Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2462 (fcc4213c48*) started at 2026-07-01T00:54:42.101 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.4s ################################################################################ # 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 v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.27.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.9 [f70d9fcc] + CommonWorldInvalidations v1.1.0 [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 v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.5+2 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.4+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.7+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.9s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.8 s ✓ BGEN 8.3 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 24.6 s ✓ MendelIHT 3 dependencies successfully precompiled in 40 seconds. 172 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 64.46s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_c15fF0/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.129 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 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nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/XAng5/src/multivariate/mvnormal.jl:207 ┌ 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 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 15.3s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 9.9s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.2s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** 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 = -1552.6161397543517, backtracks = 0, tol = 1.7579951543805101 Iteration 2: loglikelihood = -1429.808417221032, backtracks = 0, tol = 0.16111356087265716 Iteration 3: loglikelihood = -1425.229030304992, backtracks = 0, tol = 0.05763434958275648 Iteration 4: loglikelihood = -1424.9561392431347, backtracks = 0, tol = 0.004943442075807518 Iteration 5: loglikelihood = -1424.953271259867, backtracks = 1, tol = 0.00029493194761905984 Iteration 6: loglikelihood = -1424.9525096115322, backtracks = 1, tol = 0.00014241984893951517 Iteration 7: loglikelihood = -1424.9523097584558, backtracks = 1, tol = 6.786703820209071e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06378602981567383 Final loglikelihood: -1424.9523097584558 SNP PVE: 0.9293776907329964 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 2956 -0.123805 2 │ 3287 -0.950952 3 │ 3603 0.8465 4 │ 4369 1.63876 5 │ 5319 -1.08641 6 │ 6361 0.450547 7 │ 6608 0.868145 8 │ 8936 1.29332 9 │ 9430 1.49689 10 │ 9830 1.90154 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0347041Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2568.6543776487933, backtracks = 0, tol = 0.34591595277022047 Iteration 2: loglikelihood = -1610.7337218239502, backtracks = 0, tol = 0.07391985510818745 Iteration 3: loglikelihood = -1428.5587984847896, backtracks = 0, tol = 0.06773828402601495 Iteration 4: loglikelihood = -1380.2649941784914, backtracks = 0, tol = 0.09630658359553015 Iteration 5: loglikelihood = -1357.1416294805526, backtracks = 0, tol = 0.03592766996307488 Iteration 6: loglikelihood = -1344.7886337113623, backtracks = 0, tol = 0.04045131800902021 Iteration 7: loglikelihood = -1336.4328859191403, backtracks = 0, tol = 0.027663688391635986 Iteration 8: loglikelihood = -1331.5352198342684, backtracks = 0, tol = 0.021702579448698692 Iteration 9: loglikelihood = -1324.9390366583134, backtracks = 0, tol = 0.06064156359011749 Iteration 10: loglikelihood = -1323.3540960412377, backtracks = 0, tol = 0.014621287961332784 Iteration 11: loglikelihood = -1322.4859808959263, backtracks = 0, tol = 0.00778418833804231 Iteration 12: loglikelihood = -1321.9673168082857, backtracks = 0, tol = 0.00860153307721787 Iteration 13: loglikelihood = -1321.6320941696474, backtracks = 0, tol = 0.004777590962995588 Iteration 14: loglikelihood = -1321.421359929193, backtracks = 0, tol = 0.005317421979745443 Iteration 15: loglikelihood = -1321.2859997932062, backtracks = 0, tol = 0.0030424152700480977 Iteration 16: loglikelihood = -1321.2011487937039, backtracks = 0, tol = 0.003300341486157869 Iteration 17: loglikelihood = -1321.1472785574167, backtracks = 0, tol = 0.0020051072898791445 Iteration 18: loglikelihood = -1321.1136825035082, backtracks = 0, tol = 0.002046825459893244 Iteration 19: loglikelihood = -1321.0925596157078, backtracks = 0, tol = 0.00129001383736201 Iteration 20: loglikelihood = -1321.0794405648226, backtracks = 0, tol = 0.0012672919024356063 Iteration 21: loglikelihood = -1321.0712502246677, backtracks = 0, tol = 0.0008169416262158808 Iteration 22: loglikelihood = -1321.0661780143535, backtracks = 0, tol = 0.0007834309100827711 Iteration 23: loglikelihood = -1321.0630265267575, backtracks = 0, tol = 0.0005120947799582927 Iteration 24: loglikelihood = -1321.0610785615072, backtracks = 0, tol = 0.00048374558867376023 Iteration 25: loglikelihood = -1321.0598720291923, backtracks = 0, tol = 0.00031892138118168724 Iteration 26: loglikelihood = -1321.0591271747762, backtracks = 0, tol = 0.0002984577173937022 Iteration 27: loglikelihood = -1321.0586667489351, backtracks = 0, tol = 0.0001978055769581086 Iteration 28: loglikelihood = -1321.0583827248288, backtracks = 0, tol = 0.0001840424003673044 Iteration 29: loglikelihood = -1321.0582073789267, backtracks = 0, tol = 0.00012237235793116885 Iteration 30: loglikelihood = -1321.0580992653286, backtracks = 0, tol = 0.00011345017106918233 Iteration 31: loglikelihood = -1321.0580325726046, backtracks = 0, tol = 7.558554980602119e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1679.315596536357, backtracks = 0, tol = 0.3178232441761658 Iteration 2: loglikelihood = -1567.4164063171177, backtracks = 0, tol = 0.19575066082271855 Iteration 3: loglikelihood = -1545.3163763877626, backtracks = 0, tol = 0.1320671646356225 Iteration 4: loglikelihood = -1539.6163054913925, backtracks = 0, tol = 0.08925205283411874 Iteration 5: loglikelihood = -1538.3901945946027, backtracks = 0, tol = 0.02157767641330456 Iteration 6: loglikelihood = -1538.3447690492035, backtracks = 1, tol = 0.00284715649946751 Iteration 7: loglikelihood = -1538.3295906458948, backtracks = 1, tol = 0.002304410247171278 Iteration 8: loglikelihood = -1538.3255178228903, backtracks = 1, tol = 0.0013595744377296922 Iteration 9: loglikelihood = -1538.32449295057, backtracks = 1, tol = 0.0006886873795040834 Iteration 10: loglikelihood = -1538.3242389769014, backtracks = 1, tol = 0.00034604423672929594 Iteration 11: loglikelihood = -1538.3241761461031, backtracks = 1, tol = 0.00017182581016234697 Iteration 12: loglikelihood = -1538.3241606169786, backtracks = 1, tol = 8.550670435872761e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1853.7973098161258, backtracks = 0, tol = 0.8259588901869603 Iteration 2: loglikelihood = -1475.6605293261493, backtracks = 0, tol = 0.13275243720378882 Iteration 3: loglikelihood = -1418.2645885666075, backtracks = 0, tol = 0.05465528985540708 Iteration 4: loglikelihood = -1411.0951194732347, backtracks = 0, tol = 0.027836060449589903 Iteration 5: loglikelihood = -1410.7760894116113, backtracks = 0, tol = 0.002679488071866671 Iteration 6: loglikelihood = -1410.7732902140842, backtracks = 0, tol = 0.00033082438313070226 Iteration 7: loglikelihood = -1410.7732551248628, backtracks = 0, tol = 4.0143349305257325e-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 = -1631.7391864773265, backtracks = 0, tol = 0.4937280832221104 Iteration 2: loglikelihood = -1439.4947924552607, backtracks = 0, tol = 0.11188091435885855 Iteration 3: loglikelihood = -1411.1251456271875, backtracks = 0, tol = 0.0447622270146656 Iteration 4: loglikelihood = -1410.781131433829, backtracks = 0, tol = 0.0033629536127878397 Iteration 5: loglikelihood = -1410.7788602132405, backtracks = 0, tol = 0.00038633479581338747 Iteration 6: loglikelihood = -1410.7788397687864, backtracks = 0, tol = 2.785883223192417e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 11.1s **** 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 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 = -1502.409963851545, backtracks = 0, tol = 0.16855347211173824 Iteration 2: loglikelihood = -1450.2425909286644, backtracks = 0, tol = 0.08943754194301608 Iteration 3: loglikelihood = -1413.291396747708, backtracks = 0, tol = 0.09414973604994907 Iteration 4: loglikelihood = -1401.1824923830914, backtracks = 0, tol = 0.08324978117869396 Iteration 5: loglikelihood = -1394.1119266675973, backtracks = 0, tol = 0.0938373087969416 Iteration 6: loglikelihood = -1392.7491690946626, backtracks = 0, tol = 0.0181986612808526 Iteration 7: loglikelihood = -1392.3930749925808, backtracks = 1, tol = 0.007040583578080984 Iteration 8: loglikelihood = -1392.1850347496427, backtracks = 2, tol = 0.0046005597485422375 Iteration 9: loglikelihood = -1392.0532556213343, backtracks = 2, tol = 0.0040148553413499365 Iteration 10: loglikelihood = -1391.9727632174233, backtracks = 2, tol = 0.0034267518653932987 Iteration 11: loglikelihood = -1387.340865630264, backtracks = 2, tol = 0.06414636535496887 Iteration 12: loglikelihood = -1385.0047554795772, backtracks = 0, tol = 0.03236350692413106 Iteration 13: loglikelihood = -1384.5885677503495, backtracks = 0, tol = 0.011075465324278846 Iteration 14: loglikelihood = -1384.4815784535283, backtracks = 0, tol = 0.007191127150423665 Iteration 15: loglikelihood = -1384.450694030996, backtracks = 0, tol = 0.003685049712919104 Iteration 16: loglikelihood = -1384.4403908579404, backtracks = 0, tol = 0.0019075881583923504 Iteration 17: loglikelihood = -1384.4369053444746, backtracks = 0, tol = 0.0012566274808775983 Iteration 18: loglikelihood = -1384.435704201084, backtracks = 0, tol = 0.0005990094930415084 Iteration 19: loglikelihood = -1384.4352915165514, backtracks = 0, tol = 0.000430208900590107 Iteration 20: loglikelihood = -1384.4351498112048, backtracks = 0, tol = 0.00020062736862992068 Iteration 21: loglikelihood = -1384.4351013144556, backtracks = 0, tol = 0.00014666471735163677 Iteration 22: loglikelihood = -1384.4350847649825, backtracks = 0, tol = 6.822946448337284e-5 1.121257 seconds (3.38 M allocations: 62.586 MiB, 58.80% 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 **** 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 = -1545.3553220684664, backtracks = 0, tol = 0.16855347211173824 Iteration 2: loglikelihood = -1502.4276622544587, backtracks = 0, tol = 0.11425396886940374 Iteration 3: loglikelihood = -1478.265056511351, backtracks = 0, tol = 0.09745227430628324 Iteration 4: loglikelihood = -1464.3374765155522, backtracks = 0, tol = 0.04606993466415 Iteration 5: loglikelihood = -1451.1881218549156, backtracks = 0, tol = 0.11011498411444223 Iteration 6: loglikelihood = -1443.5749326467894, backtracks = 0, tol = 0.10704773599956995 Iteration 7: loglikelihood = -1435.0575464642336, backtracks = 0, tol = 0.02581431664839325 Iteration 8: loglikelihood = -1425.7396411445313, backtracks = 1, tol = 0.0027437649276669165 Iteration 9: loglikelihood = -1419.2919121840303, backtracks = 1, tol = 0.0015505343891765186 Iteration 10: loglikelihood = -1414.5584231030791, backtracks = 1, tol = 0.0008505003519140518 Iteration 11: loglikelihood = -1410.8258165848586, backtracks = 1, tol = 0.0005138813438264174 Iteration 12: loglikelihood = -1407.8338575151452, backtracks = 1, tol = 0.00043385186133023285 Iteration 13: loglikelihood = -1405.4826483733711, backtracks = 1, tol = 0.0003789206508492984 Iteration 14: loglikelihood = -1403.561256933911, backtracks = 1, tol = 0.0003357326392274965 Iteration 15: loglikelihood = -1401.9741038780692, backtracks = 1, tol = 0.00029966385325224255 Iteration 16: loglikelihood = -1400.649369168399, backtracks = 1, tol = 0.0002678335914255736 Iteration 17: loglikelihood = -1399.532842762722, backtracks = 1, tol = 0.0002393376895199979 Iteration 18: loglikelihood = -1398.5833250467415, backtracks = 1, tol = 0.00021395690887690295 Iteration 19: loglikelihood = -1397.76919888119, backtracks = 1, tol = 0.00019734227936030993 Iteration 20: loglikelihood = -1397.0659337136804, backtracks = 1, tol = 0.00018595780304431707 Iteration 21: loglikelihood = -1396.4542854219364, backtracks = 1, tol = 0.00017478884741097702 Iteration 22: loglikelihood = -1395.918996378973, backtracks = 1, tol = 0.00016411928919134094 Iteration 23: loglikelihood = -1395.447849806532, backtracks = 1, tol = 0.00015408795902697382 Iteration 24: loglikelihood = -1395.0309745709712, backtracks = 1, tol = 0.00014474813302418622 Iteration 25: loglikelihood = -1394.6603280112922, backtracks = 1, tol = 0.0001361035631335989 Iteration 26: loglikelihood = -1394.3293065842938, backtracks = 1, tol = 0.0001281301534028222 Iteration 27: loglikelihood = -1394.0324493884655, backtracks = 1, tol = 0.0001207890075742021 Iteration 28: loglikelihood = -1393.7342223733156, backtracks = 1, tol = 0.00011403430244962051 Iteration 29: loglikelihood = -1393.493959047635, backtracks = 1, tol = 0.00011328038801577702 Iteration 30: loglikelihood = -1393.2498674016229, backtracks = 1, tol = 0.00010529789380153244 Iteration 31: loglikelihood = -1393.0274374730236, backtracks = 1, tol = 0.0001036670788752931 Iteration 32: loglikelihood = -1392.8257247780787, backtracks = 1, tol = 0.00010106393130475442 Iteration 33: loglikelihood = -1392.642671446342, backtracks = 1, tol = 9.755925843409226e-5 0.447037 seconds (1.66 M allocations: 31.041 MiB, 12.83% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3540.8022, backtracks = 0, tol = 0.08193434884005275 Iteration 2: loglikelihood = -3496.742, backtracks = 0, tol = 0.04415081087849885 Iteration 3: loglikelihood = -3474.9358, backtracks = 1, tol = 0.059936477938006015 Iteration 4: loglikelihood = -3468.9414, backtracks = 1, tol = 0.01535471105805998 Iteration 5: loglikelihood = -3466.8943, backtracks = 1, tol = 0.009015759510383742 Iteration 6: loglikelihood = -3466.2974, backtracks = 1, tol = 0.004450259470654379 Iteration 7: loglikelihood = -3466.125, backtracks = 1, tol = 0.0026462980294549364 Iteration 8: loglikelihood = -3466.086, backtracks = 1, tol = 0.001471491856039676 Iteration 9: loglikelihood = -3466.0752, backtracks = 1, tol = 0.0007718120805369127 Iteration 10: loglikelihood = -3466.0715, backtracks = 1, tol = 0.00039793196440158964 Iteration 11: loglikelihood = -3466.0742, backtracks = 3, tol = 5.048184249059594e-5 27.077840 seconds (13.72 M allocations: 647.487 MiB, 1.27% gc time, 97.59% 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 = -3435.617, backtracks = 0, tol = 0.08193434884005275 Iteration 2: loglikelihood = -3322.5793, backtracks = 0, tol = 0.04553825445770038 Iteration 3: loglikelihood = -3145.2256, backtracks = 1, tol = 0.013907933894763504 Iteration 4: loglikelihood = -2927.0325, backtracks = 1, tol = 0.0072568976943577865 Iteration 5: loglikelihood = -2913.7327, backtracks = 0, tol = 0.11086122597292686 Iteration 6: loglikelihood = -2687.0046, backtracks = 0, tol = 0.11020687574662001 Iteration 7: loglikelihood = -2559.7375, backtracks = 0, tol = 0.08771807769922067 Iteration 8: loglikelihood = -2456.0352, backtracks = 0, tol = 0.08975707492830763 Iteration 9: loglikelihood = -2369.3525, backtracks = 0, tol = 0.08984787751447541 Iteration 10: loglikelihood = -2295.512, backtracks = 0, tol = 0.09083035667067499 Iteration 11: loglikelihood = -2237.8672, backtracks = 0, tol = 0.09054916508185626 Iteration 12: loglikelihood = -2210.6667, backtracks = 0, tol = 0.10701264907739183 Iteration 13: loglikelihood = -2186.0288, backtracks = 0, tol = 0.12584289513837896 Iteration 14: loglikelihood = -2158.7559, backtracks = 0, tol = 0.10937051630443352 Iteration 15: loglikelihood = -2154.9365, backtracks = 0, tol = 0.11020374505901111 Iteration 16: loglikelihood = -2141.7742, backtracks = 0, tol = 0.11177065201624602 Iteration 17: loglikelihood = -2134.6162, backtracks = 1, tol = 0.015907271689517482 Iteration 18: loglikelihood = -2133.0981, backtracks = 1, tol = 0.005475752096468781 Iteration 19: loglikelihood = -2132.7979, backtracks = 1, tol = 0.0022056186652889462 Iteration 20: loglikelihood = -2132.754, backtracks = 1, tol = 0.0012476420011815438 Iteration 21: loglikelihood = -2132.7551, backtracks = 3, tol = 0.0001816948850798181 Iteration 22: loglikelihood = -2132.755, backtracks = 2, tol = 0.0003292074203410048 Iteration 23: loglikelihood = -2132.754, backtracks = 3, tol = 0.0001314123051946633 Iteration 24: loglikelihood = -2132.754, backtracks = 3, tol = 0.00011709461141092955 Iteration 25: loglikelihood = -2132.7517, backtracks = 3, tol = 0.00010481801143483853 Iteration 26: loglikelihood = -2132.752, backtracks = 3, tol = 9.397880647807112e-5 0.233570 seconds (1.73 M allocations: 28.889 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.7s **** 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 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 5.421968 seconds (1.02 M allocations: 132.838 MiB, 7.47% gc time, 91.09% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.9s 10.317053 seconds (4.00 M allocations: 82.389 MiB, 0.19% gc time, 0.65% compilation time) 5.362761 seconds (3.98 M allocations: 91.674 MiB, 1.19% gc time) 10.957572 seconds (20.38 M allocations: 438.640 MiB, 0.95% gc time, 17.27% compilation time: 78% of which was recompilation) 8.600826 seconds (20.18 M allocations: 434.191 MiB, 1.16% gc time) 37.739891 seconds (3.36 M allocations: 4.228 GiB, 6.79% gc time, 30.55% compilation time) 56.641822 seconds (72.50 k allocations: 183.671 MiB, 0.13% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m29.1s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.530 ms (78 allocations: 4.56 KiB) 4.437 μs (0 allocations: 0 bytes) 141.089 μs (4 allocations: 288 bytes) 6.970 μs (0 allocations: 0 bytes) 45.639 μs (2 allocations: 64 bytes) 30.970 μs (0 allocations: 0 bytes) 26.550 μs (0 allocations: 0 bytes) 29.760 μs (0 allocations: 0 bytes) 106.009 μs (0 allocations: 0 bytes) 40.536 ms (78 allocations: 4.56 KiB) 18.860 μs (0 allocations: 0 bytes) 176.158 μs (4 allocations: 288 bytes) 34.560 μs (0 allocations: 0 bytes) 253.807 μs (2 allocations: 64 bytes) 87.659 μs (0 allocations: 0 bytes) 135.629 μs (0 allocations: 0 bytes) 144.759 μs (0 allocations: 0 bytes) 228.128 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m10.3s **** 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 **** **** 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 0.447518 seconds (43.84 k allocations: 5.329 MiB, 64.52% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.989497 seconds (256.79 k allocations: 167.475 MiB, 56.23% 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:53 Cross validating... 11%|███▌ | ETA: 0:01:05 Cross validating... 14%|████▋ | ETA: 0:00:49 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ 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validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 4829.45283969235 1 3648.2509337815295 2 3018.8951411200374 3 2054.4993823750033 4 1568.405968648599 5 1170.9776922935998 6 884.397956762788 7 642.3882417427529 8 409.1450843080658 9 344.6446298125192 10 345.89531976631525 11 353.3488680858382 12 357.5486430920479 13 356.0904782933435 14 355.87457273877254 15 374.83459563613445 16 354.88977021936546 17 379.3601115416351 18 372.36725186302 19 358.96852248675134 20 373.7664010264568 Best k = 9 12.527692 seconds (11.32 M allocations: 299.568 MiB, 0.84% gc time, 62.43% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 4829.45283969235 1 3648.267761929417 2 3028.4094127228245 3 2074.3150921291085 4 1630.5275317062942 5 1194.14988651104 6 912.7630956806184 7 659.2406662233017 8 420.56630283956997 9 354.6822268162873 10 358.85109846187845 11 367.7377654220054 12 370.8448299972787 13 383.5528030463509 14 381.18379368146987 15 391.30630501182617 16 385.3723678063632 17 399.45540871049656 18 400.5238861123944 19 401.52262654111814 20 403.02030484941633 Best k = 9 4.936739 seconds (10.48 M allocations: 220.799 MiB, 1.06% gc time, 1.10% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.3s **** 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: 0:06:32 Cross validating... 8%|██▌ | ETA: 0:02:30 Cross validating... 13%|████▏ | ETA: 0:01:30 Cross validating... 17%|█████▋ | ETA: 0:01:02 Cross validating... 22%|███████▏ | ETA: 0:00:47 Cross validating... 27%|████████▋ | ETA: 0:00:37 Cross validating... 32%|██████████▏ | ETA: 0:00:29 Cross validating... 37%|███████████▋ | ETA: 0:00:24 Cross validating... 41%|█████████████▎ | ETA: 0:00:20 Cross validating... 46%|██████████████▊ | ETA: 0:00:16 Cross validating... 52%|████████████████▊ | ETA: 0:00:13 Cross validating... 57%|██████████████████▎ | ETA: 0:00:11 Cross validating... 62%|███████████████████▊ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | 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 1701.0161979980467 1 1331.4331677246093 2 1066.6850285644532 3 871.3245987548828 4 675.7144366455078 5 535.7539642333984 6 462.22304565429687 7 406.1626545410156 8 369.74731036376954 9 364.55885986328127 10 362.98892572021487 11 364.2248350830078 12 365.5668962402343 13 370.9863900756836 14 367.4814439086914 15 372.6112041625977 16 370.51961077880856 17 378.0943545532226 18 395.7695609130859 19 395.87711407470704 20 386.7190158081055 Best k = 10 16.733072 seconds (12.69 M allocations: 314.654 MiB, 0.66% gc time, 84.03% 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... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | 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 validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:00 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1701.0161979980467 1 1332.2492175292969 2 1069.476988769531 3 876.7217559814453 4 677.2629409179688 5 542.1963809204101 6 464.0144713134765 7 412.19314263916016 8 374.2117954711914 9 373.53171533203124 10 376.52163549804686 11 382.25439068603515 12 395.96486022949216 13 392.8767930908203 14 392.18424139404294 15 404.0496983642578 16 402.5355182495117 17 401.75615728759766 18 405.50115777587894 19 409.61954553222654 20 418.93616662597657 Best k = 9 2.685199 seconds (10.89 M allocations: 200.118 MiB, 1.88% gc time, 1.79% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.29767530043 1 419.2660711035219 2 383.1811559245552 3 334.2080609485923 4 302.74161005736363 5 274.194798034377 6 266.1808360248384 7 246.28050090291094 8 219.9689106679833 9 223.73802470233858 10 227.27098580881744 11 232.48956331717 12 249.06926591896828 13 261.4640583968577 14 255.6945827174937 15 248.28792573746824 16 249.88501977791634 17 279.67734529980237 18 254.4966954067006 19 245.8838116776615 20 262.1635605010324 Best k = 8 8.756697 seconds (17.58 M allocations: 417.556 MiB, 1.25% gc time, 32.18% 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: 0:00:04 Cross 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0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.29767530043 1 419.99145761785996 2 384.2213706724408 3 335.2989200985186 4 304.1440529330089 5 275.90352076826684 6 270.31737431653465 7 250.325154657043 8 226.34020778036677 9 236.9482864682727 10 246.45276548213343 11 253.0485406488482 12 264.3791405238877 13 271.6963070725275 14 265.8243770378671 15 275.2314327856662 16 281.9451600248784 17 279.7702552112629 18 294.1876833716203 19 303.3965099764932 20 309.42419411229383 Best k = 8 6.079392 seconds (18.21 M allocations: 380.453 MiB, 1.38% gc time, 1.14% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.3s **** 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: 0:00:47 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.4730396665085 1 432.2545215409162 2 393.2125076585532 3 384.5355220123233 4 362.9456362961497 5 344.9753501220589 6 342.32217603789405 7 335.4424442372927 8 335.1042784856728 9 340.2666932427733 10 356.90415714934704 11 341.5632159548057 12 358.05440450664844 13 355.0187551988389 14 354.25991768485403 15 393.6273311833254 16 390.01284187395595 17 396.0368824399336 18 388.44555815558465 19 376.97252046520254 20 378.02228815068884 Best k = 8 7.195866 seconds (16.21 M allocations: 379.125 MiB, 7.00% gc time, 38.06% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 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: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 462.4730396665085 1 433.0817601678011 2 395.1439647603262 3 388.1795560294294 4 369.849461400418 5 354.9945074541878 6 354.7599021903069 7 352.26832457431027 8 355.5897755822184 9 364.6986129008681 10 356.42167698946616 11 369.80924865796845 12 379.9271926699325 13 374.57293592231406 14 399.7635677551299 15 406.4234605535372 16 426.66303044618996 17 412.0701443230265 18 402.56522994321574 19 432.3381129301748 20 425.4489295016132 Best k = 7 4.339339 seconds (17.04 M allocations: 348.097 MiB, 2.01% gc time, 1.07% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:05 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:21 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:06 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 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 1234.7703170834097 1 1098.6487444230474 2 892.8938357659842 3 709.7799643101141 4 588.0171379154705 5 499.99488719593404 6 458.6589273344658 7 405.0014702681922 8 356.5217713769938 9 355.9622139577473 10 361.066567636168 11 367.79489622049346 12 374.80494828627707 13 366.53326126515043 14 375.8320537570678 15 379.8396242996894 16 376.4681319824955 17 362.8950932153053 18 373.42683396371723 19 362.90988597108657 20 405.24035332033094 Best k = 9 8.496557 seconds (15.88 M allocations: 375.584 MiB, 0.84% gc time, 32.71% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 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... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | 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 1234.7703170834097 1 1044.2925818869264 2 840.611846527082 3 684.4034722372865 4 578.9028916644669 5 496.8320271246022 6 464.15646474407447 7 411.8268451650758 8 362.11947363510916 9 363.3447170146882 10 366.08826242460816 11 378.1622976093699 12 377.16858695100564 13 381.5178802858363 14 386.3640329005674 15 396.8734923079764 16 398.2784914519394 17 391.7510104678038 18 415.7137007691398 19 401.9325751754278 20 420.7843369464937 Best k = 8 5.881099 seconds (14.79 M allocations: 301.241 MiB, 1.02% gc time, 1.14% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 5%|█▌ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:01:02 Cross validating... 8%|██▌ | ETA: 0:01:01 Cross validating... 10%|███ | ETA: 0:00:59 Cross validating... 11%|███▌ | ETA: 0:00:58 Cross validating... 13%|████▏ | ETA: 0:00:57 Cross validating... 14%|████▋ | ETA: 0:00:56 Cross validating... 16%|█████▏ | ETA: 0:00:55 Cross validating... 17%|█████▋ | ETA: 0:00:54 Cross validating... 19%|██████▏ | ETA: 0:00:53 Cross validating... 21%|██████▋ | ETA: 0:00:48 Cross validating... 22%|███████▏ | ETA: 0:00:48 Cross validating... 24%|███████▋ | ETA: 0:00:47 Cross validating... 25%|████████▏ | ETA: 0:00:44 Cross validating... 27%|████████▋ | ETA: 0:00:43 Cross validating... 29%|█████████▏ | ETA: 0:00:43 Cross validating... 30%|█████████▋ | ETA: 0:00:40 Cross validating... 32%|██████████▏ | ETA: 0:00:40 Cross validating... 33%|██████████▋ | ETA: 0:00:39 Cross validating... 37%|███████████▋ | ETA: 0:00:36 Cross validating... 38%|████████████▎ | ETA: 0:00:35 Cross validating... 40%|████████████▊ | ETA: 0:00:34 Cross validating... 41%|█████████████▎ | ETA: 0:00:34 Cross validating... 43%|█████████████▊ | ETA: 0:00:33 Cross validating... 44%|██████████████▎ | ETA: 0:00:32 Cross validating... 48%|███████████████▎ | ETA: 0:00:30 Cross validating... 51%|████████████████▎ | ETA: 0:00:26 Cross validating... 52%|████████████████▊ | ETA: 0:00:25 Cross validating... 54%|█████████████████▎ | ETA: 0:00:24 Cross validating... 56%|█████████████████▊ | ETA: 0:00:23 Cross validating... 57%|██████████████████▎ | ETA: 0:00:22 Cross validating... 59%|██████████████████▊ | ETA: 0:00:21 Cross validating... 60%|███████████████████▎ | ETA: 0:00:21 Cross validating... 62%|███████████████████▊ | ETA: 0:00:20 Cross validating... 63%|████████████████████▍ | ETA: 0:00:20 Cross validating... 65%|████████████████████▉ | ETA: 0:00:19 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:18 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:16 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:15 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:15 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:14 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:13 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:12 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:11 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:11 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:10 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:09 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:08 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:07 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:06 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:05 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:04 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:03 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:02 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:55 Crossvalidation Results: k MSE 0 446.9925413552694 1 384.90799692179274 2 329.7877821558852 3 283.8555120664803 4 248.9003890048283 5 226.79716075691948 6 219.85556168489953 7 207.79644263614375 8 194.17790213223464 9 195.95463119024487 10 197.9906531213955 11 199.09421199838957 12 201.03208509552007 13 202.66857047883764 14 202.6320807591856 15 203.06452431215007 16 206.55134284117372 17 206.3051355845775 18 208.29259451240756 19 206.2940505475239 20 208.52047893850624 Best k = 8 55.988570 seconds (174.51 M allocations: 4.424 GiB, 1.26% gc time, 4.09% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:07 Cross validating... 8%|██▌ | ETA: 0:00:07 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross validating... 22%|███████▏ | ETA: 0:00:06 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 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65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 446.9925413552694 1 382.6253945903936 2 327.6930078075212 3 281.62336722627674 4 248.09547315993305 5 226.93665523363396 6 221.27414136747132 7 210.29237329319415 8 195.84129617184618 9 198.9668299229764 10 205.33525755519145 11 206.84200491161653 12 209.74901006023475 13 217.24814528711337 14 218.80251191127743 15 221.23714084811553 16 225.71406771486855 17 234.84788872317625 18 231.91304347279086 19 225.32823878962083 20 241.64576779375966 Best k = 8 10.367185 seconds (30.52 M allocations: 619.867 MiB, 1.55% gc time, 0.72% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m06.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:11 Cross validating... 6%|██ | ETA: 0:00:36 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 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... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | 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... 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 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 6.323025 seconds (17.19 M allocations: 341.576 MiB, 1.31% gc time, 46.88% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 3.331010 seconds (16.26 M allocations: 288.183 MiB, 1.51% gc time, 1.98% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:30 Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 4%|█▎ | ETA: 0:00:51 Cross validating... 5%|█▋ | ETA: 0:00:43 Cross validating... 6%|█▉ | ETA: 0:00:37 Cross validating... 7%|██▎ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:30 Cross validating... 9%|██▉ | ETA: 0:00:28 Cross validating... 10%|███▎ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:25 Cross validating... 12%|███▉ | 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validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 3047.468772974202 2 2752.4005723146715 3 2217.7110858334277 4 1996.7722258877254 5 1881.4277807330197 6 1834.5815785092375 7 1835.7236160902212 8 1831.4219752467588 9 1823.3019018819361 10 1838.677956987009 11 1845.8817203780063 12 1878.5406100170921 13 1879.4020772275699 14 1900.1397980178463 15 1918.3485587954813 16 1927.9022080093312 17 1920.0802698147293 18 1940.5980522356747 19 1960.256659861429 20 1959.4485560374576 Best k = 9 18.450336 seconds (311.18 k allocations: 215.384 MiB, 0.34% gc time, 9.49% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.3s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m08.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | 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2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 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... 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validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m28.1s 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] 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 [5] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:522 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.9s RNG of the outermost testset: Xoshiro(0xeb44d9968dcdb434, 0x4f1b154c9ef53d68, 0xdf1a7b1c5fe050fa, 0x5d7c0cb839ba9cc8, 0xc27eda13de294ac6) 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 1122.69s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1228.3s: package tests unexpectedly errored