Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1720 (f38c537ec6*) started at 2026-02-15T22:58:35.166 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.96s ################################################################################ # 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 v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [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 v0.10.15 [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] + 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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 v1.3.0+1 [deac9b47] + LibCURL_jll v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.92s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4609.2 ms ✓ BGEN 5766.6 ms ✓ VCFTools 27211.4 ms ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 23660.7 ms ✓ MendelIHT 4 dependencies successfully precompiled in 65 seconds. 170 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 86.44s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_dKXtaE/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.1 [2913bbd2] StatsBase v0.34.10 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v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+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 = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 22.9s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 7.9s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.4s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1582.4926021181159, backtracks = 0, tol = 1.4431863760659491 Iteration 2: loglikelihood = -1442.5035537826368, backtracks = 0, tol = 0.13432138827028509 Iteration 3: loglikelihood = -1421.0776507883804, backtracks = 0, tol = 0.06898505584933541 Iteration 4: loglikelihood = -1418.1023622297123, backtracks = 0, tol = 0.049167808983195116 Iteration 5: loglikelihood = -1417.7555220939767, backtracks = 0, tol = 0.006274313890879736 Iteration 6: loglikelihood = -1417.7528646932374, backtracks = 0, tol = 0.00045854707972897214 Iteration 7: loglikelihood = -1417.7528366984352, backtracks = 0, tol = 5.812845744199457e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05910181999206543 Final loglikelihood: -1417.7528366984352 SNP PVE: 0.8724289025598437 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1953 1.44022 2 │ 3955 0.360737 3 │ 4690 0.658759 4 │ 5190 0.757886 5 │ 5678 -0.869187 6 │ 6648 -0.408723 7 │ 7190 0.640231 8 │ 7195 1.46849 9 │ 9275 0.118424 10 │ 9720 0.127293 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.00531962Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.9s **** 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 logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.4s **** 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 = -42035.12928465302, backtracks = 0, tol = 0.3911789649974425 Iteration 2: loglikelihood = -17727.73175579435, backtracks = 0, tol = 0.026427598696750314 Iteration 3: loglikelihood = -8356.024496488966, backtracks = 0, tol = 0.02647637798474377 Iteration 4: loglikelihood = -4510.7978274239085, backtracks = 0, tol = 0.026452169926975796 Iteration 5: loglikelihood = -2612.7280065417326, backtracks = 0, tol = 0.03951609825392789 Iteration 6: loglikelihood = -1747.0471499733087, backtracks = 0, tol = 0.061320486463594524 Iteration 7: loglikelihood = -1488.3169198894248, backtracks = 0, tol = 0.05402938631356138 Iteration 8: loglikelihood = -1420.446291632135, backtracks = 0, tol = 0.03468064402600766 Iteration 9: loglikelihood = -1381.6940220332751, backtracks = 0, tol = 0.040138953144843594 Iteration 10: loglikelihood = -1352.7277012611692, backtracks = 0, tol = 0.08768945012328017 Iteration 11: loglikelihood = -1339.4161861957207, backtracks = 0, tol = 0.03836044578790272 Iteration 12: loglikelihood = -1335.224230022768, backtracks = 0, tol = 0.015453903600497986 Iteration 13: loglikelihood = -1333.3347303005423, backtracks = 1, tol = 0.008490253540112605 Iteration 14: loglikelihood = -1332.5550211006746, backtracks = 1, tol = 0.006806746021254034 Iteration 15: loglikelihood = -1331.9390507797955, backtracks = 1, tol = 0.005815812987366148 Iteration 16: loglikelihood = -1331.4956306648576, backtracks = 0, tol = 0.00843701135878505 Iteration 17: loglikelihood = -1331.1954958803342, backtracks = 0, tol = 0.005118684959111834 Iteration 18: loglikelihood = -1330.9984914378538, backtracks = 0, tol = 0.005036357829518078 Iteration 19: loglikelihood = -1330.8553522699124, backtracks = 0, tol = 0.0034856377478902716 Iteration 20: loglikelihood = -1330.753833980591, backtracks = 0, tol = 0.0033421644839939932 Iteration 21: loglikelihood = -1330.6781482989004, backtracks = 0, tol = 0.0025139866235880403 Iteration 22: loglikelihood = -1330.622655330353, backtracks = 0, tol = 0.0023330445260696304 Iteration 23: loglikelihood = -1330.58074224443, backtracks = 0, tol = 0.0018598823410076746 Iteration 24: loglikelihood = -1330.5494723090555, backtracks = 0, tol = 0.0016760024792661047 Iteration 25: loglikelihood = -1330.525684336237, backtracks = 0, tol = 0.001394786156875506 Iteration 26: loglikelihood = -1330.5077568966092, backtracks = 0, tol = 0.001225859147387468 Iteration 27: loglikelihood = -1330.4940620382488, backtracks = 0, tol = 0.0010543893535923104 Iteration 28: loglikelihood = -1330.4836761908534, backtracks = 0, tol = 0.0009074592583355147 Iteration 29: loglikelihood = -1330.4757225593694, backtracks = 0, tol = 0.0008010779210236735 Iteration 30: loglikelihood = -1330.4696659535002, backtracks = 0, tol = 0.0006774314839977605 Iteration 31: loglikelihood = -1330.4650205724588, backtracks = 0, tol = 0.000610644502082787 Iteration 32: loglikelihood = -1330.4614733009805, backtracks = 0, tol = 0.0005088049479792627 Iteration 33: loglikelihood = -1330.4587499079578, backtracks = 0, tol = 0.0004665442427073743 Iteration 34: loglikelihood = -1330.4566662261457, backtracks = 0, tol = 0.00038527746769981025 Iteration 35: loglikelihood = -1330.4550654740074, backtracks = 0, tol = 0.00035702819153702394 Iteration 36: loglikelihood = -1330.453839009432, backtracks = 0, tol = 0.00029616938456622857 Iteration 37: loglikelihood = -1330.4528963948976, backtracks = 0, tol = 0.0002735449878143939 Iteration 38: loglikelihood = -1330.4521734379339, backtracks = 0, tol = 0.00022776225051160002 Iteration 39: loglikelihood = -1330.4516176346551, backtracks = 0, tol = 0.00020976947064098978 Iteration 40: loglikelihood = -1330.451191022937, backtracks = 0, tol = 0.00017520233482402596 Iteration 41: loglikelihood = -1330.4508629774155, backtracks = 0, tol = 0.0001609724828458097 Iteration 42: loglikelihood = -1330.4506110373966, backtracks = 0, tol = 0.0001347958143700158 Iteration 43: loglikelihood = -1330.450417276307, backtracks = 0, tol = 0.0001235920158382519 Iteration 44: loglikelihood = -1330.4502684016186, backtracks = 0, tol = 0.00010372077333628256 Iteration 45: loglikelihood = -1330.4501538921572, backtracks = 0, tol = 9.493125579632583e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1550.1046998635288, backtracks = 0, tol = 0.40760948313789774 Iteration 2: loglikelihood = -1484.9884829280998, backtracks = 0, tol = 0.1099951349822128 Iteration 3: loglikelihood = -1449.440708782508, backtracks = 0, tol = 0.07005285605571836 Iteration 4: loglikelihood = -1433.6647204154804, backtracks = 0, tol = 0.07220855868067953 Iteration 5: loglikelihood = -1430.9025392212993, backtracks = 0, tol = 0.08260937203661996 Iteration 6: loglikelihood = -1429.7964522755044, backtracks = 0, tol = 0.021568821928047013 Iteration 7: loglikelihood = -1427.7200355563634, backtracks = 0, tol = 0.08862513047679868 Iteration 8: loglikelihood = -1427.500061222647, backtracks = 0, tol = 0.012644554194014834 Iteration 9: loglikelihood = -1427.4800645385862, backtracks = 0, tol = 0.0038315135416471598 Iteration 10: loglikelihood = -1427.4760788301965, backtracks = 0, tol = 0.001901742840114771 Iteration 11: loglikelihood = -1427.4750650731876, backtracks = 0, tol = 0.0007208222554213978 Iteration 12: loglikelihood = -1427.4748314040241, backtracks = 0, tol = 0.0004907862862455125 Iteration 13: loglikelihood = -1427.4747683361195, backtracks = 0, tol = 0.0001846526306582411 Iteration 14: loglikelihood = -1427.4747572174817, backtracks = 1, tol = 6.218375988796578e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1959.380670961879, backtracks = 0, tol = 0.8173002793069246 Iteration 2: loglikelihood = -1522.202993977316, backtracks = 0, tol = 0.12576193723664789 Iteration 3: loglikelihood = -1434.2142553246447, backtracks = 0, tol = 0.05326367647387358 Iteration 4: loglikelihood = -1420.253376632803, backtracks = 0, tol = 0.0288682483024928 Iteration 5: loglikelihood = -1418.5132337925345, backtracks = 0, tol = 0.02718831021855659 Iteration 6: loglikelihood = -1418.4216688555935, backtracks = 0, tol = 0.028585881695123383 Iteration 7: loglikelihood = -1418.173827217124, backtracks = 0, tol = 0.003681287333752569 Iteration 8: loglikelihood = -1418.1734755756431, backtracks = 1, tol = 4.913264260867767e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1735.1858142228443, backtracks = 0, tol = 0.4479628802950769 Iteration 2: loglikelihood = -1489.0425232328098, backtracks = 0, tol = 0.11997742338326021 Iteration 3: loglikelihood = -1422.8450931025595, backtracks = 0, tol = 0.0501641604773556 Iteration 4: loglikelihood = -1420.4094186181198, backtracks = 0, tol = 0.03185003586510081 Iteration 5: loglikelihood = -1418.7145081129186, backtracks = 0, tol = 0.031160861161324344 Iteration 6: loglikelihood = -1418.4071603737643, backtracks = 0, tol = 0.031904265938183164 Iteration 7: loglikelihood = -1418.1806968729609, backtracks = 0, tol = 0.0038167894796261167 Iteration 8: loglikelihood = -1418.1803523604895, backtracks = 1, tol = 5.83298856222893e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 9.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1515.4129860729008, backtracks = 0, tol = 0.1623002667886107 Iteration 2: loglikelihood = -1454.1123795754957, backtracks = 0, tol = 0.08546278894223618 Iteration 3: loglikelihood = -1410.5488702849148, backtracks = 0, tol = 0.11201522502157685 Iteration 4: loglikelihood = -1399.2193727165204, backtracks = 0, tol = 0.04378723221744014 Iteration 5: loglikelihood = -1388.4658295482327, backtracks = 0, tol = 0.06482475239342833 Iteration 6: loglikelihood = -1375.92449410697, backtracks = 0, tol = 0.07581092444564484 Iteration 7: loglikelihood = -1374.01831073357, backtracks = 0, tol = 0.02139620051515401 Iteration 8: loglikelihood = -1373.0419550454067, backtracks = 0, tol = 0.015013589260251904 Iteration 9: loglikelihood = -1372.39670329682, backtracks = 0, tol = 0.01422851416139463 Iteration 10: loglikelihood = -1371.9460429260578, backtracks = 0, tol = 0.009696476555760057 Iteration 11: loglikelihood = -1371.6066665238789, backtracks = 0, tol = 0.011369306039136018 Iteration 12: loglikelihood = -1371.34677267637, backtracks = 0, tol = 0.00767051087978555 Iteration 13: loglikelihood = -1365.768787898375, backtracks = 0, tol = 0.05060653181415438 Iteration 14: loglikelihood = -1363.9561859588512, backtracks = 0, tol = 0.02222772018684943 Iteration 15: loglikelihood = -1363.4428926529868, backtracks = 0, tol = 0.01059844722680611 Iteration 16: loglikelihood = -1363.2044501277728, backtracks = 0, tol = 0.009417897405477016 Iteration 17: loglikelihood = -1363.080557302181, backtracks = 0, tol = 0.005870948273308161 Iteration 18: loglikelihood = -1363.0136283184224, backtracks = 0, tol = 0.005160887997300374 Iteration 19: loglikelihood = -1362.9776399511775, backtracks = 0, tol = 0.0031326958827700624 Iteration 20: loglikelihood = -1362.9581146464031, backtracks = 0, tol = 0.002809994834864703 Iteration 21: loglikelihood = -1362.9475645167684, backtracks = 0, tol = 0.0016879267422552047 Iteration 22: loglikelihood = -1362.941845907448, backtracks = 0, tol = 0.001525717590434818 Iteration 23: loglikelihood = -1362.9387506989392, backtracks = 0, tol = 0.0009126186535773725 Iteration 24: loglikelihood = -1362.9370741811492, backtracks = 0, tol = 0.0008269007841322631 Iteration 25: loglikelihood = -1362.936166018855, backtracks = 0, tol = 0.0004942460373559248 Iteration 26: loglikelihood = -1362.935674278441, backtracks = 0, tol = 0.0004477105942739011 Iteration 27: loglikelihood = -1362.9354077852213, backtracks = 0, tol = 0.0002679096638160385 Iteration 28: loglikelihood = -1362.9352634996283, backtracks = 0, tol = 0.0002422891016178456 Iteration 29: loglikelihood = -1362.9351852850414, backtracks = 0, tol = 0.00014529912432481844 Iteration 30: loglikelihood = -1362.935142935282, backtracks = 0, tol = 0.00013109685803398862 Iteration 31: loglikelihood = -1362.9351199748432, backtracks = 0, tol = 7.882761138912884e-5 0.964155 seconds (2.71 M allocations: 52.987 MiB, 2.69% gc time, 51.38% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1545.2216689908382, backtracks = 0, tol = 0.1623002667886107 Iteration 2: loglikelihood = -1501.771632742586, backtracks = 0, tol = 0.10101086216014658 Iteration 3: loglikelihood = -1476.9411494529318, backtracks = 0, tol = 0.08345926316399987 Iteration 4: loglikelihood = -1461.4217339211364, backtracks = 0, tol = 0.048877316881875826 Iteration 5: loglikelihood = -1446.916000001851, backtracks = 0, tol = 0.0663981451869054 Iteration 6: loglikelihood = -1433.3161111342204, backtracks = 0, tol = 0.06726917117368922 Iteration 7: loglikelihood = -1426.2282365224287, backtracks = 0, tol = 0.02106164653185856 Iteration 8: loglikelihood = -1419.7622604763408, backtracks = 0, tol = 0.01343732141180764 Iteration 9: loglikelihood = -1414.8866519210953, backtracks = 0, tol = 0.012676451396891046 Iteration 10: loglikelihood = -1408.0650907151985, backtracks = 0, tol = 0.06309553887778055 Iteration 11: loglikelihood = -1401.8982903978915, backtracks = 0, tol = 0.04118356694546197 Iteration 12: loglikelihood = -1396.944219356669, backtracks = 0, tol = 0.0656643728698892 Iteration 13: loglikelihood = -1394.1590579669762, backtracks = 0, tol = 0.011249900240119326 Iteration 14: loglikelihood = -1391.5448504123203, backtracks = 0, tol = 0.0064696482401219784 Iteration 15: loglikelihood = -1389.4263180815747, backtracks = 0, tol = 0.004819549576196627 Iteration 16: loglikelihood = -1387.5805016685442, backtracks = 0, tol = 0.06423734770457168 Iteration 17: loglikelihood = -1385.4981162720187, backtracks = 0, tol = 0.00827337695128192 Iteration 18: loglikelihood = -1383.9428280235595, backtracks = 0, tol = 0.004558803827248135 Iteration 19: loglikelihood = -1381.326550149958, backtracks = 0, tol = 0.06406901298683984 Iteration 20: loglikelihood = -1378.8630352952016, backtracks = 0, tol = 0.036099958725865966 Iteration 21: loglikelihood = -1377.55634533618, backtracks = 0, tol = 0.008210764098668152 Iteration 22: loglikelihood = -1376.8868857756913, backtracks = 0, tol = 0.06749745705551839 Iteration 23: loglikelihood = -1375.1699021346212, backtracks = 0, tol = 0.06739900221396734 Iteration 24: loglikelihood = -1373.3776768814096, backtracks = 1, tol = 0.0031042096549185106 Iteration 25: loglikelihood = -1372.2167580407847, backtracks = 1, tol = 0.0017947741791463562 Iteration 26: loglikelihood = -1371.311804648311, backtracks = 1, tol = 0.0009196949934613155 Iteration 27: loglikelihood = -1370.8305123387174, backtracks = 1, tol = 0.0006092032741255156 Iteration 28: loglikelihood = -1370.7544246057046, backtracks = 1, tol = 0.000518478664067861 Iteration 29: loglikelihood = -1370.378635949931, backtracks = 2, tol = 0.00016462398774548038 Iteration 30: loglikelihood = -1370.0628226047374, backtracks = 1, tol = 0.00019005698103130583 Iteration 31: loglikelihood = -1369.659561177562, backtracks = 1, tol = 0.000131765002275628 Iteration 32: loglikelihood = -1368.9943967502575, backtracks = 1, tol = 0.0001013898755785272 Iteration 33: loglikelihood = -1368.0857953926534, backtracks = 1, tol = 0.00013415908612772554 Iteration 34: loglikelihood = -1367.2905405497556, backtracks = 1, tol = 0.00019301150424084934 Iteration 35: loglikelihood = -1366.5935312268316, backtracks = 1, tol = 0.0002170988645326748 Iteration 36: loglikelihood = -1365.9781847206004, backtracks = 1, tol = 0.00022047744005930918 Iteration 37: loglikelihood = -1365.4315048628653, backtracks = 1, tol = 0.00021444875555378602 Iteration 38: loglikelihood = -1365.0014256036795, backtracks = 1, tol = 0.00020458899431428416 Iteration 39: loglikelihood = -1364.6152946596094, backtracks = 1, tol = 0.0001832195969421286 Iteration 40: loglikelihood = -1364.2656067803177, backtracks = 1, tol = 0.0001670973015327379 Iteration 41: loglikelihood = -1363.9476977914906, backtracks = 1, tol = 0.0001543449759952092 Iteration 42: loglikelihood = -1363.6578087921637, backtracks = 1, tol = 0.00014384119765524755 Iteration 43: loglikelihood = -1363.3927554745944, backtracks = 1, tol = 0.00013487030117125627 Iteration 44: loglikelihood = -1363.1497993539713, backtracks = 1, tol = 0.00012698998002013944 Iteration 45: loglikelihood = -1362.9265683554215, backtracks = 1, tol = 0.00011993049271306849 Iteration 46: loglikelihood = -1362.7209987932931, backtracks = 1, tol = 0.00011352412872288082 Iteration 47: loglikelihood = -1362.5312892225386, backtracks = 1, tol = 0.00010766156174253752 Iteration 48: loglikelihood = -1362.3558622400903, backtracks = 1, tol = 0.00010226669310252135 Iteration 49: loglikelihood = -1362.1933323786718, backtracks = 1, tol = 9.728274295488289e-5 0.517057 seconds (2.27 M allocations: 41.955 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 = -3580.2654, backtracks = 0, tol = 0.09420144040445047 Iteration 2: loglikelihood = -3521.0918, backtracks = 0, tol = 0.0535102626196933 Iteration 3: loglikelihood = -3514.592, backtracks = 1, tol = 0.018457228599641606 Iteration 4: loglikelihood = -3499.256, backtracks = 1, tol = 0.07468796147755528 Iteration 5: loglikelihood = -3496.3628, backtracks = 1, tol = 0.00619791909922397 Iteration 6: loglikelihood = -3495.2927, backtracks = 1, tol = 0.004764260265210837 Iteration 7: loglikelihood = -3494.9485, backtracks = 1, tol = 0.0039291402320885335 Iteration 8: loglikelihood = -3494.8481, backtracks = 1, tol = 0.0023427144988186384 Iteration 9: loglikelihood = -3494.8235, backtracks = 1, tol = 0.0012757387842646376 Iteration 10: loglikelihood = -3494.8193, backtracks = 1, tol = 0.0006340613742201139 Iteration 11: loglikelihood = -3494.8171, backtracks = 2, tol = 0.00016263766232166795 Iteration 12: loglikelihood = -3494.8213, backtracks = 3, tol = 6.0527553916524666e-5 20.436515 seconds (15.57 M allocations: 676.815 MiB, 5.16% gc time, 94.05% 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 = -3459.6536, backtracks = 0, tol = 0.09420144040445047 Iteration 2: loglikelihood = -3325.67, backtracks = 0, tol = 0.05533024483662022 Iteration 3: loglikelihood = -3129.5295, backtracks = 1, tol = 0.017478462314671067 Iteration 4: loglikelihood = -2900.929, backtracks = 1, tol = 0.009107529280278902 Iteration 5: loglikelihood = -2882.7563, backtracks = 0, tol = 0.1145501267613021 Iteration 6: loglikelihood = -2656.6926, backtracks = 0, tol = 0.10168737788438507 Iteration 7: loglikelihood = -2536.9143, backtracks = 0, tol = 0.08704933710613433 Iteration 8: loglikelihood = -2436.8567, backtracks = 0, tol = 0.09416515387125926 Iteration 9: loglikelihood = -2338.4355, backtracks = 0, tol = 0.09453371271265582 Iteration 10: loglikelihood = -2268.5808, backtracks = 0, tol = 0.09950904090259816 Iteration 11: loglikelihood = -2208.521, backtracks = 0, tol = 0.09849400620173691 Iteration 12: loglikelihood = -2172.8047, backtracks = 0, tol = 0.10037450764309004 Iteration 13: loglikelihood = -2145.4531, backtracks = 0, tol = 0.10130960560654398 Iteration 14: loglikelihood = -2132.9924, backtracks = 0, tol = 0.10435160177147405 Iteration 15: loglikelihood = -2120.9055, backtracks = 0, tol = 0.10527531755848371 Iteration 16: loglikelihood = -2113.5544, backtracks = 1, tol = 0.01349595560169268 Iteration 17: loglikelihood = -2111.7373, backtracks = 1, tol = 0.006225040876318849 Iteration 18: loglikelihood = -2111.2966, backtracks = 1, tol = 0.0027566754281989135 Iteration 19: loglikelihood = -2111.1863, backtracks = 1, tol = 0.001448623030018748 Iteration 20: loglikelihood = -2111.1582, backtracks = 1, tol = 0.0007901214947853113 Iteration 21: loglikelihood = -2111.151, backtracks = 1, tol = 0.0004312115424396007 Iteration 22: loglikelihood = -2111.1482, backtracks = 1, tol = 0.0002361210176812922 Iteration 23: loglikelihood = -2111.1467, backtracks = 1, tol = 0.00012980111226594418 Iteration 24: loglikelihood = -2111.1455, backtracks = 1, tol = 7.156435805653549e-5 0.189967 seconds (1.35 M allocations: 22.361 MiB, 11.21% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 24.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 4.170312 seconds (1.11 M allocations: 137.683 MiB, 0.57% gc time, 90.69% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.5s 9.825072 seconds (4.00 M allocations: 82.482 MiB, 0.89% gc time, 0.60% compilation time) 5.609481 seconds (3.98 M allocations: 91.675 MiB, 0.18% gc time) 10.371098 seconds (20.40 M allocations: 439.318 MiB, 0.72% gc time, 17.36% compilation time: 78% of which was recompilation) 8.453208 seconds (20.18 M allocations: 434.188 MiB, 0.89% gc time) 40.807589 seconds (3.71 M allocations: 4.237 GiB, 10.82% gc time, 29.08% compilation time) 52.706671 seconds (71.97 k allocations: 183.459 MiB, 0.17% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m26.3s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.885 ms (78 allocations: 4.56 KiB) 4.953 μs (0 allocations: 0 bytes) 144.598 μs (4 allocations: 288 bytes) 6.562 μs (0 allocations: 0 bytes) 47.160 μs (2 allocations: 64 bytes) 40.549 μs (0 allocations: 0 bytes) 32.249 μs (0 allocations: 0 bytes) 28.670 μs (0 allocations: 0 bytes) 74.759 μs (0 allocations: 0 bytes) 37.913 ms (78 allocations: 4.56 KiB) 26.210 μs (0 allocations: 0 bytes) 163.829 μs (4 allocations: 288 bytes) 33.240 μs (0 allocations: 0 bytes) 195.628 μs (2 allocations: 64 bytes) 76.760 μs (0 allocations: 0 bytes) 157.889 μs (0 allocations: 0 bytes) 148.658 μs (0 allocations: 0 bytes) 186.248 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m31.7s **** 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 **** **** 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 0.423110 seconds (49.12 k allocations: 5.471 MiB, 62.12% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 2.003414 seconds (312.45 k allocations: 169.955 MiB, 61.07% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:35 Cross validating... 19%|██████▏ | ETA: 0:00:34 Cross validating... 22%|███████▏ | ETA: 0:00:28 Cross validating... 25%|████████▏ | ETA: 0:00:24 Cross validating... 29%|█████████▏ | ETA: 0:00:21 Cross validating... 32%|██████████▏ | ETA: 0:00:18 Cross validating... 35%|███████████▏ | ETA: 0:00:16 Cross validating... 38%|████████████▎ | ETA: 0:00:14 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross 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ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 2617.463263034232 1 1760.391339207103 2 1114.4063609459022 3 860.6658537838015 4 701.6798544955564 5 589.5267847850876 6 442.7921798028327 7 386.8839960071272 8 344.676946412348 9 346.74610743809643 10 347.16208814862466 11 351.5727092045743 12 354.76436855432473 13 354.6579534929626 14 363.35844531330224 15 363.39433164191536 16 377.0906553850649 17 388.27209203361843 18 376.0335209119552 19 394.26798830437724 20 412.53411192682177 Best k = 8 12.081111 seconds (11.65 M allocations: 305.178 MiB, 1.23% gc time, 59.73% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:03 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: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 2617.463263034232 1 1760.4321486786453 2 1122.9843370679368 3 866.6367008864718 4 705.6741861953311 5 594.6398912336523 6 445.17962557136605 7 390.8515843975397 8 349.30173510516397 9 356.85386359403196 10 361.67459850716784 11 369.98558645414954 12 377.6020917457289 13 373.138710353791 14 392.6167874568147 15 387.0637002052024 16 398.97399739787596 17 400.20676494487793 18 409.8916271400341 19 415.49925352700245 20 425.34271144524956 Best k = 8 4.947840 seconds (10.90 M allocations: 230.123 MiB, 0.91% gc time, 0.98% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.8s **** 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: 0:06:36 Cross validating... 8%|██▌ | ETA: 0:02:32 Cross validating... 13%|████▏ | ETA: 0:01:31 Cross validating... 17%|█████▋ | ETA: 0:01:03 Cross validating... 24%|███████▋ | ETA: 0:00:43 Cross validating... 29%|█████████▏ | ETA: 0:00:34 Cross validating... 33%|██████████▋ | ETA: 0:00:28 Cross validating... 37%|███████████▋ | ETA: 0:00:24 Cross validating... 41%|█████████████▎ | ETA: 0:00:20 Cross validating... 46%|██████████████▊ | ETA: 0:00:17 Cross validating... 51%|████████████████▎ | ETA: 0:00:14 Cross validating... 56%|█████████████████▊ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 65%|████████████████████▉ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1667.3269691162109 1 1416.8696794433595 2 1219.6492606201173 3 837.5181452636718 4 639.1953747558593 5 514.1645998535157 6 449.9824120178223 7 381.5622163085938 8 355.3608440246582 9 340.0385462341309 10 343.3624700012207 11 344.5002289428711 12 350.27699954223635 13 354.6472818603516 14 367.51775128173836 15 357.3786489257813 16 360.6690642700196 17 368.67202145385744 18 383.636067779541 19 385.1969910888672 20 411.63512042236323 Best k = 9 16.542745 seconds (12.42 M allocations: 307.376 MiB, 0.50% gc time, 84.80% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:00 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1667.3269691162109 1 1416.889658935547 2 1219.6492606201173 3 849.7257475585939 4 642.1350079345704 5 521.0572789916993 6 449.9827102050782 7 385.9804890441895 8 362.5136831054688 9 347.521581237793 10 359.1976682434082 11 366.2077940063477 12 377.8561004943848 13 385.28836389160153 14 395.73806262207034 15 393.07064657592775 16 403.91471716308604 17 404.5001268920899 18 417.8003975219727 19 421.71743927001955 20 410.04247714233395 Best k = 9 2.546972 seconds (10.78 M allocations: 198.474 MiB, 1.95% gc time, 1.58% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:54 Cross validating... 6%|██ | ETA: 0:00:29 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.2081212650693 1 380.5132193060265 2 335.06284861479674 3 327.84228643878083 4 319.86670170550224 5 315.1350891570277 6 304.6508548006966 7 298.94903028579364 8 300.75783376884635 9 298.17620677325 10 302.30442242217276 11 302.96679570295936 12 331.04388898715285 13 313.70225178136405 14 315.1796335788771 15 307.70039970676737 16 319.26027107008605 17 314.96038710942315 18 315.68946259998717 19 313.91957857798957 20 321.49805274907453 Best k = 9 8.064230 seconds (17.78 M allocations: 421.634 MiB, 1.14% gc time, 28.67% 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: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.2081212650693 1 380.54658623358534 2 335.4245445667588 3 328.1693414309 4 327.8050283933194 5 317.3798149509989 6 306.33974462366933 7 317.72026750851893 8 306.228787631834 9 309.0701564822851 10 322.4942475255775 11 331.9185108121143 12 338.725779332718 13 337.28469135207627 14 352.53664026730803 15 343.43822962608203 16 366.4733212762287 17 362.6688716520231 18 358.7443943406899 19 384.2365459612197 20 384.6293418673549 Best k = 8 5.838533 seconds (17.75 M allocations: 369.744 MiB, 1.24% gc time, 0.95% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 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 0 466.0560569622917 1 433.2021049653916 2 396.9512757882994 3 369.9731308827761 4 355.13748540214 5 329.5505970082098 6 324.22479759787626 7 327.5087078627582 8 325.91381364130143 9 331.34497405563314 10 335.3919306510668 11 339.04134515786427 12 336.67378790714423 13 330.48401849129635 14 331.90973501961696 15 357.98097758444464 16 330.679294094433 17 357.3068471574123 18 357.09269774067457 19 366.09935211247614 20 343.47409273881976 Best k = 6 7.525967 seconds (16.83 M allocations: 400.643 MiB, 12.57% gc time, 32.63% 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... 3%|█ | ETA: 0:00:05 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: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 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... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 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 0 466.0560569622917 1 433.3561842241119 2 397.1497661548106 3 370.58391852744296 4 357.2460799074597 5 331.94030542754024 6 328.03549231294375 7 331.69302362470347 8 343.61403817139353 9 360.0350105948622 10 363.50222443139717 11 378.5905746314103 12 382.54341890210344 13 376.08453972220633 14 374.70105158273725 15 409.2418563496783 16 401.44929184472755 17 404.1902853110457 18 411.33541534626136 19 441.7998012492634 20 433.1344913482948 Best k = 6 4.454717 seconds (17.40 M allocations: 357.640 MiB, 2.19% gc time, 0.89% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 775.3632067670897 1 688.1445368039196 2 554.0733204583385 3 460.95004946812713 4 433.5706882583679 5 426.12725866690755 6 410.8636607957215 7 414.76109958637073 8 416.3441506769076 9 413.6542276836263 10 404.59065644541135 11 414.40610857473666 12 415.8624672700467 13 413.12572029560835 14 412.8259528850032 15 414.4036696581078 16 417.17743852376594 17 427.47582241761785 18 416.52127275164685 19 411.1024456344002 20 419.01394459369834 Best k = 10 8.037332 seconds (14.63 M allocations: 344.036 MiB, 1.01% gc time, 31.18% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 775.3632067670897 1 664.7150678297722 2 551.5770738183802 3 461.2778504251692 4 430.713352343103 5 423.1983746710402 6 424.39806691530623 7 420.8858921678242 8 431.7991346271434 9 424.91545780804535 10 427.4310548070436 11 434.41317916527976 12 438.4346502704493 13 439.6479215773253 14 442.39104879470233 15 446.09218204490276 16 449.4026016025839 17 457.6135463034937 18 461.33214444533075 19 454.2931656049759 20 461.0052743440119 Best k = 7 5.566854 seconds (13.70 M allocations: 271.229 MiB, 1.63% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 5%|█▌ | ETA: 0:00:43 Cross validating... 6%|██ | ETA: 0:00:47 Cross validating... 8%|██▌ | ETA: 0:00:38 Cross validating... 10%|███ | ETA: 0:00:33 Cross validating... 11%|███▌ | ETA: 0:00:36 Cross validating... 13%|████▏ | ETA: 0:00:38 Cross validating... 14%|████▋ | ETA: 0:00:39 Cross validating... 16%|█████▏ | ETA: 0:00:40 Cross validating... 17%|█████▋ | ETA: 0:00:41 Cross validating... 19%|██████▏ | ETA: 0:00:42 Cross validating... 21%|██████▋ | ETA: 0:00:42 Cross validating... 22%|███████▏ | ETA: 0:00:42 Cross validating... 24%|███████▋ | ETA: 0:00:39 Cross validating... 25%|████████▏ | ETA: 0:00:39 Cross validating... 27%|████████▋ | ETA: 0:00:38 Cross 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0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:43 Crossvalidation Results: k MSE 0 367.32793856074557 1 302.3538669880218 2 254.10909562768535 3 245.6405032639131 4 226.0456904695693 5 222.95699492974467 6 220.01516028247823 7 214.96753218769481 8 215.71864817540927 9 216.46618833036786 10 221.7037870826066 11 222.42124331562826 12 223.70825375233426 13 225.0867297601136 14 226.9008312682741 15 224.13286761485966 16 223.4988470141311 17 228.47319580087526 18 232.5353022995099 19 231.60295246277673 20 226.8132796339595 Best k = 7 43.457796 seconds (135.22 M allocations: 3.468 GiB, 1.17% gc time, 4.82% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:07 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 10%|███ | ETA: 0:00:09 Cross validating... 11%|███▌ | ETA: 0:00:10 Cross validating... 13%|████▏ | ETA: 0:00:10 Cross validating... 14%|████▋ | ETA: 0:00:10 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 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ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 367.32793856074557 1 303.30820821938 2 255.73428425265303 3 247.05846203900046 4 235.80700284619093 5 225.41855252374177 6 222.6410660595388 7 226.2110226500975 8 223.72278634546933 9 230.5927244794556 10 235.47785422055892 11 236.39250583665375 12 240.35106821764649 13 246.26162701974937 14 246.10080403844296 15 249.73862474139088 16 253.82193875840846 17 259.97684856348803 18 255.17711789677247 19 266.670152325125 20 267.9361909524237 Best k = 6 11.838256 seconds (36.49 M allocations: 750.838 MiB, 1.18% gc time, 0.48% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 55.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross 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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 6.051055 seconds (17.00 M allocations: 337.796 MiB, 1.55% gc time, 42.98% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross 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228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.280047 seconds (16.17 M allocations: 286.692 MiB, 1.83% gc time, 1.67% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.8s **** 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... 2%|▋ | ETA: 0:01:19 Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 4%|█▎ | ETA: 0:00:46 Cross validating... 5%|█▋ | ETA: 0:00:40 Cross validating... 6%|█▉ | ETA: 0:00:36 Cross validating... 7%|██▎ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:31 Cross validating... 9%|██▉ | ETA: 0:00:29 Cross validating... 10%|███▎ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:26 Cross validating... 12%|███▉ | 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validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:20 Crossvalidation Results: k MSE 1 2368.1711993524796 2 2111.134264790503 3 1995.1263172858924 4 1760.6232999893425 5 1469.2166141352811 6 1381.744386779238 7 1315.047447036143 8 1316.291772767463 9 1312.8849651164257 10 1318.081212480818 11 1310.621262827564 12 1321.3713634069184 13 1332.406006075972 14 1349.046966397191 15 1366.2215872558945 16 1355.9404921201863 17 1375.5285072363445 18 1385.7792626087337 19 1401.4215867540825 20 1417.7615205121713 Best k = 11 20.328299 seconds (354.33 k allocations: 247.428 MiB, 0.53% gc time, 7.70% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 25.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m46.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 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 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... 20%|██████▍ | ETA: 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58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 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 **** 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 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | ETA: 0:00:17 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 Cross validating... 29%|█████████▎ | ETA: 0:00:16 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 31%|█████████▉ | ETA: 0:00:16 Cross validating... 32%|██████████▎ | ETA: 0:00:16 Cross validating... 33%|██████████▌ | ETA: 0:00:16 Cross validating... 34%|██████████▉ | ETA: 0:00:15 Cross validating... 35%|███████████▎ | ETA: 0:00:15 Cross validating... 36%|███████████▌ | ETA: 0:00:15 Cross validating... 37%|███████████▉ | ETA: 0:00:15 Cross validating... 38%|████████████▏ | ETA: 0:00:15 Cross validating... 39%|████████████▌ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 41%|█████████████▏ | ETA: 0:00:14 Cross validating... 42%|█████████████▌ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:12 Cross validating... 50%|████████████████ | ETA: 0:00:11 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:11 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 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: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 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 **** 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: 0:00:16 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... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:19 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | ETA: 0:00:17 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 Cross validating... 29%|█████████▎ | ETA: 0:00:16 Cross validating... 30%|█████████▋ | ETA: 0:00:16 Cross validating... 31%|█████████▉ | ETA: 0:00:16 Cross validating... 32%|██████████▎ | ETA: 0:00:16 Cross validating... 33%|██████████▌ | ETA: 0:00:16 Cross validating... 34%|██████████▉ | ETA: 0:00:16 Cross validating... 35%|███████████▎ | ETA: 0:00:16 Cross validating... 36%|███████████▌ | ETA: 0:00:15 Cross validating... 37%|███████████▉ | ETA: 0:00:15 Cross validating... 38%|████████████▏ | ETA: 0:00:15 Cross validating... 39%|████████████▌ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 41%|█████████████▏ | ETA: 0:00:14 Cross validating... 42%|█████████████▌ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:14 Cross validating... 44%|██████████████▏ | ETA: 0:00:13 Cross validating... 45%|██████████████▍ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 47%|███████████████ | ETA: 0:00:12 Cross validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:12 Cross validating... 50%|████████████████ | ETA: 0:00:12 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:11 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 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 1m27.3s 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] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.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:2244 [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:310 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:489 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 4.5s RNG of the outermost testset: Xoshiro(0xb18eea44e1dab265, 0x93f8e4691f1a74e2, 0x4359844f7b3f69f5, 0xf5f859bbd72ac311, 0x7803a1308992784b) 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 1122.79s 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:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [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] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1247.34s: package tests unexpectedly errored