Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2130 (8560e32f58*) started at 2026-05-08T01:22:10.924 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.04s ################################################################################ # 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 v7.24.0 [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 v1.4.0 [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 v1.7.1 [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 v1.0.0 [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 v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.3+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [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 6.22s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.2 s ✓ BGEN 7.7 s ✓ VCFTools 28.8 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 26.9 s ✓ MendelIHT 4 dependencies successfully precompiled in 75 seconds. 170 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 99.67s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_JjG3ai/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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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:215 └ @ LinearAlgebra ./deprecated.jl:215 Test Summary: | Pass Total Time loglikelihood | 4 4 17.1s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.6s Test Summary: | Pass Total Time _choose! | 7 7 10.5s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.4s Test Summary: | Pass Total Time project_k! | 2 2 1.1s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1657.8661454945748, backtracks = 0, tol = 1.3756387373176646 Iteration 2: loglikelihood = -1416.2789094779553, backtracks = 0, tol = 0.1407299809523737 Iteration 3: loglikelihood = -1385.3218163082154, backtracks = 0, tol = 0.05975914224509578 Iteration 4: loglikelihood = -1384.722297608014, backtracks = 0, tol = 0.007903898573235453 Iteration 5: loglikelihood = -1384.7099437694717, backtracks = 0, tol = 0.0010256237272012628 Iteration 6: loglikelihood = -1384.709651656492, backtracks = 0, tol = 0.00013200804909976633 Iteration 7: loglikelihood = -1384.7096442434588, backtracks = 0, tol = 2.5936473057750724e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.060281991958618164 Final loglikelihood: -1384.7096442434588 SNP PVE: 0.877111448617561 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 834 0.188455 2 │ 1183 -0.973066 3 │ 2344 -0.235466 4 │ 3054 -0.372268 5 │ 4002 1.70862 6 │ 4438 -0.512996 7 │ 4653 -1.47843 8 │ 5799 0.132787 9 │ 6142 0.327005 10 │ 8207 -0.392344 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0331151Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.0s **** 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 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 = -1710.9329911922332, backtracks = 0, tol = 0.468880600406798 Iteration 2: loglikelihood = -1428.37720520072, backtracks = 0, tol = 0.06244262242917805 Iteration 3: loglikelihood = -1357.8585447506991, backtracks = 0, tol = 0.05359671767860847 Iteration 4: loglikelihood = -1322.5574742824826, backtracks = 0, tol = 0.07378016110671175 Iteration 5: loglikelihood = -1313.7940141640686, backtracks = 0, tol = 0.04672718640203995 Iteration 6: loglikelihood = -1310.1823470090264, backtracks = 0, tol = 0.028715978697337458 Iteration 7: loglikelihood = -1308.2265553041939, backtracks = 0, tol = 0.020263274596179635 Iteration 8: loglikelihood = -1307.204264384484, backtracks = 0, tol = 0.014123236652097072 Iteration 9: loglikelihood = -1304.098077168619, backtracks = 0, tol = 0.05833652673346715 Iteration 10: loglikelihood = -1303.5312059734513, backtracks = 0, tol = 0.009242840927824332 Iteration 11: loglikelihood = -1303.2910027229805, backtracks = 0, tol = 0.006451810803142147 Iteration 12: loglikelihood = -1303.166092723284, backtracks = 0, tol = 0.005700105464344206 Iteration 13: loglikelihood = -1303.0968825258046, backtracks = 0, tol = 0.003602188773897436 Iteration 14: loglikelihood = -1303.0581432649944, backtracks = 0, tol = 0.0032208980968190214 Iteration 15: loglikelihood = -1303.0360429281075, backtracks = 0, tol = 0.0020370638136988422 Iteration 16: loglikelihood = -1303.0234521669702, backtracks = 0, tol = 0.0018272667371004728 Iteration 17: loglikelihood = -1303.0162146460837, backtracks = 0, tol = 0.0011629926536930002 Iteration 18: loglikelihood = -1303.0120609302526, backtracks = 0, tol = 0.0010446443113192709 Iteration 19: loglikelihood = -1303.0096656355618, backtracks = 0, tol = 0.0006679047201666239 Iteration 20: loglikelihood = -1303.008285829973, backtracks = 0, tol = 0.0006001922360608235 Iteration 21: loglikelihood = -1303.0074888730944, backtracks = 0, tol = 0.0003848610824054569 Iteration 22: loglikelihood = -1303.007028861731, backtracks = 0, tol = 0.0003458522282743414 Iteration 23: loglikelihood = -1303.0067629360437, backtracks = 0, tol = 0.0002221809225048408 Iteration 24: loglikelihood = -1303.0066092678599, backtracks = 0, tol = 0.00019963870653601332 Iteration 25: loglikelihood = -1303.0065203918077, backtracks = 0, tol = 0.00012840096837227983 Iteration 26: loglikelihood = -1303.006469000815, backtracks = 0, tol = 0.00011535768574574154 Iteration 27: loglikelihood = -1303.006439270035, backtracks = 0, tol = 7.424906333967376e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1493.7719878096618, backtracks = 0, tol = 0.4991523108789441 Iteration 2: loglikelihood = -1442.268070718093, backtracks = 0, tol = 0.10881465183559623 Iteration 3: loglikelihood = -1422.1916466438342, backtracks = 0, tol = 0.07808217212517216 Iteration 4: loglikelihood = -1417.578668127446, backtracks = 0, tol = 0.08001472523059548 Iteration 5: loglikelihood = -1416.6411611693961, backtracks = 0, tol = 0.025338554159711143 Iteration 6: loglikelihood = -1416.5187418256949, backtracks = 1, tol = 0.005696014917941559 Iteration 7: loglikelihood = -1416.4616900411415, backtracks = 1, tol = 0.0048351281810485765 Iteration 8: loglikelihood = -1416.4449813128506, backtracks = 1, tol = 0.0026216348524552785 Iteration 9: loglikelihood = -1416.440557966644, backtracks = 1, tol = 0.0013681548628763562 Iteration 10: loglikelihood = -1416.439399488246, backtracks = 1, tol = 0.0006984474017303262 Iteration 11: loglikelihood = -1416.4391007374559, backtracks = 1, tol = 0.00035572371268406043 Iteration 12: loglikelihood = -1416.4390236418446, backtracks = 1, tol = 0.0001804232989447484 Iteration 13: loglikelihood = -1416.439003838638, backtracks = 1, tol = 9.151655012263872e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1818.208953672723, backtracks = 0, tol = 0.8583097853920375 Iteration 2: loglikelihood = -1453.0594555987104, backtracks = 0, tol = 0.11843133331145418 Iteration 3: loglikelihood = -1392.1081152551117, backtracks = 0, tol = 0.05857486371356473 Iteration 4: loglikelihood = -1371.1149292108648, backtracks = 0, tol = 0.030971325293578843 Iteration 5: loglikelihood = -1370.912220456499, backtracks = 0, tol = 0.02481362530412436 Iteration 6: loglikelihood = -1369.6682446742097, backtracks = 0, tol = 0.024618999921742695 Iteration 7: loglikelihood = -1369.6056245954978, backtracks = 1, tol = 0.0006088200835854816 Iteration 8: loglikelihood = -1369.589484390682, backtracks = 1, tol = 0.0003210160886129832 Iteration 9: loglikelihood = -1369.5853366410406, backtracks = 1, tol = 0.00016621669247365828 Iteration 10: loglikelihood = -1369.5842752064707, backtracks = 1, tol = 8.464145435359154e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1521.931325638906, backtracks = 0, tol = 0.2663738829683001 Iteration 2: loglikelihood = -1393.1932885691976, backtracks = 0, tol = 0.07295511941815438 Iteration 3: loglikelihood = -1374.9742284921235, backtracks = 0, tol = 0.036504669226277854 Iteration 4: loglikelihood = -1371.7904704747634, backtracks = 0, tol = 0.031119620616705385 Iteration 5: loglikelihood = -1371.7375263114275, backtracks = 0, tol = 0.029471121050763167 Iteration 6: loglikelihood = -1370.3377983034054, backtracks = 0, tol = 0.026440608877758662 Iteration 7: loglikelihood = -1370.1107380125495, backtracks = 0, tol = 0.028854988157406544 Iteration 8: loglikelihood = -1370.043510164542, backtracks = 1, tol = 0.001194827740686162 Iteration 9: loglikelihood = -1370.0258075481177, backtracks = 1, tol = 0.0006089164371113314 Iteration 10: loglikelihood = -1370.0211588811108, backtracks = 1, tol = 0.0003021304195437968 Iteration 11: loglikelihood = -1370.019947147431, backtracks = 1, tol = 0.00014588685330009315 Iteration 12: loglikelihood = -1370.0196343909909, backtracks = 1, tol = 6.888143020999063e-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 10.8s **** 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 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 = -1498.623582610837, backtracks = 0, tol = 0.220337335308121 Iteration 2: loglikelihood = -1438.237154073625, backtracks = 0, tol = 0.10626261548520544 Iteration 3: loglikelihood = -1381.9853125715917, backtracks = 0, tol = 0.12048088361458117 Iteration 4: loglikelihood = -1367.9005977367867, backtracks = 0, tol = 0.04887788837856809 Iteration 5: loglikelihood = -1361.5392840464046, backtracks = 0, tol = 0.04824229537161613 Iteration 6: loglikelihood = -1358.3876872974083, backtracks = 0, tol = 0.02340737358051888 Iteration 7: loglikelihood = -1350.5000243680117, backtracks = 0, tol = 0.08066065425104421 Iteration 8: loglikelihood = -1342.001028869347, backtracks = 0, tol = 0.06906185420179926 Iteration 9: loglikelihood = -1340.8835683380887, backtracks = 0, tol = 0.016289266127014514 Iteration 10: loglikelihood = -1338.7303031645472, backtracks = 0, tol = 0.06927915639201254 Iteration 11: loglikelihood = -1338.4337814517612, backtracks = 0, tol = 0.009112521011690092 Iteration 12: loglikelihood = -1338.360214795336, backtracks = 0, tol = 0.0038872831913134846 Iteration 13: loglikelihood = -1338.3291896401863, backtracks = 0, tol = 0.004039568932139614 Iteration 14: loglikelihood = -1338.3157183916096, backtracks = 0, tol = 0.0015700346963770945 Iteration 15: loglikelihood = -1338.3097061527453, backtracks = 0, tol = 0.001819049779107492 Iteration 16: loglikelihood = -1338.3070618227846, backtracks = 0, tol = 0.0006780952001096879 Iteration 17: loglikelihood = -1338.3058821924533, backtracks = 0, tol = 0.0008188705544225985 Iteration 18: loglikelihood = -1338.3053678698764, backtracks = 0, tol = 0.00029446669979458584 Iteration 19: loglikelihood = -1338.3051402778378, backtracks = 0, tol = 0.00036596345339982974 Iteration 20: loglikelihood = -1338.3050424554551, backtracks = 0, tol = 0.00012674683268948177 Iteration 21: loglikelihood = -1338.3049997144258, backtracks = 0, tol = 0.000161539597945565 Iteration 22: loglikelihood = -1338.3049816848115, backtracks = 0, tol = 5.370686860381052e-5 0.981972 seconds (2.06 M allocations: 42.088 MiB, 66.64% 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 = -1530.1698049891043, backtracks = 0, tol = 0.220337335308121 Iteration 2: loglikelihood = -1485.6623998475409, backtracks = 0, tol = 0.1384637024634707 Iteration 3: loglikelihood = -1452.2256524845147, backtracks = 0, tol = 0.11737760531205556 Iteration 4: loglikelihood = -1433.5192866666316, backtracks = 0, tol = 0.05613972765106097 Iteration 5: loglikelihood = -1423.104543581618, backtracks = 0, tol = 0.04545010818777002 Iteration 6: loglikelihood = -1413.4409526053425, backtracks = 0, tol = 0.019474814342423093 Iteration 7: loglikelihood = -1400.9227277910636, backtracks = 0, tol = 0.08131240172449793 Iteration 8: loglikelihood = -1391.9327002728892, backtracks = 0, tol = 0.07431471569592604 Iteration 9: loglikelihood = -1386.1526264226127, backtracks = 0, tol = 0.01772676454652837 Iteration 10: loglikelihood = -1381.8406272986413, backtracks = 0, tol = 0.07498357551396038 Iteration 11: loglikelihood = -1377.6260481051288, backtracks = 0, tol = 0.006457773113961023 Iteration 12: loglikelihood = -1374.2683053083535, backtracks = 0, tol = 0.0013283766190820498 Iteration 13: loglikelihood = -1371.319192491259, backtracks = 0, tol = 0.0007686622433686278 Iteration 14: loglikelihood = -1369.213835482268, backtracks = 0, tol = 0.0689413394724957 Iteration 15: loglikelihood = -1366.6932984937328, backtracks = 0, tol = 0.06893421050984974 Iteration 16: loglikelihood = -1365.022236243809, backtracks = 0, tol = 0.06894542874309544 Iteration 17: loglikelihood = -1363.1271601953647, backtracks = 0, tol = 0.006898112190207541 Iteration 18: loglikelihood = -1361.5588949828639, backtracks = 0, tol = 0.0008134151200648044 Iteration 19: loglikelihood = -1360.1689550629617, backtracks = 0, tol = 0.0002981094218161912 Iteration 20: loglikelihood = -1358.9078863649943, backtracks = 0, tol = 0.00024024261161294616 Iteration 21: loglikelihood = -1357.548003234956, backtracks = 0, tol = 0.06739735487101522 Iteration 22: loglikelihood = -1356.3271208954245, backtracks = 0, tol = 0.006471584138126588 Iteration 23: loglikelihood = -1355.370055212424, backtracks = 0, tol = 0.0006261701600343414 Iteration 24: loglikelihood = -1354.4835471038798, backtracks = 0, tol = 0.00034132852009026183 Iteration 25: loglikelihood = -1354.3553140596514, backtracks = 0, tol = 0.07020798864087487 Iteration 26: loglikelihood = -1353.384534855685, backtracks = 0, tol = 0.009059722377652487 Iteration 27: loglikelihood = -1352.4203750058828, backtracks = 0, tol = 0.06306753344715445 Iteration 28: loglikelihood = -1352.2930648275133, backtracks = 0, tol = 0.06843150573266052 Iteration 29: loglikelihood = -1351.5145811663672, backtracks = 0, tol = 0.007541424815788218 Iteration 30: loglikelihood = -1350.9697578954783, backtracks = 0, tol = 0.0007091291094459699 Iteration 31: loglikelihood = -1350.4753101841825, backtracks = 0, tol = 0.00021767412369161612 Iteration 32: loglikelihood = -1350.0098561380473, backtracks = 0, tol = 0.00015613326552426838 Iteration 33: loglikelihood = -1349.2473620689457, backtracks = 0, tol = 0.06646826500604658 Iteration 34: loglikelihood = -1348.668447195183, backtracks = 0, tol = 0.00598488208049449 Iteration 35: loglikelihood = -1348.2793986610866, backtracks = 0, tol = 0.0006724606743403504 Iteration 36: loglikelihood = -1347.9072173486584, backtracks = 0, tol = 0.00032326791175162376 Iteration 37: loglikelihood = -1347.241763485257, backtracks = 1, tol = 8.363621002160358e-5 0.393096 seconds (1.37 M allocations: 24.827 MiB, 6.75% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3654.857, backtracks = 0, tol = 0.09672734163354121 Iteration 2: loglikelihood = -3604.0427, backtracks = 0, tol = 0.046529425626516 Iteration 3: loglikelihood = -3598.4194, backtracks = 1, tol = 0.01611895088191928 Iteration 4: loglikelihood = -3596.8467, backtracks = 1, tol = 0.008760328483563343 Iteration 5: loglikelihood = -3596.4321, backtracks = 1, tol = 0.0046815324887776325 Iteration 6: loglikelihood = -3596.3242, backtracks = 1, tol = 0.002382223161916529 Iteration 7: loglikelihood = -3596.299, backtracks = 1, tol = 0.0012211285994319818 Iteration 8: loglikelihood = -3596.2944, backtracks = 1, tol = 0.000611935560584148 Iteration 9: loglikelihood = -3596.2932, backtracks = 1, tol = 0.00031007655014831786 Iteration 10: loglikelihood = -3596.2927, backtracks = 1, tol = 0.00015497266403865015 Iteration 11: loglikelihood = -3596.2905, backtracks = 1, tol = 7.818064596318072e-5 26.939473 seconds (14.63 M allocations: 673.256 MiB, 1.33% gc time, 97.81% 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 = -3535.7485, backtracks = 0, tol = 0.09672734163354121 Iteration 2: loglikelihood = -3407.5251, backtracks = 0, tol = 0.04805494879453814 Iteration 3: loglikelihood = -3182.483, backtracks = 1, tol = 0.015367643033274083 Iteration 4: loglikelihood = -2925.1802, backtracks = 1, tol = 0.008336603323666232 Iteration 5: loglikelihood = -2907.5894, backtracks = 0, tol = 0.10753455986445075 Iteration 6: loglikelihood = -2683.0422, backtracks = 0, tol = 0.10840912704763181 Iteration 7: loglikelihood = -2608.739, backtracks = 0, tol = 0.09879094944810302 Iteration 8: loglikelihood = -2456.8623, backtracks = 0, tol = 0.09700761545663084 Iteration 9: loglikelihood = -2386.7356, backtracks = 0, tol = 0.09255057191038171 Iteration 10: loglikelihood = -2319.0657, backtracks = 0, tol = 0.10023397486124243 Iteration 11: loglikelihood = -2275.0544, backtracks = 0, tol = 0.10157830492234163 Iteration 12: loglikelihood = -2233.8652, backtracks = 0, tol = 0.10039481257213721 Iteration 13: loglikelihood = -2218.2817, backtracks = 0, tol = 0.10058398153320493 Iteration 14: loglikelihood = -2201.283, backtracks = 0, tol = 0.10076331305105111 Iteration 15: loglikelihood = -2200.2273, backtracks = 0, tol = 0.10118616129771849 Iteration 16: loglikelihood = -2190.933, backtracks = 0, tol = 0.100371931656004 Iteration 17: loglikelihood = -2181.0564, backtracks = 1, tol = 0.026899492504330793 Iteration 18: loglikelihood = -2179.1714, backtracks = 1, tol = 0.012641675715071916 Iteration 19: loglikelihood = -2178.8188, backtracks = 1, tol = 0.005984412076362804 Iteration 20: loglikelihood = -2175.3584, backtracks = 1, tol = 0.04678735207507814 Iteration 21: loglikelihood = -2173.892, backtracks = 1, tol = 0.024142128123205254 Iteration 22: loglikelihood = -2173.4077, backtracks = 1, tol = 0.012917226759207595 Iteration 23: loglikelihood = -2170.376, backtracks = 1, tol = 0.05231450048359295 Iteration 24: loglikelihood = -2169.5508, backtracks = 0, tol = 0.08522550239867233 Iteration 25: loglikelihood = -2168.473, backtracks = 0, tol = 0.08801334469691173 Iteration 26: loglikelihood = -2166.649, backtracks = 1, tol = 0.017044786185427777 Iteration 27: loglikelihood = -2166.1528, backtracks = 1, tol = 0.009122011129963463 Iteration 28: loglikelihood = -2165.9927, backtracks = 1, tol = 0.005097858007528411 Iteration 29: loglikelihood = -2165.938, backtracks = 1, tol = 0.002922848362342589 Iteration 30: loglikelihood = -2165.917, backtracks = 1, tol = 0.0017015876388568585 Iteration 31: loglikelihood = -2165.908, backtracks = 1, tol = 0.0010033169157866945 Iteration 32: loglikelihood = -2165.905, backtracks = 1, tol = 0.0006364735180353054 Iteration 33: loglikelihood = -2165.9038, backtracks = 1, tol = 0.00039589463429384405 Iteration 34: loglikelihood = -2165.9038, backtracks = 1, tol = 0.00024300342319619515 Iteration 35: loglikelihood = -2165.9036, backtracks = 1, tol = 0.00014783341138253588 Iteration 36: loglikelihood = -2165.8987, backtracks = 1, tol = 8.940207488888353e-5 1.040151 seconds (2.14 M allocations: 35.363 MiB, 72.12% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 32.0s **** 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 = -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 4.941449 seconds (1.14 M allocations: 136.647 MiB, 1.20% gc time, 90.78% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.3s 9.787310 seconds (4.00 M allocations: 82.494 MiB, 0.68% gc time, 0.66% compilation time) 5.021637 seconds (3.98 M allocations: 91.674 MiB, 0.18% gc time) 10.386878 seconds (20.41 M allocations: 439.369 MiB, 1.04% gc time, 17.87% compilation time: 78% of which was recompilation) 8.233574 seconds (20.18 M allocations: 434.188 MiB, 1.08% gc time) 38.659344 seconds (3.80 M allocations: 4.241 GiB, 11.44% gc time, 29.11% compilation time) 54.392585 seconds (70.38 k allocations: 183.444 MiB, 0.09% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m25.3s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 14.883 ms (78 allocations: 4.56 KiB) 4.306 μs (0 allocations: 0 bytes) 143.948 μs (4 allocations: 288 bytes) 6.886 μs (0 allocations: 0 bytes) 47.339 μs (2 allocations: 64 bytes) 30.610 μs (0 allocations: 0 bytes) 25.710 μs (0 allocations: 0 bytes) 27.950 μs (0 allocations: 0 bytes) 102.969 μs (0 allocations: 0 bytes) 37.634 ms (78 allocations: 4.56 KiB) 17.870 μs (0 allocations: 0 bytes) 175.328 μs (4 allocations: 288 bytes) 33.310 μs (0 allocations: 0 bytes) 194.708 μs (2 allocations: 64 bytes) 85.129 μs (0 allocations: 0 bytes) 131.659 μs (0 allocations: 0 bytes) 145.958 μs (0 allocations: 0 bytes) 214.728 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m17.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.416996 seconds (49.39 k allocations: 5.493 MiB, 63.09% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.8s **** 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 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 1.999984 seconds (282.34 k allocations: 168.280 MiB, 57.63% 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: 0:03:56 Cross validating... 11%|███▌ | ETA: 0:01:06 Cross validating... 14%|████▋ | ETA: 0:00:50 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:19 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 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... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 2553.1312423345657 1 1638.562761554098 2 889.4082747913825 3 568.7500262836722 4 491.257615381391 5 430.74853027220166 6 398.10766384533036 7 349.08454586655523 8 328.84868642037975 9 332.60023600674134 10 329.51418372969374 11 331.7789126573005 12 328.47060521706254 13 335.2234930411755 14 331.64627617714433 15 336.5764962088153 16 334.7622176014774 17 363.6304259672954 18 338.29032370609434 19 360.05579041448846 20 337.7640598103765 Best k = 12 12.418399 seconds (11.26 M allocations: 298.131 MiB, 1.32% gc time, 63.86% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 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 2553.1312423345657 1 1639.6464733483435 2 896.3200067237836 3 571.6772284053174 4 494.7061524039111 5 435.21140683874444 6 402.25515610214813 7 352.6540004141138 8 332.4320061789476 9 348.29225814295125 10 347.11915009693 11 356.46290007738344 12 348.67083967648335 13 359.1366758544934 14 362.1480894630535 15 373.6608749369294 16 363.560020984277 17 378.92609625314765 18 379.4502852180715 19 373.74719595475244 20 392.45366966542895 Best k = 8 4.742776 seconds (10.62 M allocations: 222.966 MiB, 0.97% gc time, 1.15% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.0s **** 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: 0:06:28 Cross validating... 6%|██ | ETA: 0:03:09 Cross validating... 10%|███ | ETA: 0:02:03 Cross validating... 13%|████▏ | ETA: 0:01:30 Cross validating... 17%|█████▋ | ETA: 0:01:02 Cross validating... 22%|███████▏ | ETA: 0:00:47 Cross validating... 25%|████████▏ | ETA: 0:00:40 Cross validating... 29%|█████████▏ | ETA: 0:00:34 Cross validating... 32%|██████████▏ | ETA: 0:00:30 Cross validating... 37%|███████████▋ | ETA: 0:00:24 Cross validating... 41%|█████████████▎ | ETA: 0:00:20 Cross validating... 46%|██████████████▊ | ETA: 0:00:17 Cross validating... 51%|████████████████▎ | ETA: 0:00:14 Cross validating... 56%|█████████████████▊ | ETA: 0:00:12 Cross validating... 59%|██████████████████▊ | ETA: 0:00:10 Cross validating... 62%|███████████████████▊ | ETA: 0:00:09 Cross validating... 65%|████████████████████▉ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | 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: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1575.1285563964843 1 1251.3835382080078 2 1045.7121467895508 3 837.8447902832031 4 666.1204063110351 5 524.798177307129 6 444.0092288513183 7 393.18341677856444 8 351.95720315551756 9 356.25832220458983 10 356.80383569335936 11 363.7074067382813 12 362.476768157959 13 362.4310644226074 14 385.5018645324707 15 363.0154051208496 16 365.9694992980957 17 378.7726589355469 18 380.66679678344724 19 400.93715170288084 20 389.384943939209 Best k = 8 17.130163 seconds (12.67 M allocations: 313.977 MiB, 0.59% gc time, 80.78% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:02 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: 0:00:01 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... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1575.1285563964843 1 1251.7135401611326 2 1047.4286554565429 3 839.9829056396484 4 670.1225612182617 5 529.5952800292969 6 448.3247809448242 7 397.6943674316406 8 360.13327993774413 9 371.9336199645996 10 376.90428955078124 11 381.5659004211426 12 390.2041018371582 13 393.7225980834961 14 396.71277359008786 15 398.4623919677734 16 407.0951874694824 17 408.1118457641602 18 403.9884376525879 19 431.00246856689455 20 430.58784777832034 Best k = 8 3.424553 seconds (11.20 M allocations: 206.378 MiB, 1.47% gc time, 1.27% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 22.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 5%|█▌ | ETA: 0:00:44 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 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Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.2619041906425 1 405.30350222619427 2 343.465484689323 3 306.55436866172545 4 295.92617886329816 5 294.1219269444265 6 288.62059403664296 7 292.0907819598368 8 301.2041289251438 9 287.5552876449779 10 302.7670947899611 11 314.9743608406675 12 321.5024732884838 13 304.4553094493965 14 320.6211887530386 15 317.2685826863723 16 308.18160602834007 17 312.8541543168561 18 304.79795627203396 19 341.47889932824876 20 314.9049166989315 Best k = 9 8.341413 seconds (17.71 M allocations: 418.226 MiB, 1.22% gc time, 32.38% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 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 0 462.2619041906425 1 405.3103714843611 2 343.9176937724525 3 311.9102992350903 4 301.4025896680528 5 302.72622778257585 6 296.7138480517678 7 306.57273651702275 8 310.69713522252323 9 318.29858840389795 10 330.1478669923042 11 340.5773853444198 12 344.74433534389607 13 356.93839779695736 14 354.94330587187613 15 361.3596067196221 16 373.8986634751704 17 373.13210427342165 18 364.6687755946456 19 402.4249162561949 20 391.9933084275966 Best k = 6 5.719777 seconds (17.58 M allocations: 363.124 MiB, 1.25% gc time, 1.12% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:12 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 464.21525869406696 1 438.92403349272433 2 407.78925513973616 3 383.11558201453806 4 356.83432731436466 5 346.3110948812499 6 329.8427090241935 7 319.5581436700429 8 322.38583139189893 9 327.846702807907 10 327.18090584185654 11 332.61920029940984 12 340.7084063449148 13 354.91560516592034 14 337.97741850423824 15 338.70958574178354 16 341.9268059830158 17 343.67677916346884 18 393.40537520541574 19 375.98150025030156 20 346.3998798159526 Best k = 7 9.005010 seconds (16.95 M allocations: 401.929 MiB, 11.21% gc time, 29.22% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 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: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross 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: 0:00:02 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 0 464.21525869406696 1 440.26352548667325 2 410.4873313273006 3 385.77582957670677 4 359.54522512590097 5 349.6293572481738 6 333.51308313676145 7 323.2598389087445 8 329.6111733713685 9 338.1266573061923 10 349.0369125493705 11 358.8013696350119 12 356.3537296352671 13 369.66622054314064 14 382.2215142669058 15 387.67558541132587 16 393.69428443920503 17 396.0537368507696 18 416.4810115804712 19 418.4696710249044 20 421.55985678231394 Best k = 7 5.781246 seconds (17.79 M allocations: 367.984 MiB, 0.99% gc time, 0.78% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 16.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 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Time: 0:00:07 Crossvalidation Results: k MSE 0 690.8989218906399 1 509.50008335521136 2 435.0434327322645 3 395.8387430636738 4 393.5081357840032 5 381.97174122192274 6 374.65828506710307 7 381.14704698071694 8 382.57181536316705 9 378.07095980444876 10 385.82027753061004 11 383.4746248807174 12 391.37514285686575 13 391.1706237592563 14 380.65553299186587 15 393.9103280875647 16 395.36198405691374 17 381.38809624634246 18 399.35373944461065 19 403.59620413176674 20 393.3798501522738 Best k = 6 8.187563 seconds (15.74 M allocations: 378.129 MiB, 0.83% gc time, 32.80% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 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 0 690.8989218906399 1 506.17225286238715 2 434.78473354538005 3 397.1751438880865 4 398.629736504819 5 387.09388011363586 6 377.7641338960402 7 386.80128271952367 8 398.99509664286916 9 406.93110674638103 10 410.3110006071069 11 421.4779107281598 12 415.77995224033987 13 427.39477936195834 14 413.2695226548458 15 413.4970848388161 16 420.4016270341457 17 450.4104278863339 18 452.4460309803448 19 446.78030161363944 20 464.05847171765186 Best k = 6 5.620340 seconds (14.56 M allocations: 295.195 MiB, 1.07% gc time, 1.09% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:46 Cross validating... 8%|██▌ | ETA: 0:00:47 Cross validating... 10%|███ | ETA: 0:00:48 Cross validating... 11%|███▌ | ETA: 0:00:48 Cross validating... 13%|████▏ | ETA: 0:00:47 Cross validating... 14%|████▋ | ETA: 0:00:47 Cross validating... 16%|█████▏ | ETA: 0:00:47 Cross validating... 17%|█████▋ | ETA: 0:00:47 Cross 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validating... 57%|██████████████████▎ | ETA: 0:00:18 Cross validating... 59%|██████████████████▊ | ETA: 0:00:18 Cross validating... 60%|███████████████████▎ | ETA: 0:00:17 Cross validating... 62%|███████████████████▊ | ETA: 0:00:17 Cross validating... 63%|████████████████████▍ | ETA: 0:00:16 Cross validating... 65%|████████████████████▉ | ETA: 0:00:16 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:15 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:13 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:12 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:11 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:10 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:09 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:08 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:08 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:07 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:45 Crossvalidation Results: k MSE 0 349.42993166074496 1 278.66809346028936 2 251.07227626794236 3 234.64180458661093 4 234.94363158481178 5 235.2769954743237 6 237.21904565991423 7 239.2609506943267 8 240.1884458328766 9 238.37716148152882 10 240.0761917653799 11 241.32570526809317 12 238.02646866604562 13 235.9917997756844 14 240.7031104222015 15 240.08365570413378 16 239.06458787796663 17 241.45766161617937 18 243.01436481703632 19 244.0560803049139 20 245.03494078034356 Best k = 3 46.304819 seconds (146.59 M allocations: 3.643 GiB, 1.16% gc time, 5.04% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross validating... 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validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 349.42993166074496 1 278.98890295334036 2 251.41319921768218 3 235.8954747989178 4 237.45411397799325 5 240.51670164813436 6 245.42899814655195 7 248.3104971195524 8 257.249755806108 9 258.1071269364595 10 263.1721626043098 11 258.249463059051 12 258.17148926889064 13 265.9583185533194 14 271.7617364613242 15 261.4508934797657 16 267.4999856289773 17 280.56792210939983 18 277.50774191855675 19 278.815724086121 20 285.8480340823285 Best k = 3 10.771252 seconds (32.25 M allocations: 659.793 MiB, 1.36% gc time, 0.64% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 57.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:11 Cross validating... 6%|██ | ETA: 0:00:36 Cross validating... 10%|███ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:16 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 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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 7.297465 seconds (17.00 M allocations: 337.719 MiB, 1.54% gc time, 39.54% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 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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 4.296988 seconds (16.18 M allocations: 286.708 MiB, 1.11% gc time, 1.47% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 12.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:22 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| ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 2364.5556329094525 2 2105.696673484389 3 2039.9337727820541 4 1923.6866773888212 5 1898.1591101723147 6 1855.375520060097 7 1832.484299199588 8 1818.0231308118396 9 1850.5830458243092 10 1834.8770469180804 11 1852.1630074210484 12 1856.5156459851084 13 1877.8750131557606 14 1878.0506125973866 15 1896.1903712663102 16 1903.6694171473596 17 1907.3871666090677 18 1917.6087400763904 19 1926.1992048975862 20 1940.3102978488291 Best k = 8 19.410965 seconds (349.00 k allocations: 283.404 MiB, 0.34% gc time, 8.77% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m58.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ 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ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 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: 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2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 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0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 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 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m25.0s 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(0xe10faa1fcd186811, 0x11688d6d559fc787, 0xef60c1f4a0618acd, 0xfdb3ec5408a96852, 0xb218927b2c814ee5) 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 1110.39s 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:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] 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 1256.04s: package tests unexpectedly errored