = -1473.7609123726095, backtracks = 2, tol = 0.0002989478457274122 Iteration 24: loglikelihood = -1473.760846575881, backtracks = 2, tol = 0.00022401519338440776 Iteration 25: loglikelihood = -1473.7608099536044, backtracks = 2, tol = 0.00016742592129964114 Iteration 26: loglikelihood = -1473.7607895827628, backtracks = 2, tol = 0.00012506166297990618 Iteration 27: loglikelihood = -1473.7607782678685, backtracks = 2, tol = 9.328859479008874e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1856.6626533081248, backtracks = 0, tol = 0.8062537494588423 Iteration 2: loglikelihood = -1457.7224364724061, backtracks = 0, tol = 0.15975109133208626 Iteration 3: loglikelihood = -1414.372739227011, backtracks = 0, tol = 0.04601688089760748 Iteration 4: loglikelihood = -1411.3481614116547, backtracks = 0, tol = 0.028591592945879863 Iteration 5: loglikelihood = -1410.985263134026, backtracks = 0, tol = 0.003725701651406573 Iteration 6: loglikelihood = -1410.9807766032384, backtracks = 1, tol = 0.00019864817300413332 Iteration 7: loglikelihood = -1410.9795781754333, backtracks = 1, tol = 9.976301667134978e-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 = -1698.2005513218621, backtracks = 0, tol = 0.6207399149218702 Iteration 2: loglikelihood = -1435.1651493796885, backtracks = 0, tol = 0.11930709704970367 Iteration 3: loglikelihood = -1412.798760621208, backtracks = 0, tol = 0.04582754539825147 Iteration 4: loglikelihood = -1411.169055076512, backtracks = 0, tol = 0.030154683812639218 Iteration 5: loglikelihood = -1411.0025840495684, backtracks = 0, tol = 0.0023368445428613876 Iteration 6: loglikelihood = -1411.0003936592846, backtracks = 0, tol = 0.00028181695276735714 Iteration 7: loglikelihood = -1411.0003548263646, backtracks = 0, tol = 3.817977094601315e-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 10.3s **** 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 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 = -1432.5385957099525, backtracks = 0, tol = 0.23347638327945375 Iteration 2: loglikelihood = -1387.7450004004165, backtracks = 0, tol = 0.09029579343881626 Iteration 3: loglikelihood = -1378.6375009380656, backtracks = 0, tol = 0.12640917293416964 Iteration 4: loglikelihood = -1346.4585994468327, backtracks = 0, tol = 0.1082971004077339 Iteration 5: loglikelihood = -1330.1942996949456, backtracks = 1, tol = 0.04881231603350173 Iteration 6: loglikelihood = -1328.2857960588844, backtracks = 0, tol = 0.047661665920928874 Iteration 7: loglikelihood = -1326.9659493136985, backtracks = 1, tol = 0.01564765635382047 Iteration 8: loglikelihood = -1326.5200032268624, backtracks = 1, tol = 0.00850361524042783 Iteration 9: loglikelihood = -1326.360378828982, backtracks = 1, tol = 0.005260369752179418 Iteration 10: loglikelihood = -1326.3289468981982, backtracks = 2, tol = 0.0019659507727220428 Iteration 11: loglikelihood = -1326.310664520247, backtracks = 2, tol = 0.0015233429240008058 Iteration 12: loglikelihood = -1326.3001743897084, backtracks = 2, tol = 0.0011766167854260132 Iteration 13: loglikelihood = -1326.2942029305946, backtracks = 2, tol = 0.0008978352274646495 Iteration 14: loglikelihood = -1326.290820484404, backtracks = 2, tol = 0.0006803602870426071 Iteration 15: loglikelihood = -1326.2889102421002, backtracks = 2, tol = 0.000513408204062011 Iteration 16: loglikelihood = -1326.2878333440224, backtracks = 2, tol = 0.0003864665094307569 Iteration 17: loglikelihood = -1326.2872268911449, backtracks = 2, tol = 0.0002904820611814643 Iteration 18: loglikelihood = -1326.286885591257, backtracks = 2, tol = 0.00021814120380550406 Iteration 19: loglikelihood = -1326.2866935925758, backtracks = 2, tol = 0.00016372505124255418 Iteration 20: loglikelihood = -1326.2865856116223, backtracks = 2, tol = 0.00012283998763638172 Iteration 21: loglikelihood = -1326.2865248929975, backtracks = 2, tol = 9.214359374097784e-5 2.178603 seconds (5.95 M allocations: 103.823 MiB, 40.32% gc time, 28.00% 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 = -1487.2599524551788, backtracks = 0, tol = 0.23347638327945375 Iteration 2: loglikelihood = -1453.1362554155694, backtracks = 0, tol = 0.1174738666790626 Iteration 3: loglikelihood = -1437.0866729693832, backtracks = 0, tol = 0.08591572536790078 Iteration 4: loglikelihood = -1418.539276930926, backtracks = 0, tol = 0.07508344937414285 Iteration 5: loglikelihood = -1401.633087288465, backtracks = 1, tol = 0.0564581343578179 Iteration 6: loglikelihood = -1386.1571580431419, backtracks = 0, tol = 0.06623829552541126 Iteration 7: loglikelihood = -1375.4671958282734, backtracks = 1, tol = 0.029706186039748433 Iteration 8: loglikelihood = -1368.1632733265496, backtracks = 1, tol = 0.015760545026071444 Iteration 9: loglikelihood = -1362.8655988679145, backtracks = 1, tol = 0.008101093793577147 Iteration 10: loglikelihood = -1359.2113210032267, backtracks = 1, tol = 0.00549357212112042 Iteration 11: loglikelihood = -1356.6103211794546, backtracks = 1, tol = 0.003021328113251863 Iteration 12: loglikelihood = -1353.0380415975606, backtracks = 2, tol = 0.0007743638484658015 Iteration 13: loglikelihood = -1351.0960650513716, backtracks = 1, tol = 0.0010166952091761497 Iteration 14: loglikelihood = -1349.3450359022324, backtracks = 1, tol = 0.0005349511265083499 Iteration 15: loglikelihood = -1347.4782292982934, backtracks = 1, tol = 0.00028152992832703615 Iteration 16: loglikelihood = -1345.6638318733956, backtracks = 1, tol = 0.0002631009806490665 Iteration 17: loglikelihood = -1344.0685180083194, backtracks = 1, tol = 0.0002822204354907146 Iteration 18: loglikelihood = -1342.7037250834562, backtracks = 1, tol = 0.0002901981108794236 Iteration 19: loglikelihood = -1341.5361236067888, backtracks = 1, tol = 0.0002820030122007453 Iteration 20: loglikelihood = -1340.5316176601398, backtracks = 1, tol = 0.00026445776745172723 Iteration 21: loglikelihood = -1339.6616184253783, backtracks = 1, tol = 0.00024314536699567599 Iteration 22: loglikelihood = -1338.9029801544143, backtracks = 1, tol = 0.0002213154031002607 Iteration 23: loglikelihood = -1338.2370543775046, backtracks = 1, tol = 0.00020060848290124662 Iteration 24: loglikelihood = -1337.6849662423062, backtracks = 1, tol = 0.00018173096874900393 Iteration 25: loglikelihood = -1337.1950359771909, backtracks = 1, tol = 0.00016041114310084284 Iteration 26: loglikelihood = -1336.7571784546192, backtracks = 1, tol = 0.0001433620253154482 Iteration 27: loglikelihood = -1336.3634693276022, backtracks = 1, tol = 0.0001294273213117089 Iteration 28: loglikelihood = -1336.0075738999662, backtracks = 1, tol = 0.0001177983015407264 Iteration 29: loglikelihood = -1335.6843650171247, backtracks = 1, tol = 0.00010791795176162363 Iteration 30: loglikelihood = -1335.3896450574127, backtracks = 1, tol = 9.939445055368921e-5 0.376630 seconds (1.53 M allocations: 28.912 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 = -3589.3877, backtracks = 0, tol = 0.09024710924650067 Iteration 2: loglikelihood = -3533.6511, backtracks = 0, tol = 0.04350441879459018 Iteration 3: loglikelihood = -3528.0933, backtracks = 1, tol = 0.015637419425484342 Iteration 4: loglikelihood = -3526.532, backtracks = 1, tol = 0.008487294855390484 Iteration 5: loglikelihood = -3526.1252, backtracks = 1, tol = 0.004605697380655845 Iteration 6: loglikelihood = -3526.0198, backtracks = 1, tol = 0.0023028841813339906 Iteration 7: loglikelihood = -3525.995, backtracks = 1, tol = 0.0011914259342321756 Iteration 8: loglikelihood = -3512.6333, backtracks = 1, tol = 0.06312945321256516 Iteration 9: loglikelihood = -3509.6384, backtracks = 0, tol = 0.013720799846722281 Iteration 10: loglikelihood = -3509.2068, backtracks = 0, tol = 0.006104964636802117 Iteration 11: loglikelihood = -3497.9004, backtracks = 0, tol = 0.07700985946675899 Iteration 12: loglikelihood = -3489.5176, backtracks = 0, tol = 0.08005875581080804 Iteration 13: loglikelihood = -3479.761, backtracks = 0, tol = 0.07757164069396638 Iteration 14: loglikelihood = -3478.505, backtracks = 0, tol = 0.008253277765407097 Iteration 15: loglikelihood = -3478.3608, backtracks = 0, tol = 0.004102983992527064 Iteration 16: loglikelihood = -3478.3352, backtracks = 1, tol = 0.0004714577270315592 Iteration 17: loglikelihood = -3478.3203, backtracks = 1, tol = 0.000617584047817861 Iteration 18: loglikelihood = -3478.3242, backtracks = 3, tol = 0.00012459543206533433 Iteration 19: loglikelihood = -3478.321, backtracks = 1, tol = 0.0004344964611179245 Iteration 20: loglikelihood = -3478.321, backtracks = 1, tol = 0.00019013880997657587 Iteration 21: loglikelihood = -3478.3274, backtracks = 3, tol = 2.8189014896539688e-5 26.441418 seconds (18.73 M allocations: 735.924 MiB, 0.83% gc time, 96.54% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3482.9873, backtracks = 0, tol = 0.09024710924650067 Iteration 2: loglikelihood = -3359.3184, backtracks = 0, tol = 0.044647209591505845 Iteration 3: loglikelihood = -3186.1814, backtracks = 1, tol = 0.014803146066573885 Iteration 4: loglikelihood = -3154.5493, backtracks = 0, tol = 0.09907569236223493 Iteration 5: loglikelihood = -2994.5337, backtracks = 0, tol = 0.09761111706452837 Iteration 6: loglikelihood = -2853.1287, backtracks = 0, tol = 0.08521180352890426 Iteration 7: loglikelihood = -2781.8572, backtracks = 0, tol = 0.08963888810242027 Iteration 8: loglikelihood = -2658.016, backtracks = 0, tol = 0.0930497930100716 Iteration 9: loglikelihood = -2542.9917, backtracks = 0, tol = 0.09189995429704141 Iteration 10: loglikelihood = -2448.9683, backtracks = 0, tol = 0.08262316430302809 Iteration 11: loglikelihood = -2370.0073, backtracks = 0, tol = 0.014978496252203955 Iteration 12: loglikelihood = -2307.4314, backtracks = 0, tol = 0.0033299846754971376 Iteration 13: loglikelihood = -2262.1052, backtracks = 0, tol = 0.0821447440552901 Iteration 14: loglikelihood = -2227.4216, backtracks = 0, tol = 0.08223560836337944 Iteration 15: loglikelihood = -2205.6055, backtracks = 0, tol = 0.0787388077047893 Iteration 16: loglikelihood = -2190.9973, backtracks = 0, tol = 0.08158431369045338 Iteration 17: loglikelihood = -2182.04, backtracks = 0, tol = 0.009769190884485041 Iteration 18: loglikelihood = -2177.2441, backtracks = 0, tol = 0.0027267386106193028 Iteration 19: loglikelihood = -2174.6152, backtracks = 0, tol = 0.000693902234469849 Iteration 20: loglikelihood = -2173.7512, backtracks = 0, tol = 0.07639062952380843 Iteration 21: loglikelihood = -2172.944, backtracks = 0, tol = 0.08267794936699077 Iteration 22: loglikelihood = -2172.0647, backtracks = 0, tol = 0.00975606475556296 Iteration 23: loglikelihood = -2171.848, backtracks = 0, tol = 0.0026899107150061266 Iteration 24: loglikelihood = -2171.7507, backtracks = 0, tol = 0.0006045623697559067 Iteration 25: loglikelihood = -2171.701, backtracks = 0, tol = 0.00018516776567238053 Iteration 26: loglikelihood = -2171.677, backtracks = 0, tol = 4.990296245670799e-5 0.182235 seconds (1.19 M allocations: 19.647 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.8s **** 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 4.765663 seconds (1.14 M allocations: 136.660 MiB, 1.02% gc time, 89.76% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.2s 10.878552 seconds (4.00 M allocations: 82.493 MiB, 0.32% gc time, 0.58% compilation time) 5.674197 seconds (3.98 M allocations: 91.677 MiB, 0.25% gc time) 11.571995 seconds (20.41 M allocations: 439.371 MiB, 0.64% gc time, 15.33% compilation time: 78% of which was recompilation) 9.234671 seconds (20.18 M allocations: 434.186 MiB, 0.77% gc time) 38.326275 seconds (3.77 M allocations: 4.239 GiB, 11.10% gc time, 27.68% compilation time) 52.950542 seconds (70.38 k allocations: 183.440 MiB, 0.19% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m26.4s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 15.252 ms (78 allocations: 4.56 KiB) 4.502 μs (0 allocations: 0 bytes) 147.618 μs (4 allocations: 288 bytes) 7.040 μs (0 allocations: 0 bytes) 48.809 μs (2 allocations: 64 bytes) 36.140 μs (0 allocations: 0 bytes) 25.780 μs (0 allocations: 0 bytes) 29.949 μs (0 allocations: 0 bytes) 118.439 μs (0 allocations: 0 bytes) 39.949 ms (78 allocations: 4.56 KiB) 18.510 μs (0 allocations: 0 bytes) 195.879 μs (4 allocations: 288 bytes) 35.719 μs (0 allocations: 0 bytes) 325.647 μs (2 allocations: 64 bytes) 97.979 μs (0 allocations: 0 bytes) 180.418 μs (0 allocations: 0 bytes) 142.449 μs (0 allocations: 0 bytes) 218.638 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m21.6s **** 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 **** **** 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 0.419038 seconds (49.39 k allocations: 5.493 MiB, 63.42% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 1.983109 seconds (282.12 k allocations: 168.122 MiB, 54.46% 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 **** Cross validating... 3%|█ | ETA: 0:03:45 Cross validating... 13%|████▏ | ETA: 0:00:55 Cross validating... 17%|█████▋ | ETA: 0:00:39 Cross validating... 21%|██████▋ | ETA: 0:00:32 Cross validating... 24%|███████▋ | ETA: 0:00:27 Cross validating... 25%|████████▏ | ETA: 0:00:25 Cross validating... 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81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | 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: 0:00:12 Crossvalidation Results: k MSE 0 6408.422635304213 1 4269.018733286979 2 3188.9567261140523 3 2435.7631208192065 4 1752.1829561580253 5 828.0016811048781 6 681.8658732963551 7 561.2579033354971 8 433.9897015304816 9 363.58192604100395 10 353.00995541376165 11 354.86037227472355 12 366.2248151662991 13 360.5220510485805 14 363.528799177233 15 367.6365011041605 16 364.60652533812566 17 368.58558139564514 18 363.69878124068737 19 379.58511827862105 20 387.98422424444556 Best k = 10 13.013659 seconds (12.01 M allocations: 320.196 MiB, 1.72% gc time, 57.96% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 22%|███████▏ | 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... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross 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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 6408.422635304213 1 4310.591467455183 2 3226.995811003778 3 2465.1914811089646 4 1777.8475981425622 5 850.158406001671 6 697.9201253870451 7 577.8366707260873 8 446.64481767922416 9 373.02076764145534 10 361.4966696227373 11 366.0582064576924 12 373.7998845369269 13 378.839872301021 14 391.0462991289172 15 403.1261904894112 16 393.93517478223004 17 406.81016091180396 18 396.4746084495554 19 409.74182290362205 20 418.55022965776175 Best k = 10 5.671314 seconds (11.38 M allocations: 238.945 MiB, 0.86% gc time, 0.84% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 19.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:06 Cross validating... 8%|██▌ | ETA: 0:02:20 Cross validating... 13%|████▏ | ETA: 0:01:24 Cross validating... 19%|██████▏ | ETA: 0:00:53 Cross validating... 24%|███████▋ | ETA: 0:00:40 Cross validating... 29%|█████████▏ | ETA: 0:00:32 Cross validating... 33%|██████████▋ | ETA: 0:00:26 Cross validating... 40%|████████████▊ | ETA: 0:00:20 Cross validating... 44%|██████████████▎ | ETA: 0:00:16 Cross validating... 51%|████████████████▎ | ETA: 0:00:13 Cross validating... 56%|█████████████████▊ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1495.3010218505858 1 1265.5885177001953 2 998.0610911254882 3 764.1196738891601 4 611.6171795043945 5 497.28303945922846 6 406.94371710205075 7 356.98626376342776 8 327.2050288391113 9 306.9110727844238 10 311.98477661132813 11 310.9307779541016 12 316.2840626831055 13 314.5188734436035 14 319.2546510009766 15 320.88111434936525 16 331.47957092285156 17 326.7463607788086 18 348.99716052246094 19 329.1093658752441 20 339.6337001342773 Best k = 9 15.630783 seconds (12.36 M allocations: 307.452 MiB, 0.57% gc time, 83.96% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | 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... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1495.3010218505858 1 1268.122744873047 2 1001.2188829345703 3 766.9320968627928 4 615.4553282470704 5 503.4480979003906 6 414.9266114196777 7 366.0354250793457 8 335.8783661804199 9 316.86376544189454 10 330.54251007080074 11 327.8414550476074 12 341.9935281677246 13 339.33848526000975 14 351.86670150756834 15 361.4517843322754 16 364.83166641235357 17 376.01960253906253 18 369.92455017089844 19 378.72825933837896 20 368.0041181945801 Best k = 9 2.699216 seconds (11.11 M allocations: 204.391 MiB, 1.75% gc time, 1.56% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.8s **** 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: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 8%|██▌ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:10 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validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.5438631409445 1 397.5788684679615 2 348.3600029578374 3 309.4746830319173 4 296.50118223093415 5 272.4696724941449 6 263.70006648774483 7 245.8471619725628 8 243.4397529645128 9 237.4078844650523 10 249.38567722645115 11 256.2222553795384 12 247.68398397108825 13 248.59146451411817 14 253.28670597551258 15 271.49706766325244 16 253.86653822949415 17 272.33072200625344 18 283.1426236678807 19 256.2462476915403 20 279.07327748007907 Best k = 9 8.702506 seconds (17.33 M allocations: 408.886 MiB, 0.86% gc time, 29.25% 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: 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Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.5438631409445 1 397.9798054034768 2 351.95471783098503 3 315.08572155426634 4 303.5194868453042 5 281.81949597069587 6 275.6099521547187 7 258.4547475048317 8 256.7116698987658 9 264.35240478459804 10 268.17634604058185 11 278.9045688974592 12 280.26473903365775 13 291.55822584397197 14 301.724104426952 15 300.00541494773415 16 313.21967281806985 17 323.37114171284657 18 328.89628621020455 19 331.5859565924449 20 340.54509953860577 Best k = 8 6.507647 seconds (18.27 M allocations: 383.128 MiB, 1.00% gc time, 1.01% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.7s **** 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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67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 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: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.1335587021768 1 424.6220374394853 2 388.5147353092139 3 372.38376898130355 4 358.25499757422756 5 350.290900863094 6 343.9778153861688 7 327.6230521042482 8 329.0989975547407 9 318.3740830440038 10 343.4294262669557 11 336.0224473277047 12 339.8666291278664 13 340.4431495298814 14 351.7981929084428 15 338.5027997335617 16 378.0180114563977 17 355.27013009180024 18 367.90187935552217 19 365.2636126126938 20 351.0047615493734 Best k = 9 7.838193 seconds (16.90 M allocations: 402.717 MiB, 12.75% gc time, 33.27% 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: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 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87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 464.1335587021768 1 426.0678600820694 2 391.17922128188434 3 376.09168355517147 4 362.9200568802321 5 355.59774224371716 6 350.2080788783852 7 336.6651809602605 8 342.1272331898027 9 333.50093713536114 10 358.3725671971562 11 359.6108127450344 12 369.63913337008967 13 380.69234709800435 14 385.44379280635053 15 395.4666337253123 16 394.7372228669003 17 411.92482794326617 18 433.6769375403661 19 434.296073941345 20 441.3165974467238 Best k = 9 4.464842 seconds (17.39 M allocations: 357.991 MiB, 1.38% gc time, 0.96% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:07 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 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94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:08 Crossvalidation Results: k MSE 0 1410.3596154768518 1 876.8771219691205 2 736.8008363429325 3 699.6880436789744 4 756.1517361857331 5 662.4419977722025 6 679.6026748276307 7 673.4065425787535 8 655.839670834082 9 670.171134128677 10 650.1642018384348 11 735.5794903305439 12 653.0199451833261 13 674.9194683407749 14 752.5788133382341 15 658.9178210922007 16 654.4399306280404 17 640.9084695604008 18 663.2514174234204 19 675.7770835185984 20 779.2737772431732 Best k = 17 8.851558 seconds (14.88 M allocations: 347.553 MiB, 1.15% gc time, 29.88% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 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... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 1410.3596154768518 1 1449.1728637232777 2 1577.1129386173768 3 1972.600467725223 4 1246.1135846365476 5 1063.0722744919747 6 831.040017308294 7 973.5940626538722 8 897.8221168057412 9 844.9804704097107 10 802.0129685822885 11 769.0866217556246 12 758.0956802146343 13 871.9749870254749 14 787.9055332111473 15 760.4265107527165 16 814.4514865168389 17 748.4501518782339 18 752.1152804457436 19 760.717806535148 20 729.4943758537697 Best k = 20 6.177856 seconds (13.69 M allocations: 270.842 MiB, 0.96% gc time, 0.95% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson 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: 0:01:03 Cross validating... 5%|█▌ | ETA: 0:01:05 Cross validating... 6%|██ | ETA: 0:01:04 Cross validating... 8%|██▌ | ETA: 0:01:04 Cross validating... 10%|███ | ETA: 0:01:03 Cross validating... 11%|███▌ | ETA: 0:01:02 Cross validating... 13%|████▏ | ETA: 0:00:54 Cross validating... 14%|████▋ | ETA: 0:00:48 Cross validating... 16%|█████▏ | ETA: 0:00:44 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 19%|██████▏ | ETA: 0:00:41 Cross validating... 21%|██████▋ | ETA: 0:00:38 Cross validating... 22%|███████▏ | ETA: 0:00:39 Cross validating... 24%|███████▋ | ETA: 0:00:36 Cross validating... 25%|████████▏ | ETA: 0:00:37 Cross validating... 27%|████████▋ | ETA: 0:00:37 Cross validating... 29%|█████████▏ | ETA: 0:00:35 Cross validating... 30%|█████████▋ | ETA: 0:00:36 Cross validating... 32%|██████████▏ | ETA: 0:00:36 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89%|████████████████████████████▌ | ETA: 0:00:06 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:05 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:02 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:53 Crossvalidation Results: k MSE 0 478.37281533462624 1 345.6156680851403 2 293.9346913137155 3 257.7140998135677 4 237.11039441840393 5 235.15909677476202 6 233.33348850284176 7 233.1367320608458 8 235.39015095949122 9 233.80006384386348 10 232.37616503487092 11 235.18087545985003 12 234.88228229864654 13 232.4165288386281 14 234.49411875297037 15 231.81270633656572 16 231.49388867462 17 232.1389987335583 18 234.96321069413233 19 234.27643973975165 20 237.54590103693437 Best k = 16 53.452763 seconds (149.23 M allocations: 3.893 GiB, 1.04% gc time, 4.29% 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: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:07 Cross validating... 8%|██▌ | ETA: 0:00:07 Cross validating... 10%|███ | ETA: 0:00:08 Cross validating... 11%|███▌ | ETA: 0:00:08 Cross validating... 13%|████▏ | ETA: 0:00:09 Cross validating... 14%|████▋ | ETA: 0:00:09 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:10 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83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:17 Crossvalidation Results: k MSE 0 478.37281533462624 1 345.5738341634018 2 294.75770057983067 3 259.9300692212493 4 240.18081972936886 5 236.75277167256675 6 241.50279393919953 7 242.72098569580652 8 246.65165666493246 9 246.8296989744238 10 248.98444005098492 11 252.69320484426316 12 251.91912425202173 13 252.4530897793635 14 254.8501139040996 15 260.23615758032133 16 253.2144280296249 17 263.33003817903176 18 264.36513251664815 19 275.0387577988771 20 268.7257344791277 Best k = 5 17.835982 seconds (50.26 M allocations: 1.028 GiB, 1.28% gc time, 0.36% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m11.8s **** 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: 0:01:08 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.308346 seconds (17.00 M allocations: 337.698 MiB, 1.38% gc time, 44.69% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 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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 3.457559 seconds (16.17 M allocations: 286.706 MiB, 1.79% gc time, 1.64% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.3s **** 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 **** 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739.6971614820919 18 748.2156259422846 19 751.0949053466545 20 756.1801656502964 Best k = 10 16.974656 seconds (312.69 k allocations: 205.829 MiB, 0.79% gc time, 9.98% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 21.8s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m05.9s **** 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... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 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97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 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 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2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross 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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 1m27.6s 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:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl: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(0xc5169277a77e1888, 0xa307d30a7067e6b2, 0x0687612bb0268389, 0xb3115206f8e4668b, 0xb44c2fa237b52c18) 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 1116.4s 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 1234.65s: package tests unexpectedly errored