Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2186 (48ff18f4cd*) started at 2026-05-14T23:47:31.689 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.47s ################################################################################ # 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 v4.5.2 [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 v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.71s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.5 s ✓ BGEN 8.0 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`. 24.8 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 68.67s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_7NLlfF/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 17.7s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 9.7s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1912.7199753597515, backtracks = 0, tol = 3.106150082028245 Iteration 2: loglikelihood = -1479.0658994728406, backtracks = 0, tol = 0.14272187601573028 Iteration 3: loglikelihood = -1412.1173110825703, backtracks = 0, tol = 0.05177428317770753 Iteration 4: loglikelihood = -1410.9536973582233, backtracks = 0, tol = 0.0060069973142010185 Iteration 5: loglikelihood = -1410.9389300294652, backtracks = 0, tol = 0.0009903432849968094 Iteration 6: loglikelihood = -1410.938724643701, backtracks = 0, tol = 7.558978587735809e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.048922061920166016 Final loglikelihood: -1410.938724643701 SNP PVE: 0.9549428668910558 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 2402 3.49039 2 │ 2983 -1.96499 3 │ 4621 1.26774 4 │ 7105 -0.487211 5 │ 7782 -0.647289 6 │ 8024 1.25434 7 │ 8053 0.219387 8 │ 9365 -0.275324 9 │ 9452 -0.551989 10 │ 9665 0.715935 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00851059Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.1s **** 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 logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -16133.666337655242, backtracks = 0, tol = 0.5917202428928972 Iteration 2: loglikelihood = -7579.477193100927, backtracks = 0, tol = 0.055807420886301876 Iteration 3: loglikelihood = -3745.887228433646, backtracks = 0, tol = 0.05613593360701806 Iteration 4: loglikelihood = -2160.402522086925, backtracks = 0, tol = 0.061057643308604165 Iteration 5: loglikelihood = -1731.3898443385074, backtracks = 0, tol = 0.05805693724678148 Iteration 6: loglikelihood = -1662.32198433355, backtracks = 0, tol = 0.03950755065819523 Iteration 7: loglikelihood = -1551.2978689101428, backtracks = 0, tol = 0.05489643182903441 Iteration 8: loglikelihood = -1528.1042140227694, backtracks = 0, tol = 0.02152641698352604 Iteration 9: loglikelihood = -1500.0703689830714, backtracks = 0, tol = 0.04452056070699338 Iteration 10: loglikelihood = -1483.026670540841, backtracks = 0, tol = 0.021316201273854012 Iteration 11: loglikelihood = -1471.2231996888042, backtracks = 0, tol = 0.06367140685243819 Iteration 12: loglikelihood = -1459.3034550703176, backtracks = 0, tol = 0.019024798685352843 Iteration 13: loglikelihood = -1455.0749826845038, backtracks = 0, tol = 0.01616483793018542 Iteration 14: loglikelihood = -1452.7957214743496, backtracks = 0, tol = 0.006935673257520535 Iteration 15: loglikelihood = -1451.4439853519593, backtracks = 1, tol = 0.004086124964905767 Iteration 16: loglikelihood = -1449.9572057406344, backtracks = 1, tol = 0.007298317857834385 Iteration 17: loglikelihood = -1448.9382952070455, backtracks = 0, tol = 0.006083120274373013 Iteration 18: loglikelihood = -1448.0851411936137, backtracks = 0, tol = 0.004804116176874842 Iteration 19: loglikelihood = -1447.4754140886464, backtracks = 1, tol = 0.0031690136512091526 Iteration 20: loglikelihood = -1446.795072109417, backtracks = 1, tol = 0.004310001821462839 Iteration 21: loglikelihood = -1446.2628589677272, backtracks = 0, tol = 0.004797944413420856 Iteration 22: loglikelihood = -1445.7995350745598, backtracks = 0, tol = 0.003583797982158299 Iteration 23: loglikelihood = -1445.4666230705102, backtracks = 1, tol = 0.002603677014681515 Iteration 24: loglikelihood = -1445.0507237881227, backtracks = 1, tol = 0.003912853070933217 Iteration 25: loglikelihood = -1444.7496695073617, backtracks = 0, tol = 0.0036778361336071252 Iteration 26: loglikelihood = -1444.4790584295995, backtracks = 0, tol = 0.0027660320032781463 Iteration 27: loglikelihood = -1444.2231990663151, backtracks = 0, tol = 0.0038397559081727968 Iteration 28: loglikelihood = -1443.9906801668758, backtracks = 0, tol = 0.0025860465243009844 Iteration 29: loglikelihood = -1443.821354299041, backtracks = 1, tol = 0.0020165941887596694 Iteration 30: loglikelihood = -1443.6753460882753, backtracks = 2, tol = 0.001838703940863002 Iteration 31: loglikelihood = -1443.5220600394293, backtracks = 3, tol = 0.0021158212217866497 Iteration 32: loglikelihood = -1443.337470971429, backtracks = 3, tol = 0.002669983371518087 Iteration 33: loglikelihood = -1443.2262269337693, backtracks = 3, tol = 0.0016637538869795521 Iteration 34: loglikelihood = -1449.7508248759748, backtracks = 3, tol = 0.05558619400988433 Iteration 35: loglikelihood = -1443.7960093858696, backtracks = 0, tol = 0.012923543206338676 Iteration 36: loglikelihood = -1441.7712545901918, backtracks = 0, tol = 0.00717531666212086 Iteration 37: loglikelihood = -1441.002844005694, backtracks = 0, tol = 0.004016468788993613 Iteration 38: loglikelihood = -1440.6459835930239, backtracks = 0, tol = 0.0033605580624149057 Iteration 39: loglikelihood = -1440.461834950427, backtracks = 0, tol = 0.002180161343885169 Iteration 40: loglikelihood = -1440.3144403399765, backtracks = 0, tol = 0.002965174024526757 Iteration 41: loglikelihood = -1440.193124547949, backtracks = 0, tol = 0.001856985249377167 Iteration 42: loglikelihood = -1439.3274749796797, backtracks = 0, tol = 0.038382722879362736 Iteration 43: loglikelihood = -1436.43647434949, backtracks = 0, tol = 0.012782540500807692 Iteration 44: loglikelihood = -1435.5132074768803, backtracks = 0, tol = 0.0062464630013455225 Iteration 45: loglikelihood = -1435.1871793231383, backtracks = 0, tol = 0.002831723766152558 Iteration 46: loglikelihood = -1435.0009039709507, backtracks = 0, tol = 0.0023305224273944144 Iteration 47: loglikelihood = -1434.8750210095855, backtracks = 0, tol = 0.0018614729584335505 Iteration 48: loglikelihood = -1434.7774811125742, backtracks = 0, tol = 0.0017938154513301584 Iteration 49: loglikelihood = -1434.6968484356855, backtracks = 0, tol = 0.001545370981847556 Iteration 50: loglikelihood = -1434.624078453364, backtracks = 0, tol = 0.0018517824618030896 Iteration 51: loglikelihood = -1434.557343022011, backtracks = 0, tol = 0.001426828784969651 Iteration 52: loglikelihood = -1434.4936022601955, backtracks = 0, tol = 0.0018776837191928672 Iteration 53: loglikelihood = -1434.433151446969, backtracks = 0, tol = 0.001365690790681509 Iteration 54: loglikelihood = -1434.3744402271027, backtracks = 0, tol = 0.0018942488415269515 Iteration 55: loglikelihood = -1434.318200905092, backtracks = 0, tol = 0.0013204156794496557 Iteration 56: loglikelihood = -1434.2632461359822, backtracks = 0, tol = 0.001910827298848194 Iteration 57: loglikelihood = -1434.2104097931956, backtracks = 0, tol = 0.0012813807648540806 Iteration 58: loglikelihood = -1434.1585990063388, backtracks = 0, tol = 0.0019300005394317316 Iteration 59: loglikelihood = -1434.1086879224688, backtracks = 0, tol = 0.0012463029613799493 Iteration 60: loglikelihood = -1434.0596064861695, backtracks = 0, tol = 0.0019525427826666804 Iteration 61: loglikelihood = -1434.0122614913803, backtracks = 0, tol = 0.0012144619249435658 Iteration 62: loglikelihood = -1433.9655796678453, backtracks = 0, tol = 0.0019788409341326457 Iteration 63: loglikelihood = -1433.9205035901375, backtracks = 0, tol = 0.0011854860387604661 Iteration 64: loglikelihood = -1433.8759422710582, backtracks = 0, tol = 0.0020092460763226168 Iteration 65: loglikelihood = -1433.8328796593705, backtracks = 0, tol = 0.0011591076988968622 Iteration 66: loglikelihood = -1433.7901958060236, backtracks = 0, tol = 0.0020441676781038256 Iteration 67: loglikelihood = -1433.7489225877484, backtracks = 0, tol = 0.0011351142579846616 Iteration 68: loglikelihood = -1433.7180247247327, backtracks = 1, tol = 0.001042055800741293 Iteration 69: loglikelihood = -1433.6828710448697, backtracks = 1, tol = 0.0012532630731683578 Iteration 70: loglikelihood = -1433.6480621001006, backtracks = 0, tol = 0.0016924154923317323 Iteration 71: loglikelihood = -1433.6142901498151, backtracks = 0, tol = 0.0010272978570671314 Iteration 72: loglikelihood = -1433.5808764099875, backtracks = 0, tol = 0.0017136538095001044 Iteration 73: loglikelihood = -1433.548437713807, backtracks = 0, tol = 0.0010073512833647775 Iteration 74: loglikelihood = -1433.5162805122677, backtracks = 0, tol = 0.0017377954113374837 Iteration 75: loglikelihood = -1433.4850457959508, backtracks = 0, tol = 0.0009886840329570608 Iteration 76: loglikelihood = -1433.4540207705336, backtracks = 0, tol = 0.0017649584613026257 Iteration 77: loglikelihood = -1433.4238737156784, backtracks = 0, tol = 0.0009715270366261052 Iteration 78: loglikelihood = -1433.4012865645145, backtracks = 1, tol = 0.0008977271458213547 Iteration 79: loglikelihood = -1433.3760597863318, backtracks = 1, tol = 0.0010469453798393087 Iteration 80: loglikelihood = -1433.35010313119, backtracks = 0, tol = 0.0014958451989729592 Iteration 81: loglikelihood = -1433.3248155169258, backtracks = 0, tol = 0.0008900871489662926 Iteration 82: loglikelihood = -1433.2997368621554, backtracks = 0, tol = 0.0015135369696612003 Iteration 83: loglikelihood = -1433.2752941455494, backtracks = 0, tol = 0.0008754730220553854 Iteration 84: loglikelihood = -1433.251016604808, backtracks = 0, tol = 0.0015332979283892599 Iteration 85: loglikelihood = -1433.2273464023224, backtracks = 0, tol = 0.0008616466210459152 Iteration 86: loglikelihood = -1433.2037998164083, backtracks = 0, tol = 0.0015551902543430095 Iteration 87: loglikelihood = -1433.180835902487, backtracks = 0, tol = 0.0008488291124204341 Iteration 88: loglikelihood = -1433.1636202321777, backtracks = 1, tol = 0.0007897091944751073 Iteration 89: loglikelihood = -1433.1447768365672, backtracks = 1, tol = 0.0008916404912254317 Iteration 90: loglikelihood = -1433.1246011092205, backtracks = 0, tol = 0.0013520961027904492 Iteration 91: loglikelihood = -1433.104884925119, backtracks = 0, tol = 0.0007866966244327877 Iteration 92: loglikelihood = -1433.0852937983339, backtracks = 0, tol = 0.0013675601301839232 Iteration 93: loglikelihood = -1433.0661432241384, backtracks = 0, tol = 0.0007756202872707267 Iteration 94: loglikelihood = -1433.047090534382, backtracks = 0, tol = 0.0013846081699592275 Iteration 95: loglikelihood = -1433.0284617912243, backtracks = 0, tol = 0.0007650504545502656 Iteration 96: loglikelihood = -1433.014503424382, backtracks = 1, tol = 0.0007016379064247108 Iteration 97: loglikelihood = -1432.998461574974, backtracks = 1, tol = 0.0008481715899868909 Iteration 98: loglikelihood = -1432.9824657929082, backtracks = 0, tol = 0.0011429480142315575 Iteration 99: loglikelihood = -1432.9667951588135, backtracks = 0, tol = 0.000701841442785337 Iteration 100: loglikelihood = -1432.9512441780469, backtracks = 0, tol = 0.0011523663872139902 Iteration 101: loglikelihood = -1432.9360045889064, backtracks = 0, tol = 0.0006923301353826984 Iteration 102: loglikelihood = -1432.920867858034, backtracks = 0, tol = 0.0011626810191515962 Iteration 103: loglikelihood = -1432.9060302094067, backtracks = 0, tol = 0.0006832037115668379 Iteration 104: loglikelihood = -1432.8912794646553, backtracks = 0, tol = 0.0011738860744146917 Iteration 105: loglikelihood = -1432.8768167783571, backtracks = 0, tol = 0.000674587193387979 Iteration 106: loglikelihood = -1432.8624256813268, backtracks = 0, tol = 0.0011860390796752558 Iteration 107: loglikelihood = -1432.8483127897143, backtracks = 0, tol = 0.0006664439020324715 Iteration 108: loglikelihood = -1432.8342566907688, backtracks = 0, tol = 0.0011992004139998774 Iteration 109: loglikelihood = -1432.8204700159672, backtracks = 0, tol = 0.000658756055974576 Iteration 110: loglikelihood = -1432.8101357850562, backtracks = 1, tol = 0.0006067201128115468 Iteration 111: loglikelihood = -1432.7984070829084, backtracks = 1, tol = 0.0007183915669049312 Iteration 112: loglikelihood = -1432.7864099815356, backtracks = 0, tol = 0.0010053884981763854 Iteration 113: loglikelihood = -1432.7746242655423, backtracks = 0, tol = 0.0006091714666392737 Iteration 114: loglikelihood = -1432.7629117487995, backtracks = 0, tol = 0.001013016686373323 Iteration 115: loglikelihood = -1432.7514030758248, backtracks = 0, tol = 0.0006021206834212227 Iteration 116: loglikelihood = -1432.7399580071992, backtracks = 0, tol = 0.0010212686885913847 Iteration 117: loglikelihood = -1432.7287099448197, backtracks = 0, tol = 0.0005953028467176597 Iteration 118: loglikelihood = -1432.7175162931396, backtracks = 0, tol = 0.0010301335865937362 Iteration 119: loglikelihood = -1432.7065134426196, backtracks = 0, tol = 0.0005888247555810427 Iteration 120: loglikelihood = -1432.6955561105738, backtracks = 0, tol = 0.001039648402869022 Iteration 121: loglikelihood = -1432.6847839591787, backtracks = 0, tol = 0.0005826611311918031 Iteration 122: loglikelihood = -1432.6740486831184, backtracks = 0, tol = 0.0010498499231852592 Iteration 123: loglikelihood = -1432.6634935091256, backtracks = 0, tol = 0.0005768025326547631 Iteration 124: loglikelihood = -1432.6555809441415, backtracks = 1, tol = 0.0005303901860063854 Iteration 125: loglikelihood = -1432.6465409310526, backtracks = 1, tol = 0.0006327167606632758 Iteration 126: loglikelihood = -1432.6373420104771, backtracks = 0, tol = 0.0008753902508199839 Iteration 127: loglikelihood = -1432.6282852548254, backtracks = 0, tol = 0.0005343582054484331 Iteration 128: loglikelihood = -1432.6192796269122, backtracks = 0, tol = 0.0008810546472773995 Iteration 129: loglikelihood = -1432.6104116265572, backtracks = 0, tol = 0.0005288712475876236 Iteration 130: loglikelihood = -1432.6015890750032, backtracks = 0, tol = 0.000887130189207785 Iteration 131: loglikelihood = -1432.5928999851399, backtracks = 0, tol = 0.0005235354876173299 Iteration 132: loglikelihood = -1432.584250885986, backtracks = 0, tol = 0.0008936035016954309 Iteration 133: loglikelihood = -1432.5757314189395, backtracks = 0, tol = 0.0005184324930992014 Iteration 134: loglikelihood = -1432.5672466553776, backtracks = 0, tol = 0.0009004951759334114 Iteration 135: loglikelihood = -1432.5588880075043, backtracks = 0, tol = 0.0005135455169209206 Iteration 136: loglikelihood = -1432.5505589229247, backtracks = 0, tol = 0.0009078247759547201 Iteration 137: loglikelihood = -1432.5423527296675, backtracks = 0, tol = 0.0005088684489804825 Iteration 138: loglikelihood = -1432.5341710814344, backtracks = 0, tol = 0.000915614493748821 Iteration 139: loglikelihood = -1432.5261093738013, backtracks = 0, tol = 0.0005043948579328726 Iteration 140: loglikelihood = -1432.52006608359, backtracks = 1, tol = 0.00046194449107059694 Iteration 141: loglikelihood = -1432.5130591552133, backtracks = 1, tol = 0.0005618233024811683 Iteration 142: loglikelihood = -1432.5060555142222, backtracks = 0, tol = 0.0007527533333328107 Iteration 143: loglikelihood = -1432.4991465374997, backtracks = 0, tol = 0.00046698766106637615 Iteration 144: loglikelihood = -1432.4922742151725, backtracks = 0, tol = 0.000756737225564803 Iteration 145: loglikelihood = -1432.4854938120907, backtracks = 0, tol = 0.000462701402022993 Iteration 146: loglikelihood = -1432.478746755849, backtracks = 0, tol = 0.0007609802613855997 Iteration 147: loglikelihood = -1432.4720890687577, backtracks = 0, tol = 0.00045851382989916986 Iteration 148: loglikelihood = -1432.4654615437175, backtracks = 0, tol = 0.0007654696661869724 Iteration 149: loglikelihood = -1432.4589210155598, backtracks = 0, tol = 0.0004544839000456278 Iteration 150: loglikelihood = -1432.4524075633756, backtracks = 0, tol = 0.0007702158576080931 Iteration 151: loglikelihood = -1432.44597890231, backtracks = 0, tol = 0.0004506011878587561 Iteration 152: loglikelihood = -1432.4395743190896, backtracks = 0, tol = 0.0007752283242273003 Iteration 153: loglikelihood = -1432.4332524772813, backtracks = 0, tol = 0.00044686157133529977 Iteration 154: loglikelihood = -1432.4269517919126, backtracks = 0, tol = 0.0007805177075326266 Iteration 155: loglikelihood = -1432.4207319449704, backtracks = 0, tol = 0.00044326078450612 Iteration 156: loglikelihood = -1432.4145303991165, backtracks = 0, tol = 0.000786095683481882 Iteration 157: loglikelihood = -1432.4084079270647, backtracks = 0, tol = 0.0004397950226620453 Iteration 158: loglikelihood = -1432.4023009565099, backtracks = 0, tol = 0.0007919750732500378 Iteration 159: loglikelihood = -1432.396271426055, backtracks = 0, tol = 0.0004364608562317846 Iteration 160: loglikelihood = -1432.391751226714, backtracks = 1, tol = 0.00039908497153805857 Iteration 161: loglikelihood = -1432.3864759540963, backtracks = 1, tol = 0.0004890899705032165 Iteration 162: loglikelihood = -1432.3812327397193, backtracks = 0, tol = 0.0006475660314539519 Iteration 163: loglikelihood = -1432.3760509524348, backtracks = 0, tol = 0.0004046456828036198 Iteration 164: loglikelihood = -1432.3708937098645, backtracks = 0, tol = 0.0006504504823592698 Iteration 165: loglikelihood = -1432.3657963233622, backtracks = 0, tol = 0.00040139335129965185 Iteration 166: loglikelihood = -1432.3607216149796, backtracks = 0, tol = 0.0006535004633165985 Iteration 167: loglikelihood = -1432.355705288466, backtracks = 0, tol = 0.00039820130837778304 Iteration 168: loglikelihood = -1432.3507098364262, backtracks = 0, tol = 0.000656705218694785 Iteration 169: loglikelihood = -1432.3457713809821, backtracks = 0, tol = 0.00039511336210194196 Iteration 170: loglikelihood = -1432.3408520477412, backtracks = 0, tol = 0.0006600703680809611 Iteration 171: loglikelihood = -1432.3359884097342, backtracks = 0, tol = 0.0003921228976355852 Iteration 172: loglikelihood = -1432.331142188457, backtracks = 0, tol = 0.000663600732362789 Iteration 173: loglikelihood = -1432.3263504402096, backtracks = 0, tol = 0.0003892274372402832 Iteration 174: loglikelihood = -1432.321574445163, backtracks = 0, tol = 0.0006673016760766254 Iteration 175: loglikelihood = -1432.316851775821, backtracks = 0, tol = 0.0003864243735930692 Iteration 176: loglikelihood = -1432.3121432334904, backtracks = 0, tol = 0.0006711790183929334 Iteration 177: loglikelihood = -1432.3074869405066, backtracks = 0, tol = 0.0003837113355986875 Iteration 178: loglikelihood = -1432.3028431812352, backtracks = 0, tol = 0.0006752390760712368 Iteration 179: loglikelihood = -1432.29825066238, backtracks = 0, tol = 0.0003810861423274761 Iteration 180: loglikelihood = -1432.2936691125376, backtracks = 0, tol = 0.0006794886979699193 Iteration 181: loglikelihood = -1432.2891378583715, backtracks = 0, tol = 0.00037854679994905194 Iteration 182: loglikelihood = -1432.285741514972, backtracks = 1, tol = 0.0003419676527278521 Iteration 183: loglikelihood = -1432.2816032429614, backtracks = 1, tol = 0.0004449591513232131 Iteration 184: loglikelihood = -1432.2777224886179, backtracks = 0, tol = 0.0005329953698143819 Iteration 185: loglikelihood = -1432.2738811568095, backtracks = 0, tol = 0.0003485593444489818 Iteration 186: loglikelihood = -1432.270058319125, backtracks = 0, tol = 0.0005346509737196337 Iteration 187: loglikelihood = -1432.266273948598, backtracks = 0, tol = 0.0003460028853947442 Iteration 188: loglikelihood = -1432.2625070385207, backtracks = 0, tol = 0.0005363968850638469 Iteration 189: loglikelihood = -1432.2587776900352, backtracks = 0, tol = 0.0003434879150756222 Iteration 190: loglikelihood = -1432.2550648032188, backtracks = 0, tol = 0.0005382252242840065 Iteration 191: loglikelihood = -1432.2513886186857, backtracks = 0, tol = 0.00034104112734206456 Iteration 192: loglikelihood = -1432.2477279271725, backtracks = 0, tol = 0.000540137888393925 Iteration 193: loglikelihood = -1432.2441031224023, backtracks = 0, tol = 0.00033865932882158335 Iteration 194: loglikelihood = -1432.2404928700687, backtracks = 0, tol = 0.0005421365082048954 Iteration 195: loglikelihood = -1432.2369177303387, backtracks = 0, tol = 0.0003363407332459285 Iteration 196: loglikelihood = -1432.2333562284769, backtracks = 0, tol = 0.0005442228788978203 Iteration 197: loglikelihood = -1432.2298291043292, backtracks = 0, tol = 0.00033408359980049475 Iteration 198: loglikelihood = -1432.2263147275387, backtracks = 0, tol = 0.0005463989431081981 Iteration 199: loglikelihood = -1432.2228340308197, backtracks = 0, tol = 0.0003318862954478985 Did not converge after 200 iterations! IHT run time was 1.7176649570465088 seconds Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 4.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1794.0697105051354, backtracks = 0, tol = 0.6206581720915431 Iteration 2: loglikelihood = -1634.7828428302564, backtracks = 0, tol = 0.15756708780149237 Iteration 3: loglikelihood = -1569.433800105497, backtracks = 0, tol = 0.10925794223941487 Iteration 4: loglikelihood = -1536.06365709906, backtracks = 0, tol = 0.06965228194953091 Iteration 5: loglikelihood = -1523.8731820522485, backtracks = 0, tol = 0.07515118844497377 Iteration 6: loglikelihood = -1522.3491931150081, backtracks = 0, tol = 0.07146274316201909 Iteration 7: loglikelihood = -1520.286142302737, backtracks = 0, tol = 0.07140893251474442 Iteration 8: loglikelihood = -1519.5828109558245, backtracks = 1, tol = 0.01207930381508081 Iteration 9: loglikelihood = -1519.1346159158725, backtracks = 2, tol = 0.014297419251459798 Iteration 10: loglikelihood = -1518.8829257823197, backtracks = 2, tol = 0.07366724915320945 Iteration 11: loglikelihood = -1517.8536820744814, backtracks = 0, tol = 0.07360703111181943 Iteration 12: loglikelihood = -1517.6491736495207, backtracks = 1, tol = 0.005687633837964986 Iteration 13: loglikelihood = -1517.483739120545, backtracks = 2, tol = 0.0089592312647065 Iteration 14: loglikelihood = -1517.362772948566, backtracks = 3, tol = 0.007856468629962754 Iteration 15: loglikelihood = -1517.7155619116188, backtracks = 3, tol = 0.06306701486108149 Iteration 16: loglikelihood = -1517.408330422863, backtracks = 0, tol = 0.07193475134603897 Iteration 17: loglikelihood = -1517.0813452332318, backtracks = 0, tol = 0.013974224355159843 Iteration 18: loglikelihood = -1517.0390102999413, backtracks = 2, tol = 0.0034389663600678136 Iteration 19: loglikelihood = -1521.650010616163, backtracks = 3, tol = 0.07766241984250163 Iteration 20: loglikelihood = -1518.649969993851, backtracks = 0, tol = 0.07378952269345605 Iteration 21: loglikelihood = -1518.516684766278, backtracks = 0, tol = 0.005389453537818685 Iteration 22: loglikelihood = -1518.4855119156994, backtracks = 1, tol = 0.0026578958602292944 Iteration 23: loglikelihood = -1518.7056058348487, backtracks = 3, tol = 0.08078933015492948 Iteration 24: loglikelihood = -1516.8329001477268, backtracks = 0, tol = 0.068752810450303 Iteration 25: loglikelihood = -1516.778299661555, backtracks = 0, tol = 0.0034481745349613816 Iteration 26: loglikelihood = -1516.756199663555, backtracks = 1, tol = 0.0024561083375214112 Iteration 27: loglikelihood = -1533.1777722160566, backtracks = 3, tol = 0.08489162113324772 Iteration 28: loglikelihood = -1520.7440903475203, backtracks = 0, tol = 0.08490831933966073 Iteration 29: loglikelihood = -1517.2955868064662, backtracks = 0, tol = 0.05490433470143612 Iteration 30: loglikelihood = -1516.704032618744, backtracks = 0, tol = 0.019383198722926147 Iteration 31: loglikelihood = -1516.6621643618491, backtracks = 0, tol = 0.003438314496438117 Iteration 32: loglikelihood = -1516.651475645422, backtracks = 2, tol = 0.0014585083329224594 Iteration 33: loglikelihood = -1526.5253568531361, backtracks = 3, tol = 0.07993678042420048 Iteration 34: loglikelihood = -1520.221351828609, backtracks = 0, tol = 0.07989184803440273 Iteration 35: loglikelihood = -1517.494469963078, backtracks = 0, tol = 0.053047258068343525 Iteration 36: loglikelihood = -1516.998314576648, backtracks = 0, tol = 0.0591406558367702 Iteration 37: loglikelihood = -1516.901371853912, backtracks = 0, tol = 0.0049950862681346206 Iteration 38: loglikelihood = -1516.8835596722865, backtracks = 0, tol = 0.0026889903466771467 Iteration 39: loglikelihood = -1516.873258741462, backtracks = 1, tol = 0.0015066332084615484 Iteration 40: loglikelihood = -1530.0905900221926, backtracks = 3, tol = 0.09135094245818268 Iteration 41: loglikelihood = -1520.2955358592735, backtracks = 0, tol = 0.09132884289273525 Iteration 42: loglikelihood = -1516.6890137509197, backtracks = 0, tol = 0.07151180129046487 Iteration 43: loglikelihood = -1516.5399033691128, backtracks = 0, tol = 0.0061388434350479045 Iteration 44: loglikelihood = -1516.5283111816307, backtracks = 1, tol = 0.0011728137627880465 Iteration 45: loglikelihood = -1516.5234884996871, backtracks = 3, tol = 0.0009862020770482303 Iteration 46: loglikelihood = -1517.1765119887036, backtracks = 3, tol = 0.07208780887721054 Iteration 47: loglikelihood = -1516.8113348382988, backtracks = 0, tol = 0.016957261945138837 Iteration 48: loglikelihood = -1516.8002499012036, backtracks = 0, tol = 0.002122535819067531 Iteration 49: loglikelihood = -1516.7936710868312, backtracks = 1, tol = 0.0014482621753381364 Iteration 50: loglikelihood = -1516.7873004064638, backtracks = 3, tol = 0.0016922623154393556 Iteration 51: loglikelihood = -1533.2458182747193, backtracks = 3, tol = 0.0969652290817899 Iteration 52: loglikelihood = -1521.860999728818, backtracks = 0, tol = 0.0886137485731168 Iteration 53: loglikelihood = -1517.0464433585603, backtracks = 0, tol = 0.07151766778986482 Iteration 54: loglikelihood = -1516.7937839696726, backtracks = 0, tol = 0.008572176509592336 Iteration 55: loglikelihood = -1516.7641547495675, backtracks = 0, tol = 0.0033215024845019273 Iteration 56: loglikelihood = -1516.672295017318, backtracks = 0, tol = 0.0706957962061915 Iteration 57: loglikelihood = -1516.4583770867978, backtracks = 0, tol = 0.011978501263031956 Iteration 58: loglikelihood = -1516.4516841026632, backtracks = 0, tol = 0.0016139818541880426 Iteration 59: loglikelihood = -1516.4480964371085, backtracks = 1, tol = 0.0009865327687087104 Iteration 60: loglikelihood = -1521.1341123351394, backtracks = 3, tol = 0.07778691126346833 Iteration 61: loglikelihood = -1518.1877191174838, backtracks = 0, tol = 0.07377452976398116 Iteration 62: loglikelihood = -1518.0748115928952, backtracks = 0, tol = 0.0050163380488784095 Iteration 63: loglikelihood = -1518.0637385518692, backtracks = 0, tol = 0.0018912475243518323 Iteration 64: loglikelihood = -1518.0354060506827, backtracks = 0, tol = 0.07622859014870666 Iteration 65: loglikelihood = -1516.4631367431632, backtracks = 0, tol = 0.0649142740948712 Iteration 66: loglikelihood = -1516.428027316841, backtracks = 0, tol = 0.002473852569533793 Iteration 67: loglikelihood = -1516.4237457091333, backtracks = 1, tol = 0.0006812602492809008 Iteration 68: loglikelihood = -1516.4203783364776, backtracks = 2, tol = 0.001112145042821163 Iteration 69: loglikelihood = -1791.8137127550597, backtracks = 3, tol = 0.1807464560723484 Iteration 70: loglikelihood = -1740.102102835342, backtracks = 0, tol = 0.5700141758834711 Iteration 71: loglikelihood = -1660.398962456305, backtracks = 0, tol = 0.06625907163255634 Iteration 72: loglikelihood = -1604.687220829495, backtracks = 0, tol = 0.07008831610975853 Iteration 73: loglikelihood = -1564.2043748458507, backtracks = 0, tol = 0.06829783211028873 Iteration 74: loglikelihood = -1540.5926368119603, backtracks = 0, tol = 0.06923786451988695 Iteration 75: loglikelihood = -1527.3313646231152, backtracks = 0, tol = 0.06005506471945397 Iteration 76: loglikelihood = -1521.5865906460244, backtracks = 0, tol = 0.04402570260644639 Iteration 77: loglikelihood = -1520.5139635824114, backtracks = 0, tol = 0.021535770168194204 Iteration 78: loglikelihood = -1518.3259371592576, backtracks = 0, tol = 0.05769090678299028 Iteration 79: loglikelihood = -1516.669008621306, backtracks = 0, tol = 0.05985832913069396 Iteration 80: loglikelihood = -1516.419426842316, backtracks = 0, tol = 0.011451625272565116 Iteration 81: loglikelihood = -1516.396453408525, backtracks = 0, tol = 0.002542101071434984 Iteration 82: loglikelihood = -1516.392727696261, backtracks = 1, tol = 0.0007777033910867743 Iteration 83: loglikelihood = -1516.3903689664867, backtracks = 2, tol = 0.000813915518783907 Iteration 84: loglikelihood = -1551.4615141343882, backtracks = 3, tol = 0.10718376744786136 Iteration 85: loglikelihood = -1521.5358690265002, backtracks = 0, tol = 0.10716943530326706 Iteration 86: loglikelihood = -1518.5353197599206, backtracks = 0, tol = 0.05566309822580755 Iteration 87: loglikelihood = -1516.6971333223066, backtracks = 0, tol = 0.057218015198926116 Iteration 88: loglikelihood = -1516.4085220289421, backtracks = 0, tol = 0.011956783042516825 Iteration 89: loglikelihood = -1516.3827926784966, backtracks = 0, tol = 0.0030279829745810485 Iteration 90: loglikelihood = -1516.3781465303534, backtracks = 0, tol = 0.0012337289527378427 Iteration 91: loglikelihood = -1516.3765591080007, backtracks = 1, tol = 0.0005372390621796153 Iteration 92: loglikelihood = -1548.4525570180713, backtracks = 3, tol = 0.1021453545680224 Iteration 93: loglikelihood = -1521.377266517631, backtracks = 0, tol = 0.10212717212208616 Iteration 94: loglikelihood = -1518.512051081777, backtracks = 0, tol = 0.055260184197765023 Iteration 95: loglikelihood = -1516.7083949734567, backtracks = 0, tol = 0.056414076158552026 Iteration 96: loglikelihood = -1516.3973599516546, backtracks = 0, tol = 0.012783608680979998 Iteration 97: loglikelihood = -1516.371205750311, backtracks = 0, tol = 0.003069953252323179 Iteration 98: loglikelihood = -1516.366705124283, backtracks = 0, tol = 0.0011934688357910512 Iteration 99: loglikelihood = -1516.3653318438107, backtracks = 1, tol = 0.0004696615840270754 Iteration 100: loglikelihood = -1534.0093678112335, backtracks = 3, tol = 0.08841164534512154 Iteration 101: loglikelihood = -1520.4779561612563, backtracks = 0, tol = 0.08839612722578052 Iteration 102: loglikelihood = -1516.9947668661882, backtracks = 0, tol = 0.05478093326575082 Iteration 103: loglikelihood = -1516.3925165893327, backtracks = 0, tol = 0.019728799819354003 Iteration 104: loglikelihood = -1516.3618073851, backtracks = 0, tol = 0.002729047263726079 Iteration 105: loglikelihood = -1516.3587506744468, backtracks = 1, tol = 0.0006482612731909357 Iteration 106: loglikelihood = -1516.357339025347, backtracks = 2, tol = 0.0005045113101155566 Iteration 107: loglikelihood = -1516.3560551718817, backtracks = 3, tol = 0.0006851128981140989 Iteration 108: loglikelihood = -1888.3699777991715, backtracks = 3, tol = 0.22162068291367668 Iteration 109: loglikelihood = -1767.7578082690259, backtracks = 0, tol = 0.5888844183936065 Iteration 110: loglikelihood = -1675.0282460308488, backtracks = 0, tol = 0.06398284802253255 Iteration 111: loglikelihood = -1619.3995989083835, backtracks = 0, tol = 0.07017840738745627 Iteration 112: loglikelihood = -1574.8509911036276, backtracks = 0, tol = 0.06499399904091001 Iteration 113: loglikelihood = -1544.7862828419286, backtracks = 0, tol = 0.07276880257163544 Iteration 114: loglikelihood = -1528.6288020985637, backtracks = 0, tol = 0.06459019198165686 Iteration 115: loglikelihood = -1520.959916960349, backtracks = 0, tol = 0.049424001288384166 Iteration 116: loglikelihood = -1519.1063384985096, backtracks = 0, tol = 0.02741788076108431 Iteration 117: loglikelihood = -1517.626160511499, backtracks = 0, tol = 0.051272240551656585 Iteration 118: loglikelihood = -1516.566348182784, backtracks = 0, tol = 0.06813146082261914 Iteration 119: loglikelihood = -1516.3589825794443, backtracks = 0, tol = 0.007906821881125473 Iteration 120: loglikelihood = -1516.344869884471, backtracks = 0, tol = 0.0023333161961651555 Iteration 121: loglikelihood = -1516.342804722961, backtracks = 0, tol = 0.0007183372147694087 Iteration 122: loglikelihood = -1516.3420283688774, backtracks = 1, tol = 0.00036594673297296034 Iteration 123: loglikelihood = -2223.19149121873, backtracks = 3, tol = 0.32982600617113944 Iteration 124: loglikelihood = -1901.343658549014, backtracks = 0, tol = 0.6382357142903813 Iteration 125: loglikelihood = -1749.0885798089917, backtracks = 0, tol = 0.09402262169322968 Iteration 126: loglikelihood = -1645.722226142586, backtracks = 0, tol = 0.08451418463626167 Iteration 127: loglikelihood = -1593.546579430352, backtracks = 0, tol = 0.06884905808481907 Iteration 128: loglikelihood = -1556.8966873957136, backtracks = 0, tol = 0.07218896734479274 Iteration 129: loglikelihood = -1537.8874944066688, backtracks = 0, tol = 0.06808175303123858 Iteration 130: loglikelihood = -1525.616869390438, backtracks = 0, tol = 0.05900012494717286 Iteration 131: loglikelihood = -1520.117103314137, backtracks = 0, tol = 0.043415420777378366 Iteration 132: loglikelihood = -1519.0910663402342, backtracks = 0, tol = 0.02096077322900258 Iteration 133: loglikelihood = -1517.4271393207723, backtracks = 0, tol = 0.05965470428439184 Iteration 134: loglikelihood = -1517.1879197398518, backtracks = 0, tol = 0.008306589888224036 Iteration 135: loglikelihood = -1517.154378651963, backtracks = 0, tol = 0.003728440166729148 Iteration 136: loglikelihood = -1517.148726366889, backtracks = 0, tol = 0.0013937173461296187 Iteration 137: loglikelihood = -1516.4017988912656, backtracks = 0, tol = 0.059809729028721406 Iteration 138: loglikelihood = -1516.3335295650836, backtracks = 0, tol = 0.004862574207490792 Iteration 139: loglikelihood = -1516.3284641032203, backtracks = 0, tol = 0.001311598133053795 Iteration 140: loglikelihood = -1516.3276540078532, backtracks = 1, tol = 0.00031118691269358995 Iteration 141: loglikelihood = -1516.327104793281, backtracks = 3, tol = 0.0004117801834567824 Iteration 142: loglikelihood = -1826.55003337025, backtracks = 3, tol = 0.20736764116866077 Iteration 143: loglikelihood = -1675.919522874424, backtracks = 0, tol = 0.4919455653292221 Iteration 144: loglikelihood = -1615.7601349790536, backtracks = 0, tol = 0.0600269994018493 Iteration 145: loglikelihood = -1576.8017452022655, backtracks = 0, tol = 0.0659102704295944 Iteration 146: loglikelihood = -1547.8275739560233, backtracks = 0, tol = 0.06242529600828595 Iteration 147: loglikelihood = -1529.493396643113, backtracks = 0, tol = 0.06322446960682565 Iteration 148: loglikelihood = -1522.4384911602247, backtracks = 0, tol = 0.04653486276607993 Iteration 149: loglikelihood = -1521.2442903737815, backtracks = 0, tol = 0.02218316087232439 Iteration 150: loglikelihood = -1519.31590439281, backtracks = 0, tol = 0.05069048686596112 Iteration 151: loglikelihood = -1516.7208246482073, backtracks = 0, tol = 0.06060750219428622 Iteration 152: loglikelihood = -1516.3686447321697, backtracks = 0, tol = 0.010930976519771813 Iteration 153: loglikelihood = -1516.327603293476, backtracks = 0, tol = 0.0039011418917525792 Iteration 154: loglikelihood = -1516.3207811314699, backtracks = 0, tol = 0.001468313289625669 Iteration 155: loglikelihood = -1516.3192280470957, backtracks = 0, tol = 0.0008499881702424762 Iteration 156: loglikelihood = -1516.318619993555, backtracks = 1, tol = 0.0003444603565484547 Iteration 157: loglikelihood = -1516.318222691591, backtracks = 3, tol = 0.000332566793382248 Iteration 158: loglikelihood = -1794.7120413472708, backtracks = 3, tol = 0.19261709710424454 Iteration 159: loglikelihood = -1669.400224154526, backtracks = 0, tol = 0.4879423940830795 Iteration 160: loglikelihood = -1612.942705888459, backtracks = 0, tol = 0.06077907189359784 Iteration 161: loglikelihood = -1575.499487470683, backtracks = 0, tol = 0.06336163855937639 Iteration 162: loglikelihood = -1546.9669245680777, backtracks = 0, tol = 0.06234326102192599 Iteration 163: loglikelihood = -1528.9709809861934, backtracks = 0, tol = 0.06286846860984141 Iteration 164: loglikelihood = -1522.2802322862942, backtracks = 0, tol = 0.04556358196044365 Iteration 165: loglikelihood = -1521.2257333450973, backtracks = 0, tol = 0.020925713057094956 Iteration 166: loglikelihood = -1517.9517042684529, backtracks = 0, tol = 0.053321889699834236 Iteration 167: loglikelihood = -1516.5423802197554, backtracks = 0, tol = 0.06657494416930608 Iteration 168: loglikelihood = -1516.3292447440576, backtracks = 0, tol = 0.007802019216862815 Iteration 169: loglikelihood = -1516.3144165119977, backtracks = 0, tol = 0.002297208418106792 Iteration 170: loglikelihood = -1516.3124489822756, backtracks = 0, tol = 0.0007135892136269502 Iteration 171: loglikelihood = -1516.311823697591, backtracks = 0, tol = 0.0005487835200809776 Iteration 172: loglikelihood = -1516.3114278070148, backtracks = 1, tol = 0.0003158907428837195 Iteration 173: loglikelihood = -1516.6963287679241, backtracks = 3, tol = 0.06233436574024735 Iteration 174: loglikelihood = -1516.5959896941122, backtracks = 0, tol = 0.007546604789522048 Iteration 175: loglikelihood = -1516.5931502789797, backtracks = 0, tol = 0.001115763489073082 Iteration 176: loglikelihood = -1516.354593580174, backtracks = 1, tol = 0.06026836953104792 Iteration 177: loglikelihood = -1516.311070233627, backtracks = 0, tol = 0.004101471731187329 Iteration 178: loglikelihood = -1516.309339833784, backtracks = 0, tol = 0.0008602371588291469 Iteration 179: loglikelihood = -1516.3088495758586, backtracks = 1, tol = 0.00034728207153987523 Iteration 180: loglikelihood = -1516.3085663565369, backtracks = 3, tol = 0.00028531837088622083 Iteration 181: loglikelihood = -1807.2018550893426, backtracks = 3, tol = 0.1985692259753878 Iteration 182: loglikelihood = -1671.7876663523352, backtracks = 0, tol = 0.4892551338641554 Iteration 183: loglikelihood = -1613.9245770219798, backtracks = 0, tol = 0.06048145851888798 Iteration 184: loglikelihood = -1575.9143102769783, backtracks = 0, tol = 0.06435326815064248 Iteration 185: loglikelihood = -1547.2270040607784, backtracks = 0, tol = 0.06236334507876255 Iteration 186: loglikelihood = -1529.121561485288, backtracks = 0, tol = 0.06297755620054558 Iteration 187: loglikelihood = -1522.3167751219892, backtracks = 0, tol = 0.045868497458464254 Iteration 188: loglikelihood = -1521.220128557258, backtracks = 0, tol = 0.021314515319943047 Iteration 189: loglikelihood = -1518.0092754233538, backtracks = 0, tol = 0.052406673912682014 Iteration 190: loglikelihood = -1516.5360449345317, backtracks = 0, tol = 0.06650490495632963 Iteration 191: loglikelihood = -1516.3210932502063, backtracks = 0, tol = 0.007860422731089974 Iteration 192: loglikelihood = -1516.30612337164, backtracks = 0, tol = 0.002295585319722575 Iteration 193: loglikelihood = -1516.3042036378, backtracks = 0, tol = 0.000703522254575626 Iteration 194: loglikelihood = -1516.3036652216754, backtracks = 0, tol = 0.0005054892232102344 Iteration 195: loglikelihood = -1516.3033466994948, backtracks = 1, tol = 0.00028840699928311226 Iteration 196: loglikelihood = -1516.3030574065267, backtracks = 3, tol = 0.000336432659168836 Iteration 197: loglikelihood = -1620.1084336567828, backtracks = 3, tol = 0.16006613247452983 Iteration 198: loglikelihood = -1536.0091627451193, backtracks = 0, tol = 0.1600623113272462 Iteration 199: loglikelihood = -1523.4723283757035, backtracks = 0, tol = 0.06002770685186804 Did not converge after 200 iterations! IHT run time was 1.8527448177337646 seconds Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 3.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1824.0916841628675, backtracks = 0, tol = 0.8205900613955586 Iteration 2: loglikelihood = -1463.234110888505, backtracks = 0, tol = 0.15343317721724248 Iteration 3: loglikelihood = -1405.4392287135931, backtracks = 0, tol = 0.04353591166352193 Iteration 4: loglikelihood = -1402.6119467978253, backtracks = 0, tol = 0.02457497460250581 Iteration 5: loglikelihood = -1402.508998557636, backtracks = 0, tol = 0.02578552154365372 Iteration 6: loglikelihood = -1402.4417296057477, backtracks = 0, tol = 0.001772246773782522 Iteration 7: loglikelihood = -1402.4413713019615, backtracks = 1, tol = 6.380393535727335e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1682.6079290154394, backtracks = 0, tol = 0.3810903313964997 Iteration 2: loglikelihood = -1430.1989731462443, backtracks = 0, tol = 0.1149521776631829 Iteration 3: loglikelihood = -1405.2723657158663, backtracks = 0, tol = 0.04050980972922926 Iteration 4: loglikelihood = -1403.8374472885864, backtracks = 0, tol = 0.0317179126158593 Iteration 5: loglikelihood = -1403.5716953640926, backtracks = 1, tol = 0.002510124740835121 Iteration 6: loglikelihood = -1403.502483168827, backtracks = 1, tol = 0.0013295675404793525 Iteration 7: loglikelihood = -1403.452776681477, backtracks = 0, tol = 0.030596325902685517 Iteration 8: loglikelihood = -1403.1858614936345, backtracks = 1, tol = 0.0020180074034885686 Iteration 9: loglikelihood = -1402.4910711093094, backtracks = 0, tol = 0.02857831849919695 Iteration 10: loglikelihood = -1402.4565252880193, backtracks = 1, tol = 0.0010298882148592453 Iteration 11: loglikelihood = -1402.4475841009364, backtracks = 1, tol = 0.0005231785560115555 Iteration 12: loglikelihood = -1402.4452864005495, backtracks = 1, tol = 0.00026117450527842964 Iteration 13: loglikelihood = -1402.4447004208823, backtracks = 1, tol = 0.00012868477233041124 Iteration 14: loglikelihood = -1402.4445519520316, backtracks = 1, tol = 6.29236766680285e-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 10.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1457.8859273584035, backtracks = 0, tol = 0.16895397771513074 Iteration 2: loglikelihood = -1423.7880167111778, backtracks = 0, tol = 0.08364085199486125 Iteration 3: loglikelihood = -1383.2179775773766, backtracks = 0, tol = 0.07155189713592937 Iteration 4: loglikelihood = -1351.122730494904, backtracks = 0, tol = 0.06754273326146595 Iteration 5: loglikelihood = -1333.5504836737698, backtracks = 0, tol = 0.06531877771444686 Iteration 6: loglikelihood = -1323.630631276739, backtracks = 0, tol = 0.0608332208323967 Iteration 7: loglikelihood = -1314.0186170834936, backtracks = 0, tol = 0.053928293729582785 Iteration 8: loglikelihood = -1311.8163488498978, backtracks = 1, tol = 0.018516647913854777 Iteration 9: loglikelihood = -1308.00597103293, backtracks = 1, tol = 0.06283973772012864 Iteration 10: loglikelihood = -1306.8657433320798, backtracks = 1, tol = 0.012453571288751976 Iteration 11: loglikelihood = -1306.4463098392375, backtracks = 1, tol = 0.008464140236889909 Iteration 12: loglikelihood = -1306.3542915702192, backtracks = 2, tol = 0.0032031763143832042 Iteration 13: loglikelihood = -1306.2982788521806, backtracks = 2, tol = 0.0027422583721375556 Iteration 14: loglikelihood = -1306.265371137791, backtracks = 2, tol = 0.002034094895990824 Iteration 15: loglikelihood = -1306.2462813973607, backtracks = 2, tol = 0.0015495846142106725 Iteration 16: loglikelihood = -1306.2352886955584, backtracks = 2, tol = 0.0012031949887972317 Iteration 17: loglikelihood = -1306.2289819108412, backtracks = 2, tol = 0.0009376268886775473 Iteration 18: loglikelihood = -1306.2253749934955, backtracks = 2, tol = 0.0007330897050739144 Iteration 19: loglikelihood = -1306.2233167039944, backtracks = 2, tol = 0.0005662685927080778 Iteration 20: loglikelihood = -1306.222144741732, backtracks = 2, tol = 0.0004372266158617875 Iteration 21: loglikelihood = -1306.2214786276365, backtracks = 2, tol = 0.000335047443356489 Iteration 22: loglikelihood = -1306.2211006741559, backtracks = 2, tol = 0.000256390676282052 Iteration 23: loglikelihood = -1306.2208865226987, backtracks = 2, tol = 0.00019521073170011111 Iteration 24: loglikelihood = -1306.2207653372775, backtracks = 2, tol = 0.0001484267235060866 Iteration 25: loglikelihood = -1306.220696830448, backtracks = 2, tol = 0.00011247056639110803 Iteration 26: loglikelihood = -1306.2206581379291, backtracks = 2, tol = 8.513460025601792e-5 1.812246 seconds (11.22 M allocations: 185.237 MiB, 4.38% gc time, 32.89% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1481.2466507040517, backtracks = 0, tol = 0.16895397771513074 Iteration 2: loglikelihood = -1450.0651067521092, backtracks = 0, tol = 0.08364085199486125 Iteration 3: loglikelihood = -1424.7445906281202, backtracks = 0, tol = 0.08520253507155294 Iteration 4: loglikelihood = -1401.0459512745356, backtracks = 0, tol = 0.06349463248381747 Iteration 5: loglikelihood = -1386.4282029125745, backtracks = 0, tol = 0.05415641203807396 Iteration 6: loglikelihood = -1372.3258257562638, backtracks = 0, tol = 0.0718816949209802 Iteration 7: loglikelihood = -1361.3120566658424, backtracks = 0, tol = 0.05995167908851002 Iteration 8: loglikelihood = -1353.891499118702, backtracks = 0, tol = 0.07521683046195862 Iteration 9: loglikelihood = -1348.2977797981557, backtracks = 0, tol = 0.01747335541786205 Iteration 10: loglikelihood = -1343.4714324475294, backtracks = 0, tol = 0.006890945173181753 Iteration 11: loglikelihood = -1339.4961283154278, backtracks = 0, tol = 0.06450100313008988 Iteration 12: loglikelihood = -1336.7400280676075, backtracks = 0, tol = 0.07011645498058723 Iteration 13: loglikelihood = -1333.7168151244646, backtracks = 0, tol = 0.009419908108205026 Iteration 14: loglikelihood = -1331.290343798034, backtracks = 0, tol = 0.0013302314914038675 Iteration 15: loglikelihood = -1328.2912406073378, backtracks = 0, tol = 0.06889919158838602 Iteration 16: loglikelihood = -1326.2172414243676, backtracks = 0, tol = 0.010313817789880678 Iteration 17: loglikelihood = -1324.6315085531933, backtracks = 0, tol = 0.0034510273106348106 Iteration 18: loglikelihood = -1323.1638285615782, backtracks = 0, tol = 0.001798895257425049 Iteration 19: loglikelihood = -1321.9066222241688, backtracks = 0, tol = 0.0015319314265771055 Iteration 20: loglikelihood = -1320.7554220717304, backtracks = 0, tol = 0.0007649235839959403 Iteration 21: loglikelihood = -1319.7431112519675, backtracks = 0, tol = 0.0007189839985803361 Iteration 22: loglikelihood = -1318.8199457429027, backtracks = 0, tol = 0.0003122165595177213 Iteration 23: loglikelihood = -1317.9946991955646, backtracks = 0, tol = 0.0003419802376938532 Iteration 24: loglikelihood = -1317.2414567100188, backtracks = 0, tol = 0.00014610511089896172 Iteration 25: loglikelihood = -1316.5608657308153, backtracks = 0, tol = 0.00016882338636719873 Iteration 26: loglikelihood = -1315.9375618510708, backtracks = 0, tol = 0.00012515431015027565 Iteration 27: loglikelihood = -1315.3701596499895, backtracks = 0, tol = 0.00010560036692029556 Iteration 28: loglikelihood = -1314.8482800684499, backtracks = 0, tol = 0.00011100658321195258 Iteration 29: loglikelihood = -1314.3704897922871, backtracks = 0, tol = 9.592744725410603e-5 0.283981 seconds (1.04 M allocations: 19.095 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 = -3564.9192, backtracks = 0, tol = 0.09218019162020546 Iteration 2: loglikelihood = -3508.9045, backtracks = 0, tol = 0.052245908195142264 Iteration 3: loglikelihood = -3503.4792, backtracks = 1, tol = 0.016328657072110717 Iteration 4: loglikelihood = -3501.9614, backtracks = 1, tol = 0.008590290346046166 Iteration 5: loglikelihood = -3501.5618, backtracks = 1, tol = 0.004691003150047607 Iteration 6: loglikelihood = -3501.4573, backtracks = 1, tol = 0.0023497504555408124 Iteration 7: loglikelihood = -3501.4365, backtracks = 1, tol = 0.0012167958645221114 Iteration 8: loglikelihood = -3501.423, backtracks = 1, tol = 0.0006035143648758887 Iteration 9: loglikelihood = -3501.427, backtracks = 3, tol = 7.689907108908496e-5 25.926580 seconds (14.22 M allocations: 666.860 MiB, 4.52% gc time, 94.93% 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 = -3455.0273, backtracks = 0, tol = 0.09218019162020546 Iteration 2: loglikelihood = -3332.794, backtracks = 0, tol = 0.05388024681543617 Iteration 3: loglikelihood = -3167.0261, backtracks = 1, tol = 0.015493769077423303 Iteration 4: loglikelihood = -2964.5688, backtracks = 1, tol = 0.008096260200955167 Iteration 5: loglikelihood = -2749.6719, backtracks = 1, tol = 0.0039257427591855775 Iteration 6: loglikelihood = -2675.5935, backtracks = 0, tol = 0.09896988737981124 Iteration 7: loglikelihood = -2529.7795, backtracks = 0, tol = 0.09934567519087391 Iteration 8: loglikelihood = -2430.558, backtracks = 0, tol = 0.08506011791710746 Iteration 9: loglikelihood = -2351.9543, backtracks = 0, tol = 0.08218140820217586 Iteration 10: loglikelihood = -2290.1526, backtracks = 0, tol = 0.08566311363708208 Iteration 11: loglikelihood = -2239.666, backtracks = 0, tol = 0.08536541298341337 Iteration 12: loglikelihood = -2210.5957, backtracks = 0, tol = 0.09486395001120199 Iteration 13: loglikelihood = -2184.8672, backtracks = 0, tol = 0.09453467269426016 Iteration 14: loglikelihood = -2175.7737, backtracks = 0, tol = 0.09572423431095814 Iteration 15: loglikelihood = -2164.1074, backtracks = 0, tol = 0.09547304261737533 Iteration 16: loglikelihood = -2163.77, backtracks = 0, tol = 0.09589265352052917 Iteration 17: loglikelihood = -2157.6653, backtracks = 0, tol = 0.09569760111325025 Iteration 18: loglikelihood = -2155.6462, backtracks = 1, tol = 0.008331417339531605 Iteration 19: loglikelihood = -2155.151, backtracks = 1, tol = 0.00421639326098095 Iteration 20: loglikelihood = -2155.0515, backtracks = 1, tol = 0.002163679216687386 Iteration 21: loglikelihood = -2155.0378, backtracks = 1, tol = 0.0011268885404789053 Iteration 22: loglikelihood = -2155.0396, backtracks = 3, tol = 0.0001490892631956806 Iteration 23: loglikelihood = -2155.039, backtracks = 1, tol = 0.0005279285651706048 Iteration 24: loglikelihood = -2155.038, backtracks = 3, tol = 7.098312367420218e-5 0.172942 seconds (1.44 M allocations: 23.959 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 30.7s **** 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 = -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 4.736881 seconds (1.14 M allocations: 136.629 MiB, 0.56% gc time, 91.12% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.2s 9.917452 seconds (4.00 M allocations: 82.494 MiB, 0.66% gc time, 0.67% compilation time) 5.260164 seconds (3.98 M allocations: 91.678 MiB, 0.10% gc time) 9.910717 seconds (20.41 M allocations: 439.369 MiB, 1.08% gc time, 17.32% compilation time: 78% of which was recompilation) 7.868243 seconds (20.18 M allocations: 434.187 MiB, 0.96% gc time) 37.888468 seconds (3.77 M allocations: 4.239 GiB, 10.20% gc time, 28.91% compilation time) 56.504131 seconds (70.38 k allocations: 183.448 MiB, 1.88% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m25.0s Test Summary: | Pass Total Time update_support! | 10 10 0.5s 13.712 ms (78 allocations: 4.56 KiB) 3.799 μs (0 allocations: 0 bytes) 132.538 μs (4 allocations: 288 bytes) 6.576 μs (0 allocations: 0 bytes) 39.270 μs (2 allocations: 64 bytes) 30.379 μs (0 allocations: 0 bytes) 22.170 μs (0 allocations: 0 bytes) 23.959 μs (0 allocations: 0 bytes) 90.369 μs (0 allocations: 0 bytes) 38.681 ms (78 allocations: 4.56 KiB) 18.400 μs (0 allocations: 0 bytes) 148.059 μs (4 allocations: 288 bytes) 34.000 μs (0 allocations: 0 bytes) 231.548 μs (2 allocations: 64 bytes) 70.919 μs (0 allocations: 0 bytes) 114.889 μs (0 allocations: 0 bytes) 142.789 μs (0 allocations: 0 bytes) 199.898 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m16.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.441532 seconds (49.38 k allocations: 5.492 MiB, 65.20% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.962401 seconds (282.13 k allocations: 168.426 MiB, 58.05% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** 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: 0:03:54 Cross validating... 11%|███▌ | ETA: 0:01:05 Cross validating... 14%|████▋ | ETA: 0:00:50 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 62%|███████████████████▊ | ETA: 0:00:07 Cross validating... 65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 7335.131333942434 1 3246.112108235974 2 1936.1419910558348 3 1454.1933376135764 4 859.8985854806805 5 694.8984565211779 6 556.0411460042926 7 450.5858326949266 8 370.065662937357 9 345.9885692740926 10 329.7353415162658 11 334.4006992122049 12 334.7663025087288 13 335.45596995339326 14 337.66779886708775 15 340.83854130155044 16 342.49369905660797 17 348.01179363702374 18 358.7780120692455 19 346.1431598934271 20 368.85471302454465 Best k = 10 12.451028 seconds (11.33 M allocations: 298.085 MiB, 1.33% gc time, 63.23% 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: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 7335.131333942434 1 3250.074898327025 2 1941.206111993807 3 1465.4508328842749 4 866.9883206049722 5 705.6141063324034 6 565.7797063975511 7 459.2267073126716 8 378.3957326345105 9 354.5772324664107 10 338.12286879181806 11 349.91334901468895 12 353.2522727804736 13 354.9951721466955 14 359.6413071498921 15 368.8183629875142 16 370.8925245340961 17 374.8826871951552 18 371.0440562043891 19 381.2592519284076 20 387.9828619768562 Best k = 10 4.851952 seconds (10.91 M allocations: 228.333 MiB, 0.99% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:04 Cross validating... 6%|██ | ETA: 0:02:58 Cross validating... 11%|███▌ | ETA: 0:01:37 Cross validating... 13%|████▏ | ETA: 0:01:24 Cross validating... 17%|█████▋ | ETA: 0:00:59 Cross validating... 21%|██████▋ | ETA: 0:00:48 Cross validating... 24%|███████▋ | ETA: 0:00:40 Cross validating... 27%|████████▋ | ETA: 0:00:35 Cross validating... 30%|█████████▋ | ETA: 0:00:30 Cross validating... 33%|██████████▋ | ETA: 0:00:26 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:19 Cross validating... 46%|██████████████▊ | ETA: 0:00:16 Cross validating... 51%|████████████████▎ | ETA: 0:00:13 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 63%|████████████████████▍ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1539.671846191406 1 1190.4674372558593 2 981.1968695068358 3 807.2351911621095 4 599.0221610107423 5 492.7096502685547 6 416.39904162597657 7 377.42371850585937 8 358.64867193603516 9 342.06587927246096 10 345.11444421386716 11 347.85982354736325 12 349.9496339111328 13 352.58761267089847 14 356.24058459472656 15 350.0478428955078 16 357.2275770874024 17 354.5951737060547 18 383.2155658569336 19 386.518241027832 20 375.77038079833983 Best k = 9 16.594281 seconds (12.61 M allocations: 313.629 MiB, 0.77% gc time, 79.21% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 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... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1539.671846191406 1 1190.4674372558593 2 982.1091949462889 3 825.0763044433593 4 601.4380343017579 5 496.3603852539063 6 418.31926843261715 7 379.75890753173826 8 361.9710319213867 9 345.31159301757816 10 353.74599829101567 11 359.32893200683594 12 366.7822255859375 13 380.6466221313476 14 375.86011199951173 15 386.26240924072266 16 394.16756713867187 17 389.2491221313477 18 399.76038568115234 19 396.24675122070306 20 425.1860821533203 Best k = 9 3.496218 seconds (10.77 M allocations: 197.561 MiB, 1.54% gc time, 1.19% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 22.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 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: 0:00:07 Crossvalidation Results: k MSE 0 461.97979786656225 1 287.89733147041704 2 259.1497979865822 3 246.4690556725862 4 233.5912087993299 5 227.80600996950037 6 214.57924523169368 7 215.1488476427389 8 215.52158764932443 9 219.260222671059 10 237.15142010128739 11 235.7257205507372 12 245.27260573190705 13 239.99883578881338 14 267.9847919641505 15 253.34122593219996 16 231.68492333111152 17 274.8450953523934 18 237.18508921857728 19 249.99334741373514 20 242.17315158313755 Best k = 6 8.210678 seconds (17.46 M allocations: 405.408 MiB, 1.18% gc time, 31.25% 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: 0:00:04 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: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 461.97979786656225 1 287.76253761089083 2 260.1126422900363 3 248.15800564319636 4 235.6528820380861 5 232.2546333698569 6 223.72946257665066 7 220.49550675113082 8 226.10279275132098 9 229.06312752986693 10 248.3641264275009 11 259.2186210305422 12 260.40216460613965 13 269.6513211949276 14 272.1120734680134 15 287.6723763039692 16 284.4345655132694 17 289.60062113546144 18 292.7400783238626 19 311.9635414725909 20 309.6155567593261 Best k = 7 5.714621 seconds (17.21 M allocations: 353.281 MiB, 1.43% gc time, 1.04% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:50 Cross validating... 6%|██ | ETA: 0:00:27 Cross validating... 10%|███ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:11 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:08 Crossvalidation Results: k MSE 0 462.5109710878566 1 423.57128168219435 2 394.5536283184374 3 370.80771841742006 4 347.94048407418995 5 314.2643942750254 6 306.5875489146888 7 298.16513833143483 8 289.05130984153857 9 291.38172434633356 10 304.47536794978214 11 311.8720630788578 12 310.1111251219188 13 314.86321527137824 14 305.91492999639684 15 313.88122939266447 16 319.01567972170636 17 317.81304423427224 18 317.0828394843862 19 340.32112492232096 20 338.5318523830434 Best k = 8 9.597656 seconds (16.79 M allocations: 394.510 MiB, 11.24% gc time, 28.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:05 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 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... 79%|█████████████████████████▍ | 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... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.5109710878566 1 423.8978427303024 2 395.07595631749206 3 371.110399710082 4 350.177152011575 5 318.3414487425442 6 312.2575662927961 7 305.12177838603634 8 302.43044065439636 9 311.9275731018481 10 323.5305345454749 11 329.7781030940418 12 343.8242890270192 13 343.3764767045491 14 358.079872393579 15 352.89236108665716 16 362.99669781968464 17 369.37222768358015 18 395.3690583198876 19 389.87823763092297 20 386.2372825268001 Best k = 8 6.246709 seconds (17.05 M allocations: 349.781 MiB, 1.36% gc time, 0.75% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 18.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 8%|██▌ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross 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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: 0:00:07 Crossvalidation Results: k MSE 0 1711.4778670598168 1 769.8873541634327 2 698.2908115438455 3 756.6633881769774 4 758.7732309136102 5 711.5781798171915 6 654.8147042104523 7 761.3010524046532 8 693.1151460388921 9 670.4520921444698 10 629.3012136536574 11 627.1180732863379 12 639.9551014823287 13 651.1642584497729 14 667.5800243585973 15 658.7888813009858 16 665.2863941586569 17 622.0571667342165 18 606.0020778924646 19 607.4550029370785 20 638.8900109167089 Best k = 18 7.903016 seconds (14.79 M allocations: 339.226 MiB, 0.82% gc time, 32.79% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1711.4778670598168 1 717.0647797687877 2 631.8494405818783 3 578.8541772499552 4 605.8595745390503 5 612.2853278236862 6 589.9967916313526 7 600.3154465531821 8 599.6824046382301 9 603.8524368839823 10 602.3243339655013 11 615.0238203116385 12 628.527943281309 13 641.4682725838784 14 647.8217635422185 15 634.4549798593063 16 669.0219364705407 17 636.6511410176224 18 641.7871736875566 19 670.6989967943871 20 664.1575749545136 Best k = 3 5.445773 seconds (13.71 M allocations: 271.498 MiB, 0.99% gc time, 1.18% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:27 Cross validating... 5%|█▌ | ETA: 0:01:17 Cross validating... 6%|██ | ETA: 0:01:11 Cross validating... 10%|███ | ETA: 0:00:47 Cross validating... 11%|███▌ | ETA: 0:00:48 Cross validating... 13%|████▏ | ETA: 0:00:42 Cross validating... 14%|████▋ | ETA: 0:00:43 Cross validating... 16%|█████▏ | ETA: 0:00:43 Cross validating... 17%|█████▋ | ETA: 0:00:43 Cross validating... 19%|██████▏ | ETA: 0:00:39 Cross validating... 21%|██████▋ | ETA: 0:00:36 Cross validating... 22%|███████▏ | ETA: 0:00:34 Cross validating... 24%|███████▋ | ETA: 0:00:34 Cross validating... 25%|████████▏ | ETA: 0:00:34 Cross validating... 27%|████████▋ | ETA: 0:00:35 Cross validating... 29%|█████████▏ | ETA: 0:00:35 Cross validating... 30%|█████████▋ | ETA: 0:00:35 Cross validating... 32%|██████████▏ | ETA: 0:00:35 Cross validating... 33%|██████████▋ | ETA: 0:00:33 Cross validating... 37%|███████████▋ | ETA: 0:00:30 Cross validating... 40%|████████████▊ | ETA: 0:00:27 Cross validating... 41%|█████████████▎ | ETA: 0:00:25 Cross validating... 43%|█████████████▊ | ETA: 0:00:24 Cross validating... 44%|██████████████▎ | ETA: 0:00:23 Cross validating... 48%|███████████████▎ | ETA: 0:00:20 Cross validating... 49%|███████████████▊ | ETA: 0:00:19 Cross validating... 51%|████████████████▎ | ETA: 0:00:18 Cross validating... 52%|████████████████▊ | ETA: 0:00:17 Cross validating... 54%|█████████████████▎ | ETA: 0:00:17 Cross validating... 56%|█████████████████▊ | ETA: 0:00:17 Cross validating... 57%|██████████████████▎ | ETA: 0:00:16 Cross validating... 59%|██████████████████▊ | ETA: 0:00:16 Cross validating... 60%|███████████████████▎ | ETA: 0:00:16 Cross validating... 62%|███████████████████▊ | ETA: 0:00:15 Cross validating... 63%|████████████████████▍ | ETA: 0:00:14 Cross validating... 65%|████████████████████▉ | ETA: 0:00:14 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:14 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:12 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:12 Cross validating... 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0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:43 Crossvalidation Results: k MSE 0 571.5170060082016 1 296.3350354428538 2 253.7946544180458 3 236.83925616449358 4 234.57973833451234 5 231.54122030422246 6 231.05296038239584 7 229.4015285310168 8 226.20671013509997 9 233.1096938150854 10 227.38525200526732 11 229.57375697129675 12 230.7747822361566 13 232.97166415003983 14 232.39399404004536 15 235.14831840190027 16 232.8765267393191 17 235.3153786218324 18 233.78285621065658 19 231.75702520301667 20 234.56011750644663 Best k = 8 43.577420 seconds (135.21 M allocations: 3.484 GiB, 1.22% gc time, 4.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:06 Cross 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0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 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: 0:00:29 Crossvalidation Results: k MSE 0 571.5170060082016 1 297.24092975189615 2 255.5441539839798 3 240.1518290840507 4 238.10050124674518 5 238.57867938825893 6 238.95936173364964 7 240.12833736697894 8 236.3638460033199 9 248.21288654047356 10 246.45897613258666 11 249.00387051171617 12 253.2613004804864 13 265.0330629932016 14 258.5775463094798 15 265.22446042503555 16 273.9164577523476 17 282.537065611862 18 278.48094114420223 19 309.34775557103274 20 314.7951200856861 Best k = 8 29.996268 seconds (97.30 M allocations: 1.956 GiB, 1.07% gc time, 0.21% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m14.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:08 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 7.174371 seconds (17.00 M allocations: 337.698 MiB, 1.60% gc time, 39.47% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 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75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 4.207954 seconds (16.18 M allocations: 286.708 MiB, 1.16% gc time, 1.34% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 12.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:19 Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 4%|█▎ | ETA: 0:00:46 Cross validating... 5%|█▋ | ETA: 0:00:39 Cross validating... 6%|█▉ | ETA: 0:00:35 Cross validating... 7%|██▎ | ETA: 0:00:32 Cross validating... 8%|██▌ | ETA: 0:00:30 Cross validating... 9%|██▉ | ETA: 0:00:28 Cross validating... 10%|███▎ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:25 Cross validating... 12%|███▉ | 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98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 3300.2280007763475 2 2269.9824837032975 3 1949.7175063366808 4 1734.2543565492808 5 1533.1784086482078 6 1471.2353985615705 7 1442.5194501047226 8 1447.8533311751935 9 1457.0799027326705 10 1449.208942975371 11 1473.2605498207922 12 1481.5925594373107 13 1482.4647944250707 14 1486.129353007051 15 1480.4819617701014 16 1485.5888156624897 17 1501.2299025810921 18 1514.539978181174 19 1516.1853862955654 20 1520.6456936669288 Best k = 7 18.674291 seconds (341.04 k allocations: 255.117 MiB, 0.44% gc time, 8.66% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m58.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 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 validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:18 Cross 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Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 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ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m25.9s 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:318 [18] _start() @ Base ./client.jl:593 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.0s RNG of the outermost testset: Xoshiro(0x22202c0e2583d0c4, 0x04871f121a911183, 0x52c0761b083cce71, 0x87dbb763c4382604, 0x8479db85fbf0179e) 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 1110.54s 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:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1225.7s: package tests unexpectedly errored