Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2082 (4fdd12e277*) started at 2026-04-26T23:31:57.437 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.57s ################################################################################ # 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 v1.4.0+0 [deac9b47] + LibCURL_jll v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.30+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 6.61s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.4 s ✓ BGEN 8.3 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 29.0 s ✓ MendelIHT 3 dependencies successfully precompiled in 46 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 73.53s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_axDGdU/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 25.6s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.6s Test Summary: | Pass Total Time _choose! | 7 7 11.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.5s Test Summary: | Pass Total Time project_k! | 2 2 1.2s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1788.4250336219955, backtracks = 0, tol = 2.261228072634515 Iteration 2: loglikelihood = -1456.3661471465698, backtracks = 0, tol = 0.14500592330958192 Iteration 3: loglikelihood = -1415.7818621681902, backtracks = 0, tol = 0.0517096355135645 Iteration 4: loglikelihood = -1415.4425515268483, backtracks = 0, tol = 0.0330226474878251 Iteration 5: loglikelihood = -1414.7341455309772, backtracks = 0, tol = 0.032503757288304694 Iteration 6: loglikelihood = -1414.6426130052414, backtracks = 0, tol = 0.0018418835214763707 Iteration 7: loglikelihood = -1414.6417901544205, backtracks = 0, tol = 0.00021463513899734504 Iteration 8: loglikelihood = -1414.6417805654, backtracks = 0, tol = 2.4514876743611172e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.07616281509399414 Final loglikelihood: -1414.6417805654 SNP PVE: 0.9387200909373079 Iterations: 8 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 715 -0.118353 2 │ 1530 0.557307 3 │ 1754 -1.11813 4 │ 2300 -0.465003 5 │ 3447 0.837013 6 │ 5857 -1.89484 7 │ 5968 0.975992 8 │ 6432 -2.67431 9 │ 7058 -0.512981 10 │ 7243 -0.657706 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0198885Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 26.0s **** 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 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 4.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -2292.696242688054, backtracks = 0, tol = 0.2828896381960402 Iteration 2: loglikelihood = -1722.3892306540963, backtracks = 0, tol = 0.05476345071200429 Iteration 3: loglikelihood = -1537.234331363168, backtracks = 0, tol = 0.04609170917433263 Iteration 4: loglikelihood = -1481.3369428552794, backtracks = 0, tol = 0.04424230133409312 Iteration 5: loglikelihood = -1388.8854163225828, backtracks = 0, tol = 0.11953951979192788 Iteration 6: loglikelihood = -1366.4104562690677, backtracks = 0, tol = 0.03772020726224805 Iteration 7: loglikelihood = -1355.3620553395622, backtracks = 0, tol = 0.07020174322757615 Iteration 8: loglikelihood = -1349.0924260340464, backtracks = 0, tol = 0.02189314383064726 Iteration 9: loglikelihood = -1342.4277039490667, backtracks = 0, tol = 0.07024059794722945 Iteration 10: loglikelihood = -1340.033111776667, backtracks = 0, tol = 0.011842454776380504 Iteration 11: loglikelihood = -1338.84730351426, backtracks = 1, tol = 0.009213773914456576 Iteration 12: loglikelihood = -1338.243837481226, backtracks = 0, tol = 0.010835746060220353 Iteration 13: loglikelihood = -1337.847725409219, backtracks = 0, tol = 0.005862211350428397 Iteration 14: loglikelihood = -1337.5911978962456, backtracks = 0, tol = 0.006840614819018308 Iteration 15: loglikelihood = -1337.4151572309484, backtracks = 0, tol = 0.003792052449194535 Iteration 16: loglikelihood = -1337.2958833230416, backtracks = 0, tol = 0.004469212747625799 Iteration 17: loglikelihood = -1337.2125946159713, backtracks = 0, tol = 0.002585459883322059 Iteration 18: loglikelihood = -1337.1549650689233, backtracks = 0, tol = 0.0030236582931620765 Iteration 19: loglikelihood = -1337.1143576258623, backtracks = 0, tol = 0.0017927928079691851 Iteration 20: loglikelihood = -1337.0859325831827, backtracks = 0, tol = 0.002084076824467038 Iteration 21: loglikelihood = -1337.0658014240487, backtracks = 0, tol = 0.0012562664615905306 Iteration 22: loglikelihood = -1337.051612013807, backtracks = 0, tol = 0.0014533058982503936 Iteration 23: loglikelihood = -1337.041532479928, backtracks = 0, tol = 0.0008859473344085873 Iteration 24: loglikelihood = -1337.0343971011534, backtracks = 0, tol = 0.001021120772205583 Iteration 25: loglikelihood = -1337.029319021473, backtracks = 0, tol = 0.0006273454946717334 Iteration 26: loglikelihood = -1337.0257140773274, backtracks = 0, tol = 0.0007210750074664723 Iteration 27: loglikelihood = -1337.0231454922375, backtracks = 0, tol = 0.00044542338417343717 Iteration 28: loglikelihood = -1337.021318619627, backtracks = 0, tol = 0.0005109377519735526 Iteration 29: loglikelihood = -1337.0200159370568, backtracks = 0, tol = 0.00031682919435090123 Iteration 30: loglikelihood = -1337.0190882382644, backtracks = 0, tol = 0.0003628934669843696 Iteration 31: loglikelihood = -1337.0184263865103, backtracks = 0, tol = 0.00022563955603209298 Iteration 32: loglikelihood = -1337.0179546376155, backtracks = 0, tol = 0.00025816870193132104 Iteration 33: loglikelihood = -1337.0176179584935, backtracks = 0, tol = 0.00016083397952624693 Iteration 34: loglikelihood = -1337.0173778364308, backtracks = 0, tol = 0.00018387759312443478 Iteration 35: loglikelihood = -1337.0172064243036, backtracks = 0, tol = 0.00011470983993770542 Iteration 36: loglikelihood = -1337.0170841194501, backtracks = 0, tol = 0.00013107127919308236 Iteration 37: loglikelihood = -1337.0169967970792, backtracks = 0, tol = 8.184772050496391e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1663.3221868947126, backtracks = 0, tol = 0.28851355413105423 Iteration 2: loglikelihood = -1578.9919157110478, backtracks = 0, tol = 0.1598212036448505 Iteration 3: loglikelihood = -1546.8180071121312, backtracks = 0, tol = 0.13433889292984 Iteration 4: loglikelihood = -1541.7012667554004, backtracks = 0, tol = 0.07270415977275492 Iteration 5: loglikelihood = -1533.3576447255264, backtracks = 0, tol = 0.06836861941414879 Iteration 6: loglikelihood = -1532.3146030113553, backtracks = 1, tol = 0.013627999100673572 Iteration 7: loglikelihood = -1531.995168279595, backtracks = 1, tol = 0.05491437952235015 Iteration 8: loglikelihood = -1531.7375988040299, backtracks = 1, tol = 0.005641939799734164 Iteration 9: loglikelihood = -1531.6344889585364, backtracks = 1, tol = 0.0044545887501190005 Iteration 10: loglikelihood = -1531.6080113163243, backtracks = 2, tol = 0.001964566116500693 Iteration 11: loglikelihood = -1531.5912431235279, backtracks = 2, tol = 0.0016170848876525246 Iteration 12: loglikelihood = -1531.5809959637922, backtracks = 2, tol = 0.0012736076901178155 Iteration 13: loglikelihood = -1531.5748839184423, backtracks = 2, tol = 0.0009766831166395011 Iteration 14: loglikelihood = -1531.571288577214, backtracks = 2, tol = 0.0007391529074343928 Iteration 15: loglikelihood = -1531.5691902564886, backtracks = 2, tol = 0.0005559461140538428 Iteration 16: loglikelihood = -1531.5679715243734, backtracks = 2, tol = 0.00041689493989750234 Iteration 17: loglikelihood = -1531.5672659493237, backtracks = 2, tol = 0.0003121282067501762 Iteration 18: loglikelihood = -1531.566858405469, backtracks = 2, tol = 0.00023348013540809307 Iteration 19: loglikelihood = -1531.566623413918, backtracks = 2, tol = 0.00017455805409039187 Iteration 20: loglikelihood = -1531.566488098602, backtracks = 2, tol = 0.0001304678603405976 Iteration 21: loglikelihood = -1531.5664102627456, backtracks = 2, tol = 9.750118232236189e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1832.8334083441157, backtracks = 0, tol = 0.7604466132011113 Iteration 2: loglikelihood = -1447.308153510224, backtracks = 0, tol = 0.12105594998385284 Iteration 3: loglikelihood = -1394.5674680461802, backtracks = 0, tol = 0.04929972781826346 Iteration 4: loglikelihood = -1388.3668270648861, backtracks = 0, tol = 0.02775804285919044 Iteration 5: loglikelihood = -1387.946636716812, backtracks = 0, tol = 0.025373342430963838 Iteration 6: loglikelihood = -1387.851049110031, backtracks = 1, tol = 0.0007715122360940078 Iteration 7: loglikelihood = -1387.8263695119713, backtracks = 1, tol = 0.0003842876487686569 Iteration 8: loglikelihood = -1387.8200155781626, backtracks = 1, tol = 0.00019296321379670686 Iteration 9: loglikelihood = -1387.818386499004, backtracks = 1, tol = 0.00010257619866432853 Iteration 10: loglikelihood = -1387.8179707274196, backtracks = 1, tol = 5.902574523321379e-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 = -1639.0972609014689, backtracks = 0, tol = 0.4300997703910655 Iteration 2: loglikelihood = -1434.2850173497252, backtracks = 0, tol = 0.08862516455706901 Iteration 3: loglikelihood = -1396.7407302735817, backtracks = 0, tol = 0.04106976779017113 Iteration 4: loglikelihood = -1389.0537171877995, backtracks = 0, tol = 0.02804319105669019 Iteration 5: loglikelihood = -1387.585430446655, backtracks = 0, tol = 0.029644656991977547 Iteration 6: loglikelihood = -1386.3180519689968, backtracks = 0, tol = 0.0294423299764571 Iteration 7: loglikelihood = -1386.2182172927821, backtracks = 0, tol = 0.0018339884210078763 Iteration 8: loglikelihood = -1386.2168986872089, backtracks = 0, tol = 0.00023147120984721496 Iteration 9: loglikelihood = -1386.2168776048127, backtracks = 0, tol = 2.887780222025296e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 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 11.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1629.6790532971406, backtracks = 0, tol = 0.2735569875708762 Iteration 2: loglikelihood = -1518.8261233579126, backtracks = 0, tol = 0.10668565891108199 Iteration 3: loglikelihood = -1432.3672371053992, backtracks = 0, tol = 0.17688170581743823 Iteration 4: loglikelihood = -1420.2435888241916, backtracks = 0, tol = 0.03517030994132127 Iteration 5: loglikelihood = -1413.3431775199494, backtracks = 0, tol = 0.05521596201363445 Iteration 6: loglikelihood = -1408.8115723069088, backtracks = 0, tol = 0.01722658206941166 Iteration 7: loglikelihood = -1406.089834658205, backtracks = 1, tol = 0.02102356560744525 Iteration 8: loglikelihood = -1399.1390878668092, backtracks = 1, tol = 0.04484542261154022 Iteration 9: loglikelihood = -1394.800924922976, backtracks = 0, tol = 0.02876287623583523 Iteration 10: loglikelihood = -1393.0733727600038, backtracks = 0, tol = 0.012639974261449052 Iteration 11: loglikelihood = -1392.0581750063575, backtracks = 0, tol = 0.015331999143236722 Iteration 12: loglikelihood = -1391.3604246269533, backtracks = 0, tol = 0.007848184934143652 Iteration 13: loglikelihood = -1385.4984815415323, backtracks = 0, tol = 0.04315619498080624 Iteration 14: loglikelihood = -1383.591066741278, backtracks = 1, tol = 0.011268748408035796 Iteration 15: loglikelihood = -1374.9198599197832, backtracks = 1, tol = 0.042333299232862956 Iteration 16: loglikelihood = -1371.2036794345245, backtracks = 0, tol = 0.022018242267764512 Iteration 17: loglikelihood = -1370.2647508752864, backtracks = 0, tol = 0.009366851842928061 Iteration 18: loglikelihood = -1369.9381295964736, backtracks = 0, tol = 0.006907522408904269 Iteration 19: loglikelihood = -1369.800554527235, backtracks = 0, tol = 0.004859773302955351 Iteration 20: loglikelihood = -1369.7323617419079, backtracks = 0, tol = 0.0032604553614057185 Iteration 21: loglikelihood = -1369.696689397366, backtracks = 0, tol = 0.0026783679218748266 Iteration 22: loglikelihood = -1369.677392680104, backtracks = 0, tol = 0.001847763817520727 Iteration 23: loglikelihood = -1369.6668722035818, backtracks = 0, tol = 0.001475999284438605 Iteration 24: loglikelihood = -1369.6611087912938, backtracks = 0, tol = 0.0010240938603371934 Iteration 25: loglikelihood = -1369.6579434538282, backtracks = 0, tol = 0.00081286563807002 Iteration 26: loglikelihood = -1369.6562055282218, backtracks = 0, tol = 0.0005640265064471712 Iteration 27: loglikelihood = -1369.6552490490255, backtracks = 0, tol = 0.0004478992340899391 Iteration 28: loglikelihood = -1369.654723449349, backtracks = 0, tol = 0.0003102181258366862 Iteration 29: loglikelihood = -1369.6544338655658, backtracks = 0, tol = 0.0002470184040203098 Iteration 30: loglikelihood = -1369.6542746231864, backtracks = 0, tol = 0.00017062931000582792 Iteration 31: loglikelihood = -1369.6541868135575, backtracks = 0, tol = 0.00013635609961904407 Iteration 32: loglikelihood = -1369.6541384930383, backtracks = 0, tol = 9.3895528809608e-5 1.245104 seconds (3.30 M allocations: 62.360 MiB, 1.95% gc time, 53.40% 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 = -1646.698297305928, backtracks = 0, tol = 0.2735569875708762 Iteration 2: loglikelihood = -1582.5928328046239, backtracks = 0, tol = 0.12016070433099905 Iteration 3: loglikelihood = -1526.4303029557802, backtracks = 0, tol = 0.17683392769288395 Iteration 4: loglikelihood = -1499.188838292914, backtracks = 0, tol = 0.09856782591955404 Iteration 5: loglikelihood = -1482.2693461690856, backtracks = 0, tol = 0.07484067300153062 Iteration 6: loglikelihood = -1467.4968701899895, backtracks = 0, tol = 0.025957402107954112 Iteration 7: loglikelihood = -1452.9340267980142, backtracks = 0, tol = 0.06730626942754846 Iteration 8: loglikelihood = -1443.4983569163392, backtracks = 0, tol = 0.062145159245385884 Iteration 9: loglikelihood = -1434.4631432210022, backtracks = 0, tol = 0.04777815063616987 Iteration 10: loglikelihood = -1430.1495078175026, backtracks = 0, tol = 0.06468409057528787 Iteration 11: loglikelihood = -1424.123006941102, backtracks = 0, tol = 0.06618533161907203 Iteration 12: loglikelihood = -1415.8339923850951, backtracks = 0, tol = 0.056221841344887495 Iteration 13: loglikelihood = -1411.3649695132485, backtracks = 0, tol = 0.009788170896278082 Iteration 14: loglikelihood = -1408.1912440536764, backtracks = 0, tol = 0.0034762841773142866 Iteration 15: loglikelihood = -1405.3238786296713, backtracks = 0, tol = 0.0016837404557600388 Iteration 16: loglikelihood = -1402.8563807982687, backtracks = 0, tol = 0.0008093170034926755 Iteration 17: loglikelihood = -1400.6493842993727, backtracks = 0, tol = 0.0004412678987520914 Iteration 18: loglikelihood = -1397.234651154052, backtracks = 0, tol = 0.05060403108909425 Iteration 19: loglikelihood = -1395.008054028094, backtracks = 0, tol = 0.0070965807970513935 Iteration 20: loglikelihood = -1393.3423080556604, backtracks = 0, tol = 0.0012120827821219717 Iteration 21: loglikelihood = -1391.8231102574775, backtracks = 0, tol = 0.0005892372804997665 Iteration 22: loglikelihood = -1390.473802357313, backtracks = 0, tol = 0.0003087219631887821 Iteration 23: loglikelihood = -1389.2372178388146, backtracks = 0, tol = 0.00023895229172996222 Iteration 24: loglikelihood = -1388.1226298687882, backtracks = 0, tol = 0.00022080383938807575 Iteration 25: loglikelihood = -1387.0964650410776, backtracks = 0, tol = 0.00015832461877251494 Iteration 26: loglikelihood = -1387.0951043921011, backtracks = 0, tol = 0.054357952125827336 Iteration 27: loglikelihood = -1385.3392975947709, backtracks = 0, tol = 0.054350391493022156 Iteration 28: loglikelihood = -1384.5103830689786, backtracks = 0, tol = 0.0039843103538478725 Iteration 29: loglikelihood = -1383.7661730767675, backtracks = 0, tol = 0.001078751624674127 Iteration 30: loglikelihood = -1383.0954473810964, backtracks = 0, tol = 0.00025490918020893577 Iteration 31: loglikelihood = -1382.4683069503076, backtracks = 0, tol = 7.273552558524456e-5 0.349887 seconds (1.18 M allocations: 21.321 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3434.7744, backtracks = 0, tol = 0.08512729835801514 Iteration 2: loglikelihood = -3393.979, backtracks = 0, tol = 0.043046162795045584 Iteration 3: loglikelihood = -3365.4485, backtracks = 1, tol = 0.0650353042878907 Iteration 4: loglikelihood = -3358.4177, backtracks = 0, tol = 0.099777748893464 Iteration 5: loglikelihood = -3314.7788, backtracks = 0, tol = 0.08391854181305337 Iteration 6: loglikelihood = -3313.793, backtracks = 1, tol = 0.004753905307685495 Iteration 7: loglikelihood = -3313.402, backtracks = 1, tol = 0.002979924251714351 Iteration 8: loglikelihood = -3313.2712, backtracks = 1, tol = 0.0027648086682635687 Iteration 9: loglikelihood = -3313.236, backtracks = 1, tol = 0.001421333847227529 Iteration 10: loglikelihood = -3313.2268, backtracks = 1, tol = 0.0007437741043744608 Iteration 11: loglikelihood = -3313.2275, backtracks = 3, tol = 9.072154633202218e-5 27.803707 seconds (14.74 M allocations: 677.467 MiB, 1.78% gc time, 97.09% 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 = -3347.4502, backtracks = 0, tol = 0.08512729835801514 Iteration 2: loglikelihood = -3249.7878, backtracks = 0, tol = 0.04404777388567668 Iteration 3: loglikelihood = -3070.3206, backtracks = 1, tol = 0.06481333845322382 Iteration 4: loglikelihood = -2986.328, backtracks = 0, tol = 0.09985100368533932 Iteration 5: loglikelihood = -2867.8435, backtracks = 0, tol = 0.08591576106165327 Iteration 6: loglikelihood = -2829.75, backtracks = 0, tol = 0.10012961010383947 Iteration 7: loglikelihood = -2699.894, backtracks = 0, tol = 0.0878615198895793 Iteration 8: loglikelihood = -2599.696, backtracks = 0, tol = 0.0886406910199339 Iteration 9: loglikelihood = -2514.7166, backtracks = 0, tol = 0.00739937226897789 Iteration 10: loglikelihood = -2436.1633, backtracks = 0, tol = 0.0845815236193417 Iteration 11: loglikelihood = -2361.3896, backtracks = 0, tol = 0.08457863735687028 Iteration 12: loglikelihood = -2300.0137, backtracks = 0, tol = 0.08293965876455013 Iteration 13: loglikelihood = -2249.1682, backtracks = 0, tol = 0.08272149805649034 Iteration 14: loglikelihood = -2210.8242, backtracks = 0, tol = 0.09388574145481879 Iteration 15: loglikelihood = -2179.2275, backtracks = 0, tol = 0.08722894358642841 Iteration 16: loglikelihood = -2160.2175, backtracks = 0, tol = 0.01645399102871873 Iteration 17: loglikelihood = -2148.5928, backtracks = 0, tol = 0.002766988278857078 Iteration 18: loglikelihood = -2141.5022, backtracks = 0, tol = 0.0008016936257581508 Iteration 19: loglikelihood = -2137.3318, backtracks = 0, tol = 0.0003142129512195812 Iteration 20: loglikelihood = -2134.955, backtracks = 0, tol = 0.00028993996076200377 Iteration 21: loglikelihood = -2132.974, backtracks = 1, tol = 0.00010305802554318577 Iteration 22: loglikelihood = -2132.5593, backtracks = 0, tol = 0.0004014319219194691 Iteration 23: loglikelihood = -2132.2402, backtracks = 1, tol = 3.940841704859684e-5 0.168895 seconds (1.09 M allocations: 18.062 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 32.5s **** 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 **** Initializing β to univariate regression values... 13%|▎ | ETA: 0:00:33Running 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 6.184027 seconds (1.19 M allocations: 140.149 MiB, 14.81% gc time, 78.48% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 6.7s 10.844458 seconds (4.00 M allocations: 82.500 MiB, 0.19% gc time, 0.63% compilation time) 5.737182 seconds (3.98 M allocations: 91.677 MiB, 0.43% gc time) 11.828959 seconds (20.41 M allocations: 439.459 MiB, 0.86% gc time, 16.89% compilation time: 79% of which was recompilation) 9.660968 seconds (20.18 M allocations: 434.187 MiB, 1.07% gc time) 40.801206 seconds (3.85 M allocations: 4.244 GiB, 11.41% gc time, 29.27% compilation time) 54.221435 seconds (70.38 k allocations: 183.441 MiB, 0.15% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m32.5s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.794 ms (78 allocations: 4.56 KiB) 4.974 μs (0 allocations: 0 bytes) 136.699 μs (4 allocations: 288 bytes) 7.407 μs (0 allocations: 0 bytes) 56.859 μs (2 allocations: 64 bytes) 33.130 μs (0 allocations: 0 bytes) 27.579 μs (0 allocations: 0 bytes) 29.890 μs (0 allocations: 0 bytes) 136.398 μs (0 allocations: 0 bytes) 39.505 ms (78 allocations: 4.56 KiB) 27.410 μs (0 allocations: 0 bytes) 207.948 μs (4 allocations: 288 bytes) 45.870 μs (0 allocations: 0 bytes) 329.387 μs (2 allocations: 64 bytes) 110.869 μs (0 allocations: 0 bytes) 124.409 μs (0 allocations: 0 bytes) 190.038 μs (0 allocations: 0 bytes) 219.598 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m23.0s **** 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 **** **** 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 0.445189 seconds (49.46 k allocations: 5.502 MiB, 63.68% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 1.922871 seconds (282.38 k allocations: 168.157 MiB, 57.83% 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: 0:03:49 Cross 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65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 5409.0855919367505 1 3121.5143316535004 2 1774.7744105842926 3 1419.693309486451 4 973.7074358873809 5 746.1508308763597 6 591.0905792486097 7 491.5189020331703 8 405.23469040650355 9 337.59692440196034 10 341.4674234378996 11 346.9513957601155 12 348.52441251846886 13 348.2521441882482 14 351.5357175594996 15 353.14189627015776 16 365.2150608654701 17 370.25452398461624 18 360.13849923741657 19 357.5221582523245 20 384.74955492174854 Best k = 9 12.755558 seconds (11.20 M allocations: 291.896 MiB, 1.90% gc time, 58.68% 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: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 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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... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 5409.0855919367505 1 3122.7490748090227 2 1776.711370905124 3 1426.369366345735 4 987.143327686716 5 754.3782956816372 6 603.1324700355879 7 504.51355308527855 8 416.8000597462433 9 349.4531250786755 10 357.6066909957743 11 369.4953805447258 12 375.3366817587314 13 376.1546795232828 14 384.0802086190315 15 386.6208247031063 16 385.7130248981514 17 398.74877230728185 18 408.9187486001439 19 406.4072187453773 20 406.7167381147411 Best k = 9 5.173734 seconds (10.06 M allocations: 210.263 MiB, 0.86% gc time, 0.94% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:26 Cross validating... 8%|██▌ | ETA: 0:02:28 Cross validating... 13%|████▏ | ETA: 0:01:28 Cross validating... 17%|█████▋ | ETA: 0:01:01 Cross validating... 22%|███████▏ | ETA: 0:00:46 Cross validating... 25%|████████▏ | ETA: 0:00:39 Cross validating... 30%|█████████▋ | ETA: 0:00:31 Cross validating... 35%|███████████▏ | ETA: 0:00:25 Cross validating... 40%|████████████▊ | ETA: 0:00:21 Cross validating... 44%|██████████████▎ | ETA: 0:00:17 Cross 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389.0242094116211 8 354.6585098266602 9 336.85617321777346 10 340.82626113891604 11 342.82771688842774 12 344.63028427124027 13 348.23344006347656 14 356.6096476135254 15 353.1322117614746 16 372.30685565185547 17 357.81841784667967 18 359.6927371826172 19 363.64991482543945 20 357.8770882873535 Best k = 9 16.719042 seconds (12.75 M allocations: 316.849 MiB, 0.56% gc time, 82.63% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | 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... 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100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1546.502358276367 1 1324.623536376953 2 982.5618372192382 3 801.7137897338866 4 654.1447257080079 5 528.5126165771485 6 449.1202112731934 7 393.82921606445314 8 363.8958520812988 9 344.79574102783204 10 353.89556799316404 11 361.5222179260254 12 364.64080200195315 13 376.7667213134766 14 384.36426919555663 15 390.6222038269043 16 401.52322088623043 17 403.10411532592775 18 409.0989605407715 19 421.3892825927734 20 411.0791355285645 Best k = 9 2.914156 seconds (11.30 M allocations: 207.695 MiB, 1.49% gc time, 1.54% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 21.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | 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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... 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: 0:00:08 Crossvalidation Results: k MSE 0 465.0128227494747 1 367.3398134192089 2 281.84026466545794 3 268.701829649755 4 247.91868136001395 5 235.38911744862784 6 222.04220705329197 7 222.9635199399599 8 225.5558086992724 9 229.4395452222994 10 218.65460401651364 11 231.7274433016754 12 241.60107569857888 13 225.20607751893698 14 232.0650313466938 15 232.84012525017187 16 237.22044425690643 17 248.779645005367 18 257.8419815605818 19 225.61376013678384 20 248.612201951688 Best k = 10 9.101365 seconds (17.52 M allocations: 408.495 MiB, 0.88% gc time, 31.75% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross 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ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 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: 0:00:06 Crossvalidation Results: k MSE 0 465.0128227494747 1 368.29608558261407 2 283.0291424117851 3 270.75392158670087 4 251.46171855698896 5 238.82196697325904 6 227.24917549704014 7 231.3030737638141 8 234.64058127107376 9 236.8476363863857 10 238.41234992420436 11 238.36011823040025 12 258.0064635833803 13 260.3241207795028 14 255.49045744998435 15 277.01602046158956 16 283.83500763472205 17 282.0637852165516 18 261.4263822337739 19 277.4815560765852 20 278.33875139882895 Best k = 6 6.528539 seconds (18.04 M allocations: 376.183 MiB, 1.03% gc time, 0.91% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 16.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:49 Cross validating... 6%|██ | ETA: 0:00:26 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... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.3008055592543 1 420.74506057006806 2 395.83641532125864 3 358.4859180937463 4 340.14432708087816 5 319.3771444378954 6 303.4143312953784 7 292.82589467820105 8 296.2861588689632 9 298.9010434061134 10 303.1303745706787 11 307.40628154133924 12 305.6789958391213 13 309.7397587102118 14 320.290367686802 15 310.082540561566 16 310.4528197755256 17 323.29571736257407 18 327.88084664826926 19 306.5693993300599 20 324.77825415557044 Best k = 7 7.823985 seconds (16.54 M allocations: 391.511 MiB, 12.23% gc time, 34.75% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 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: 0:00:03 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: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 463.3008055592543 1 422.20591669317315 2 397.41020267182836 3 368.7734049040911 4 339.7901116292817 5 321.96748506935444 6 307.0829464444231 7 297.58810626312714 8 307.0047239555945 9 315.926619002952 10 328.12989234320435 11 328.00125199237164 12 332.7636157855045 13 348.11198357530765 14 354.6360936304241 15 355.68026754331737 16 357.56729500276157 17 353.52725137458185 18 366.90423153423365 19 382.77236848366925 20 383.3630652354991 Best k = 7 4.509868 seconds (17.49 M allocations: 361.293 MiB, 1.68% gc time, 0.96% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:07 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 8%|██▌ | ETA: 0:00:29 Cross validating... 11%|███▌ | ETA: 0:00:22 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:15 Cross validating... 21%|██████▋ | ETA: 0:00:13 Cross validating... 24%|███████▋ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:11 Cross validating... 29%|█████████▏ | ETA: 0:00:10 Cross validating... 32%|██████████▏ | ETA: 0:00:09 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:07 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:06 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:05 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:08 Crossvalidation Results: k MSE 0 968.6600276039992 1 847.8605339218313 2 605.0432284586443 3 531.2469936725255 4 416.48300420444554 5 396.9721611211577 6 374.6794413259206 7 376.8980569868801 8 375.171963633027 9 387.2182466733567 10 370.83916502903475 11 397.67813338321406 12 371.66513367577454 13 378.5315734999957 14 388.0484864769577 15 390.5439703391294 16 376.0389237589103 17 414.59779269340004 18 427.1750041456667 19 422.79109645831795 20 417.6294526614722 Best k = 10 9.076794 seconds (15.82 M allocations: 374.460 MiB, 1.05% gc time, 31.48% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | 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100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 968.6600276039992 1 807.2419401812479 2 587.7778733758497 3 524.1987487662151 4 422.0578658275494 5 390.68302749921565 6 384.4275670583253 7 375.67805407902824 8 378.3217740290553 9 386.5750158319014 10 393.9050937537054 11 405.892336208164 12 412.67779587655696 13 417.63008902838067 14 421.6618051223966 15 412.96397842871943 16 421.17209635943084 17 448.35162679762664 18 460.2196510777671 19 466.34103308700594 20 469.1464650525603 Best k = 7 6.223825 seconds (14.58 M allocations: 295.603 MiB, 1.01% gc time, 1.01% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 15.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:39 Cross validating... 6%|██ | ETA: 0:00:51 Cross validating... 10%|███ | ETA: 0:00:34 Cross validating... 11%|███▌ | ETA: 0:00:38 Cross validating... 13%|████▏ | ETA: 0:00:41 Cross validating... 14%|████▋ | ETA: 0:00:42 Cross validating... 16%|█████▏ | ETA: 0:00:44 Cross validating... 17%|█████▋ | ETA: 0:00:45 Cross validating... 19%|██████▏ | ETA: 0:00:45 Cross validating... 21%|██████▋ | ETA: 0:00:45 Cross validating... 22%|███████▏ | ETA: 0:00:45 Cross validating... 24%|███████▋ | ETA: 0:00:41 Cross validating... 25%|████████▏ | ETA: 0:00:42 Cross validating... 27%|████████▋ | ETA: 0:00:41 Cross validating... 29%|█████████▏ | ETA: 0:00:41 Cross validating... 30%|█████████▋ | ETA: 0:00:41 Cross validating... 32%|██████████▏ | ETA: 0:00:39 Cross validating... 33%|██████████▋ | ETA: 0:00:38 Cross validating... 37%|███████████▋ | ETA: 0:00:35 Cross validating... 38%|████████████▎ | ETA: 0:00:35 Cross validating... 40%|████████████▊ | ETA: 0:00:34 Cross validating... 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70%|██████████████████████▍ | ETA: 0:00:15 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:14 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:14 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:13 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:12 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:12 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:11 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:10 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:09 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:08 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:07 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:05 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:46 Crossvalidation Results: k MSE 0 403.9802863175602 1 310.64875537624556 2 249.5002877884705 3 220.9816644146823 4 197.80265414524524 5 189.88416795426292 6 186.8289962413948 7 187.77537042359157 8 185.2067392596495 9 185.58396327426306 10 185.92298305599536 11 187.88709905475343 12 187.69959766320954 13 189.1380656123432 14 192.15282343108998 15 193.42718705802542 16 192.9694323350111 17 195.454375618443 18 194.86405053485424 19 195.94370080711437 20 195.5657683796066 Best k = 8 47.094639 seconds (133.90 M allocations: 3.321 GiB, 1.12% gc time, 5.26% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:06 Cross validating... 5%|█▌ | ETA: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:09 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 10%|███ | ETA: 0:00:09 Cross validating... 11%|███▌ | ETA: 0:00:08 Cross validating... 13%|████▏ | ETA: 0:00:08 Cross validating... 14%|████▋ | ETA: 0:00:09 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:10 Cross validating... 30%|█████████▋ | ETA: 0:00:10 Cross 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87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 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: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 403.9802863175602 1 306.4684786470997 2 249.35754094935 3 221.4260675247781 4 199.20295689966682 5 192.409351590122 6 189.55863994490068 7 192.20177137367017 8 190.66873801126965 9 190.7193563020325 10 194.25606713547913 11 194.3113222260145 12 204.63448372692926 13 205.32009928689865 14 207.01315095953828 15 214.058924617873 16 215.7556232527906 17 217.43936250623324 18 219.6860287013393 19 227.8715518356917 20 235.2549594557966 Best k = 6 14.623402 seconds (41.87 M allocations: 877.992 MiB, 1.18% gc time, 0.47% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m02.2s **** 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: 0:01:12 Cross validating... 6%|██ | ETA: 0:00:36 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 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... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.575577 seconds (17.01 M allocations: 337.914 MiB, 1.64% gc time, 45.23% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 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: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.553384 seconds (16.18 M allocations: 286.714 MiB, 2.48% gc time, 1.71% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:25 Cross validating... 3%|█ | ETA: 0:01:01 Cross validating... 4%|█▎ | ETA: 0:00:49 Cross validating... 5%|█▋ | 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94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 1361.9994395346453 2 1304.2134976730395 3 1276.9660894430785 4 1231.7738654971483 5 1234.9075404455855 6 1242.0217051856393 7 1237.7828881100863 8 1241.2120988305599 9 1250.193289817974 10 1255.5743782514285 11 1260.6116752671203 12 1267.9007747317448 13 1283.5884194347677 14 1277.222825551792 15 1288.0838986284177 16 1297.5492981252803 17 1319.9719085683355 18 1287.1929528705364 19 1290.1220750886791 20 1308.2966324095842 Best k = 4 20.094598 seconds (340.19 k allocations: 255.705 MiB, 0.44% gc time, 8.36% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 25.4s 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 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94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:14 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 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74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 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: 0:00:03 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: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m29.3s 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] getproperty(x::Nothing, f::Symbol) @ Base ~/.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 3.1s RNG of the outermost testset: Xoshiro(0xbe2893282563ac01, 0xc1cbff29d331a379, 0x438ae2672bb02a09, 0x75e1d999ac02046c, 0x8e6fefdd2d77878d) 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 1149.22s 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 1270.08s: package tests unexpectedly errored