Package evaluation to test MendelIHT on Julia 1.11.8 (29b3528cce*) started at 2026-01-20T14:31:51.358 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.11` Set-up completed after 8.52s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.11/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.15 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 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 To see why use `status --outdated -m` Installation completed after 5.64s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 10654.3 ms ✓ BGEN 6500.9 ms ✓ VCFTools 206668.8 ms ✓ MendelIHT 3 dependencies successfully precompiled in 231 seconds. 170 already precompiled. Precompilation completed after 246.33s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_UMz8iM/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.2 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.10 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.11.0 [44cfe95a] Pkg v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_UMz8iM/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 [67c07d97] Automa v1.1.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools 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[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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 WARNING: using deprecated binding Distributions.MatrixReshaped in MendelIHT. , use Distributions.ReshapedDistribution{2, S, D} where D<:Distributions.Distribution{Distributions.ArrayLikeVariate{1}, S} where S<:Distributions.ValueSupport instead. ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:BlasReal, <:StridedMatrix}, ::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 13.1s Test Summary: | Pass Total Time deviance | 1 1 0.6s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 8.2s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.7s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 2.1s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1706.0485081344252, backtracks = 0, tol = 1.9903464134934614 Iteration 2: loglikelihood = -1403.6095768370674, backtracks = 0, tol = 0.146023724776058 Iteration 3: loglikelihood = -1373.147538792011, backtracks = 0, tol = 0.06338065222876181 Iteration 4: loglikelihood = -1372.5957293656152, backtracks = 0, tol = 0.006882643182059074 Iteration 5: loglikelihood = -1372.5892904481248, backtracks = 0, tol = 0.0006299119337477573 Iteration 6: loglikelihood = -1372.5891777445365, backtracks = 0, tol = 8.196623772338748e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05706906318664551 Final loglikelihood: -1372.5891777445365 SNP PVE: 0.9221145925920944 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 449 -0.29647 2 │ 682 -0.13738 3 │ 2296 -1.26833 4 │ 2624 0.740156 5 │ 3039 1.16326 6 │ 4855 -1.00922 7 │ 5440 -2.2942 8 │ 5563 -0.849637 9 │ 6068 0.35118 10 │ 6740 -0.403047 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00764676Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 20.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -357.05406929589384, backtracks = 0, tol = 0.8380082173781972 Iteration 2: loglikelihood = -253.69247673658248, backtracks = 0, tol = 0.38139022833574177 Iteration 3: loglikelihood = -242.78890265594725, backtracks = 0, tol = 0.21772646553308606 Iteration 4: loglikelihood = -211.3640910919962, backtracks = 0, tol = 0.18632794312765352 Iteration 5: loglikelihood = -206.07758041780974, backtracks = 1, tol = 0.051383518206643046 Iteration 6: loglikelihood = -204.018617087407, backtracks = 3, tol = 0.020052933740041072 Iteration 7: loglikelihood = -202.12440666162166, backtracks = 3, tol = 0.022394307327778626 Iteration 8: loglikelihood = -200.51339216597611, backtracks = 3, tol = 0.021600855513207017 Iteration 9: loglikelihood = -199.1607521139652, backtracks = 3, tol = 0.020205916063858787 Iteration 10: loglikelihood = -198.03368293305746, backtracks = 3, tol = 0.018747980180644195 Iteration 11: loglikelihood = -197.1010787346633, backtracks = 3, tol = 0.01730311555883611 Iteration 12: loglikelihood = -199.1081399043643, backtracks = 3, tol = 0.10742989707378812 Iteration 13: loglikelihood = -196.35077450026276, backtracks = 0, tol = 0.10574886891481221 Iteration 14: loglikelihood = -195.5179886251886, backtracks = 1, tol = 0.016488769010944707 Iteration 15: loglikelihood = -195.26353610431914, backtracks = 3, tol = 0.005398010607219295 Iteration 16: loglikelihood = -194.94618143558304, backtracks = 3, tol = 0.008296620982687967 Iteration 17: loglikelihood = -198.1603861597454, backtracks = 3, tol = 0.1191184942601117 Iteration 18: loglikelihood = -196.08507656080548, backtracks = 0, tol = 0.04091866505365408 Iteration 19: loglikelihood = -194.68771845520706, backtracks = 2, tol = 0.08627046961582337 Iteration 20: loglikelihood = -194.18573370488792, backtracks = 1, tol = 0.012532615214018756 Iteration 21: loglikelihood = -194.04409249060237, backtracks = 2, tol = 0.0045289192218591345 Iteration 22: loglikelihood = -193.89081161879778, backtracks = 2, tol = 0.005408550068552711 Iteration 23: loglikelihood = -197.78991514558754, backtracks = 3, tol = 0.12418846818411548 Iteration 24: loglikelihood = -195.3458651891717, backtracks = 0, tol = 0.04474686356665713 Iteration 25: loglikelihood = -193.85329270192864, backtracks = 1, tol = 0.11642705219079118 Iteration 26: loglikelihood = -193.5872888252266, backtracks = 1, tol = 0.005994529796500222 Iteration 27: loglikelihood = -193.49244103087173, backtracks = 1, tol = 0.003977497505879251 Iteration 28: loglikelihood = -193.43959542357507, backtracks = 2, tol = 0.00330084983993103 Iteration 29: loglikelihood = -197.2834449493823, backtracks = 3, tol = 0.14332949891400917 Iteration 30: loglikelihood = -191.1561814374434, backtracks = 0, tol = 0.14271551862933007 Iteration 31: loglikelihood = -190.2589777412173, backtracks = 1, tol = 0.018296148237923138 Iteration 32: loglikelihood = -189.9878891870221, backtracks = 1, tol = 0.010701165536450384 Iteration 33: loglikelihood = -189.867470684632, backtracks = 1, tol = 0.007473112269951343 Iteration 34: loglikelihood = -193.0058316555954, backtracks = 3, tol = 0.1141647124557401 Iteration 35: loglikelihood = -191.61778833782117, backtracks = 0, tol = 0.033257092226161265 Iteration 36: loglikelihood = -190.26592749131268, backtracks = 0, tol = 0.12758732776034531 Iteration 37: loglikelihood = -189.83372327320802, backtracks = 1, tol = 0.008553392013129577 Iteration 38: loglikelihood = -189.70612855593623, backtracks = 1, tol = 0.0044027459232161385 Iteration 39: loglikelihood = -189.65408637483733, backtracks = 1, tol = 0.003586549894028387 Iteration 40: loglikelihood = -189.6305816735391, backtracks = 3, tol = 0.0019965524261909384 Iteration 41: loglikelihood = -200.89359611814402, backtracks = 3, tol = 0.14583347899126511 Iteration 42: loglikelihood = -193.27097139861027, backtracks = 0, tol = 0.14535809468532176 Iteration 43: loglikelihood = -192.2935217503592, backtracks = 1, tol = 0.015904619777886927 Iteration 44: loglikelihood = -192.0507085557377, backtracks = 1, tol = 0.008141180826631752 Iteration 45: loglikelihood = -191.98876965234143, backtracks = 1, tol = 0.0042025046810855214 Iteration 46: loglikelihood = -191.9726936044892, backtracks = 1, tol = 0.0021655324830217207 Iteration 47: loglikelihood = -191.96846706923031, backtracks = 1, tol = 0.0011055332529237927 Iteration 48: loglikelihood = -191.96734266484526, backtracks = 1, tol = 0.0005555964548322557 Iteration 49: loglikelihood = -191.9670386960076, backtracks = 1, tol = 0.0002733997501911196 Iteration 50: loglikelihood = -191.96695335555074, backtracks = 1, tol = 0.00013154922168130258 Iteration 51: loglikelihood = -191.96692620413978, backtracks = 1, tol = 7.105685194739283e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 2.8s **** 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 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 = -1443.3138074366282, backtracks = 0, tol = 0.26284556457231717 Iteration 2: loglikelihood = -1370.195557660929, backtracks = 0, tol = 0.0795426095160743 Iteration 3: loglikelihood = -1346.0346100824127, backtracks = 1, tol = 0.07863886530427744 Iteration 4: loglikelihood = -1328.043634950906, backtracks = 0, tol = 0.06577167923734324 Iteration 5: loglikelihood = -1321.5668451506426, backtracks = 1, tol = 0.06514574021063788 Iteration 6: loglikelihood = -1316.9808193087174, backtracks = 0, tol = 0.02391679394731476 Iteration 7: loglikelihood = -1314.7231032549048, backtracks = 2, tol = 0.016297098255187065 Iteration 8: loglikelihood = -1313.0256510344675, backtracks = 2, tol = 0.04947452052025023 Iteration 9: loglikelihood = -1311.4134192367378, backtracks = 1, tol = 0.012060770164303713 Iteration 10: loglikelihood = -1310.6386938142346, backtracks = 2, tol = 0.008830996562509399 Iteration 11: loglikelihood = -1310.2891051585475, backtracks = 3, tol = 0.004899895118496582 Iteration 12: loglikelihood = -1309.9957257690785, backtracks = 3, tol = 0.004661138713979139 Iteration 13: loglikelihood = -1309.7626923962512, backtracks = 3, tol = 0.004272926024179129 Iteration 14: loglikelihood = -1309.579389940976, backtracks = 3, tol = 0.0038791167439823832 Iteration 15: loglikelihood = -1309.4360191786407, backtracks = 3, tol = 0.0034936412963890557 Iteration 16: loglikelihood = -1309.3243029029816, backtracks = 3, tol = 0.0031289487132661353 Iteration 17: loglikelihood = -1309.2374889154178, backtracks = 3, tol = 0.00279086058784812 Iteration 18: loglikelihood = -1309.170168651954, backtracks = 3, tol = 0.002481432690611709 Iteration 19: loglikelihood = -1309.118054544563, backtracks = 3, tol = 0.002200731266780527 Iteration 20: loglikelihood = -1309.0777699529376, backtracks = 3, tol = 0.0019477484359929796 Iteration 21: loglikelihood = -1309.046667896622, backtracks = 3, tol = 0.0017208963388593733 Iteration 22: loglikelihood = -1309.0226806767591, backtracks = 3, tol = 0.0015182923554022281 Iteration 23: loglikelihood = -1309.0041976588948, backtracks = 3, tol = 0.0013379333829833407 Iteration 24: loglikelihood = -1308.989967167823, backtracks = 3, tol = 0.0011778055973926589 Iteration 25: loglikelihood = -1308.9790184007948, backtracks = 3, tol = 0.00103595359146049 Iteration 26: loglikelihood = -1308.9705996632529, backtracks = 3, tol = 0.0009105225960830759 Iteration 27: loglikelihood = -1308.9641297549895, backtracks = 3, tol = 0.0007997824385860431 Iteration 28: loglikelihood = -1308.959159858766, backtracks = 3, tol = 0.0007021390643961982 Iteration 29: loglikelihood = -1308.9553437606244, backtracks = 3, tol = 0.0006161376759907016 Iteration 30: loglikelihood = -1308.952414644512, backtracks = 3, tol = 0.0005404603466817425 Iteration 31: loglikelihood = -1308.9501670519926, backtracks = 3, tol = 0.0004739201262088837 Iteration 32: loglikelihood = -1308.948442885345, backtracks = 3, tol = 0.0004154530542663602 Iteration 33: loglikelihood = -1308.947120566301, backtracks = 3, tol = 0.0003641090662567343 Iteration 34: loglikelihood = -1308.946106651428, backtracks = 3, tol = 0.000319042465271083 Iteration 35: loglikelihood = -1308.9453293557292, backtracks = 3, tol = 0.0002795024120326442 Iteration 36: loglikelihood = -1308.9447335557431, backtracks = 3, tol = 0.00024482372613998676 Iteration 37: loglikelihood = -1308.944276937914, backtracks = 3, tol = 0.00021441817985804054 Iteration 38: loglikelihood = -1308.9439270321927, backtracks = 3, tol = 0.0001877663871329375 Iteration 39: loglikelihood = -1308.9436589291643, backtracks = 3, tol = 0.00016441033615253 Iteration 40: loglikelihood = -1308.9434535242763, backtracks = 3, tol = 0.0001439465768402207 Iteration 41: loglikelihood = -1308.9432961682523, backtracks = 3, tol = 0.00012602005022778847 Iteration 42: loglikelihood = -1308.9431756302415, backtracks = 3, tol = 0.00011031853110443762 Iteration 43: loglikelihood = -1308.9430833015456, backtracks = 3, tol = 9.656764607094533e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1570.6205482973521, backtracks = 0, tol = 0.2514826710501483 Iteration 2: loglikelihood = -1524.0572438313548, backtracks = 0, tol = 0.17284173582292814 Iteration 3: loglikelihood = -1519.4920269230402, backtracks = 0, tol = 0.1284434661088158 Iteration 4: loglikelihood = -1511.3948933908994, backtracks = 0, tol = 0.10493612579038174 Iteration 5: loglikelihood = -1510.927808393647, backtracks = 1, tol = 0.009642915570534627 Iteration 6: loglikelihood = -1509.1615738629193, backtracks = 1, tol = 0.07110262398418934 Iteration 7: loglikelihood = -1509.012618036431, backtracks = 1, tol = 0.0038521974882149844 Iteration 8: loglikelihood = -1508.9592568683518, backtracks = 1, tol = 0.003027066098751489 Iteration 9: loglikelihood = -1508.9340682969112, backtracks = 1, tol = 0.06535618745773955 Iteration 10: loglikelihood = -1508.602385716977, backtracks = 0, tol = 0.06615131927408961 Iteration 11: loglikelihood = -1508.527955968152, backtracks = 1, tol = 0.0033111641033152536 Iteration 12: loglikelihood = -1508.508480017122, backtracks = 1, tol = 0.0016735014818378062 Iteration 13: loglikelihood = -1508.503342677268, backtracks = 1, tol = 0.0008410803744543762 Iteration 14: loglikelihood = -1508.5019089634209, backtracks = 1, tol = 0.0004251017135601371 Iteration 15: loglikelihood = -1508.5014569353664, backtracks = 1, tol = 0.000272022123238274 Iteration 16: loglikelihood = -1508.5012888086778, backtracks = 1, tol = 0.0002519778494127357 Iteration 17: loglikelihood = -1508.5012530750948, backtracks = 2, tol = 9.866647448719999e-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 = -1661.950150052616, backtracks = 0, tol = 0.7369632352001478 Iteration 2: loglikelihood = -1381.3595989334667, backtracks = 0, tol = 0.13689931248132806 Iteration 3: loglikelihood = -1354.8073919042356, backtracks = 0, tol = 0.03916712193455077 Iteration 4: loglikelihood = -1350.4795744865964, backtracks = 0, tol = 0.027125200451818834 Iteration 5: loglikelihood = -1350.270751980041, backtracks = 1, tol = 0.0015327702292442151 Iteration 6: loglikelihood = -1350.21695113773, backtracks = 1, tol = 0.0007538083519300594 Iteration 7: loglikelihood = -1350.2031271178591, backtracks = 1, tol = 0.0003656305783683589 Iteration 8: loglikelihood = -1350.1995882929255, backtracks = 1, tol = 0.00017502375850226353 Iteration 9: loglikelihood = -1350.198686160325, backtracks = 1, tol = 8.286280625097989e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1471.0932275548353, backtracks = 0, tol = 0.37847306291143973 Iteration 2: loglikelihood = -1364.7454834084904, backtracks = 0, tol = 0.06659121032931833 Iteration 3: loglikelihood = -1352.7952221664668, backtracks = 0, tol = 0.034176672857932563 Iteration 4: loglikelihood = -1352.524965558838, backtracks = 0, tol = 0.002886801721910454 Iteration 5: loglikelihood = -1351.7679441604034, backtracks = 0, tol = 0.029004262301780503 Iteration 6: loglikelihood = -1351.6178425836654, backtracks = 0, tol = 0.0025104597657368334 Iteration 7: loglikelihood = -1351.616139970462, backtracks = 0, tol = 0.00024545226675119227 Iteration 8: loglikelihood = -1351.6161148526016, backtracks = 0, tol = 3.755526125532914e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1523.5958299921442, backtracks = 0, tol = 0.129071945392328 Iteration 2: loglikelihood = -1477.249859294593, backtracks = 0, tol = 0.08696841134209665 Iteration 3: loglikelihood = -1476.0121270981692, backtracks = 0, tol = 0.1343225194224959 Iteration 4: loglikelihood = -1447.8443838957955, backtracks = 0, tol = 0.11013528966572202 Iteration 5: loglikelihood = -1427.8242345986778, backtracks = 0, tol = 0.08209060918136464 Iteration 6: loglikelihood = -1414.2794725041153, backtracks = 0, tol = 0.10123294488164228 Iteration 7: loglikelihood = -1411.2564308202386, backtracks = 0, tol = 0.048387448547542636 Iteration 8: loglikelihood = -1411.050772541226, backtracks = 0, tol = 0.009770585645740737 Iteration 9: loglikelihood = -1411.015046678896, backtracks = 0, tol = 0.0044797142739283246 Iteration 10: loglikelihood = -1411.0073439042797, backtracks = 0, tol = 0.001416636381297378 Iteration 11: loglikelihood = -1411.005269199528, backtracks = 0, tol = 0.0009276879819342229 Iteration 12: loglikelihood = -1411.0045554592828, backtracks = 0, tol = 0.0004610425460981298 Iteration 13: loglikelihood = -1411.0042923301237, backtracks = 0, tol = 0.0003630593339154695 Iteration 14: loglikelihood = -1411.0041913953814, backtracks = 0, tol = 0.00018097289114187264 Iteration 15: loglikelihood = -1411.004151515616, backtracks = 0, tol = 0.0001478056297443225 Iteration 16: loglikelihood = -1411.0041354814252, backtracks = 0, tol = 7.383869781080513e-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 = -1576.5944043258398, backtracks = 0, tol = 0.2463131288927061 Iteration 2: loglikelihood = -1505.7732565165654, backtracks = 0, tol = 0.2064188478236517 Iteration 3: loglikelihood = -1447.9586527011343, backtracks = 0, tol = 0.12175655579203716 Iteration 4: loglikelihood = -1435.2881744666033, backtracks = 0, tol = 0.10768352613090407 Iteration 5: loglikelihood = -1429.51454262393, backtracks = 0, tol = 0.07586033223139907 Iteration 6: loglikelihood = -1427.7139178076804, backtracks = 0, tol = 0.04177042151609518 Iteration 7: loglikelihood = -1427.4217897418478, backtracks = 0, tol = 0.012310297064338293 Iteration 8: loglikelihood = -1427.3437566906503, backtracks = 0, tol = 0.004079249115440825 Iteration 9: loglikelihood = -1427.318944353514, backtracks = 0, tol = 0.0023015635627460663 Iteration 10: loglikelihood = -1427.3106426516142, backtracks = 0, tol = 0.001486332592774629 Iteration 11: loglikelihood = -1427.307785188213, backtracks = 0, tol = 0.0008216441158313917 Iteration 12: loglikelihood = -1427.3067826218225, backtracks = 0, tol = 0.0005535056526890428 Iteration 13: loglikelihood = -1427.3064222471853, backtracks = 0, tol = 0.00030122218778151324 Iteration 14: loglikelihood = -1427.306290594537, backtracks = 0, tol = 0.000210435184027697 Iteration 15: loglikelihood = -1427.3062415375573, backtracks = 0, tol = 0.00011334289016943538 Iteration 16: loglikelihood = -1427.3062230242942, backtracks = 0, tol = 8.120447775564562e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 8.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1572.3915368377072, backtracks = 0, tol = 0.14080018581046247 Iteration 2: loglikelihood = -1493.6245782297347, backtracks = 0, tol = 0.08621019484241597 Iteration 3: loglikelihood = -1407.1652360801602, backtracks = 0, tol = 0.12099534937569155 Iteration 4: loglikelihood = -1391.7078680089248, backtracks = 0, tol = 0.0691376240275615 Iteration 5: loglikelihood = -1383.9805348503648, backtracks = 0, tol = 0.042823323085311886 Iteration 6: loglikelihood = -1380.1034733419135, backtracks = 0, tol = 0.028017100278663127 Iteration 7: loglikelihood = -1372.3201304063814, backtracks = 0, tol = 0.08415392191922313 Iteration 8: loglikelihood = -1362.2737023620432, backtracks = 0, tol = 0.07448924480240789 Iteration 9: loglikelihood = -1359.47340589822, backtracks = 0, tol = 0.023506716232255965 Iteration 10: loglikelihood = -1358.8064157954009, backtracks = 0, tol = 0.011666959591951373 Iteration 11: loglikelihood = -1358.5516607564778, backtracks = 0, tol = 0.00962805665196859 Iteration 12: loglikelihood = -1358.4372145321552, backtracks = 0, tol = 0.005027123924121157 Iteration 13: loglikelihood = -1358.3825146226272, backtracks = 0, tol = 0.0046305865946471405 Iteration 14: loglikelihood = -1358.3556855365855, backtracks = 0, tol = 0.0024237215896914513 Iteration 15: loglikelihood = -1358.3424523366712, backtracks = 0, tol = 0.0022885025559492163 Iteration 16: loglikelihood = -1358.3358823687886, backtracks = 0, tol = 0.0011885134049852194 Iteration 17: loglikelihood = -1358.33261749307, backtracks = 0, tol = 0.0011412607884869431 Iteration 18: loglikelihood = -1358.3309912175648, backtracks = 0, tol = 0.0005862985642893317 Iteration 19: loglikelihood = -1358.3301807712444, backtracks = 0, tol = 0.0005711347031319384 Iteration 20: loglikelihood = -1358.3297765542738, backtracks = 0, tol = 0.000290111254621256 Iteration 21: loglikelihood = -1358.329574867071, backtracks = 0, tol = 0.000286182156069357 Iteration 22: loglikelihood = -1358.3294742224423, backtracks = 0, tol = 0.00014382433841254364 Iteration 23: loglikelihood = -1358.3294239801924, backtracks = 0, tol = 0.00014343733039542933 Iteration 24: loglikelihood = -1358.329398905633, backtracks = 0, tol = 7.13902451226632e-5 0.929378 seconds (1.94 M allocations: 38.370 MiB, 5.00% gc time, 58.51% 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 = -1593.9809728910454, backtracks = 0, tol = 0.14080018581046247 Iteration 2: loglikelihood = -1544.351253128312, backtracks = 0, tol = 0.08621019484241597 Iteration 3: loglikelihood = -1490.9684053184892, backtracks = 0, tol = 0.11687671295482013 Iteration 4: loglikelihood = -1465.9453575092134, backtracks = 0, tol = 0.09960325047797518 Iteration 5: loglikelihood = -1449.8123278668186, backtracks = 0, tol = 0.07912777210881844 Iteration 6: loglikelihood = -1435.0466766810218, backtracks = 0, tol = 0.07421923802661005 Iteration 7: loglikelihood = -1425.372249167962, backtracks = 0, tol = 0.046564086946209574 Iteration 8: loglikelihood = -1417.7079017831968, backtracks = 0, tol = 0.012423160429511474 Iteration 9: loglikelihood = -1412.2116845189535, backtracks = 0, tol = 0.08105088750011849 Iteration 10: loglikelihood = -1406.5457052790036, backtracks = 0, tol = 0.007933806465054231 Iteration 11: loglikelihood = -1402.141155826082, backtracks = 0, tol = 0.002800331519993929 Iteration 12: loglikelihood = -1398.314113857163, backtracks = 0, tol = 0.0018327636375316204 Iteration 13: loglikelihood = -1395.0780179207422, backtracks = 0, tol = 0.07397390270936535 Iteration 14: loglikelihood = -1392.2583106893333, backtracks = 0, tol = 0.005408083891834477 Iteration 15: loglikelihood = -1389.7887579620574, backtracks = 0, tol = 0.0013438487051811976 Iteration 16: loglikelihood = -1387.6339441444336, backtracks = 0, tol = 0.0005208980855832824 Iteration 17: loglikelihood = -1385.7064765919245, backtracks = 0, tol = 0.00021848077589064384 Iteration 18: loglikelihood = -1383.9887368566694, backtracks = 0, tol = 0.0003399559931026791 Iteration 19: loglikelihood = -1382.4446796711875, backtracks = 0, tol = 0.00024248625741129398 Iteration 20: loglikelihood = -1381.0549737784927, backtracks = 0, tol = 0.00027799492515684214 Iteration 21: loglikelihood = -1379.7959286236112, backtracks = 0, tol = 0.00022867159725619308 Iteration 22: loglikelihood = -1378.7660237388839, backtracks = 0, tol = 0.07225404612696285 Iteration 23: loglikelihood = -1377.4279506639855, backtracks = 0, tol = 0.005689285124324149 Iteration 24: loglikelihood = -1376.4364948507648, backtracks = 0, tol = 0.0016601791512934857 Iteration 25: loglikelihood = -1375.5105786715917, backtracks = 0, tol = 0.0011565944126823496 Iteration 26: loglikelihood = -1374.6837935376943, backtracks = 0, tol = 0.0005469725516860141 Iteration 27: loglikelihood = -1373.9105219464086, backtracks = 0, tol = 0.00042069585572179 Iteration 28: loglikelihood = -1372.3703384216888, backtracks = 1, tol = 0.00013652934269600494 Iteration 29: loglikelihood = -1371.0431222277648, backtracks = 1, tol = 0.0002053641284340976 Iteration 30: loglikelihood = -1369.9034088545486, backtracks = 1, tol = 0.0002060034364499193 Iteration 31: loglikelihood = -1368.9094437469564, backtracks = 1, tol = 0.00019710028153740477 Iteration 32: loglikelihood = -1368.0362208895733, backtracks = 1, tol = 0.00018594796184699013 Iteration 33: loglikelihood = -1367.2637690874178, backtracks = 1, tol = 0.00017402147848183126 Iteration 34: loglikelihood = -1366.5759786222904, backtracks = 1, tol = 0.00016218797860385932 Iteration 35: loglikelihood = -1365.959896778257, backtracks = 1, tol = 0.0001509584460642536 Iteration 36: loglikelihood = -1365.3467676663722, backtracks = 1, tol = 0.00014059221006394273 Iteration 37: loglikelihood = -1364.7907825174223, backtracks = 1, tol = 0.00013576328223373425 Iteration 38: loglikelihood = -1364.2884864167065, backtracks = 1, tol = 0.00013038762905952966 Iteration 39: loglikelihood = -1363.8336809329437, backtracks = 1, tol = 0.000124413279375894 Iteration 40: loglikelihood = -1363.4206400004807, backtracks = 1, tol = 0.00011825365026063021 Iteration 41: loglikelihood = -1363.0443224376354, backtracks = 1, tol = 0.00011218599688957055 Iteration 42: loglikelihood = -1362.7004052794614, backtracks = 1, tol = 0.00010638357924313299 Iteration 43: loglikelihood = -1362.3852117718493, backtracks = 1, tol = 0.00010093820033384457 Iteration 44: loglikelihood = -1362.0956148730857, backtracks = 1, tol = 9.588544488763406e-5 0.487775 seconds (2.00 M allocations: 36.603 MiB, 3.46% 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 = -3539.852, backtracks = 0, tol = 0.08821764416884652 Iteration 2: loglikelihood = -3491.2432, backtracks = 0, tol = 0.046802512249206625 Iteration 3: loglikelihood = -3463.0735, backtracks = 1, tol = 0.06287033551380643 Iteration 4: loglikelihood = -3458.403, backtracks = 1, tol = 0.011214285681949262 Iteration 5: loglikelihood = -3456.741, backtracks = 1, tol = 0.007106107617807631 Iteration 6: loglikelihood = -3456.2373, backtracks = 1, tol = 0.004036432561373568 Iteration 7: loglikelihood = -3440.7673, backtracks = 1, tol = 0.06440588649836018 Iteration 8: loglikelihood = -3433.4094, backtracks = 0, tol = 0.08050420263112916 Iteration 9: loglikelihood = -3423.0574, backtracks = 0, tol = 0.08582027377977818 Iteration 10: loglikelihood = -3421.7314, backtracks = 0, tol = 0.007466232819402108 Iteration 11: loglikelihood = -3421.6938, backtracks = 0, tol = 0.0010819839128892996 Iteration 12: loglikelihood = -3421.693, backtracks = 0, tol = 0.0003535372689089754 Iteration 13: loglikelihood = -3421.693, backtracks = 1, tol = 4.77786285806382e-5 24.600903 seconds (17.62 M allocations: 746.771 MiB, 0.94% gc time, 98.12% 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 = -3436.909, backtracks = 0, tol = 0.08821764416884652 Iteration 2: loglikelihood = -3322.399, backtracks = 0, tol = 0.0482432048439139 Iteration 3: loglikelihood = -3133.975, backtracks = 1, tol = 0.06156323448518673 Iteration 4: loglikelihood = -3052.958, backtracks = 0, tol = 0.08879361368038732 Iteration 5: loglikelihood = -2938.0352, backtracks = 0, tol = 0.08941097362993038 Iteration 6: loglikelihood = -2841.1313, backtracks = 0, tol = 0.010693850457679033 Iteration 7: loglikelihood = -2736.5935, backtracks = 0, tol = 0.09145340809397823 Iteration 8: loglikelihood = -2624.4836, backtracks = 0, tol = 0.09656689400430352 Iteration 9: loglikelihood = -2521.5078, backtracks = 0, tol = 0.08667802408522263 Iteration 10: loglikelihood = -2428.391, backtracks = 0, tol = 0.012273613208424631 Iteration 11: loglikelihood = -2348.5583, backtracks = 0, tol = 0.002091239978803023 Iteration 12: loglikelihood = -2288.545, backtracks = 0, tol = 0.09422996320390277 Iteration 13: loglikelihood = -2229.7317, backtracks = 0, tol = 0.08593118992877084 Iteration 14: loglikelihood = -2193.09, backtracks = 0, tol = 0.011174383931792157 Iteration 15: loglikelihood = -2174.057, backtracks = 0, tol = 0.09335292181291807 Iteration 16: loglikelihood = -2161.6824, backtracks = 0, tol = 0.11061422323786693 Iteration 17: loglikelihood = -2146.1787, backtracks = 0, tol = 0.10927031932786929 Iteration 18: loglikelihood = -2136.0198, backtracks = 1, tol = 0.013363788143002816 Iteration 19: loglikelihood = -2133.4402, backtracks = 1, tol = 0.006690785793901782 Iteration 20: loglikelihood = -2132.8374, backtracks = 1, tol = 0.003412980061667367 Iteration 21: loglikelihood = -2132.7024, backtracks = 1, tol = 0.001759764272633646 Iteration 22: loglikelihood = -2132.6975, backtracks = 1, tol = 0.0009216576724426933 Iteration 23: loglikelihood = -2132.6975, backtracks = 3, tol = 0.00012281003532032457 Iteration 24: loglikelihood = -2132.6953, backtracks = 3, tol = 0.00010865046046537538 Iteration 25: loglikelihood = -2132.6968, backtracks = 3, tol = 9.61168476681262e-5 0.238168 seconds (1.54 M allocations: 25.649 MiB, 12.45% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 29.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Initializing β to univariate regression values... 0%| | ETA: 8:18:47Running 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 = -2973.20721158067, backtracks = 0, tol = 0.9753037901485436 Iteration 2: loglikelihood = -1640.6694321323835, backtracks = 0, tol = 0.2999151154493682 Iteration 3: loglikelihood = -1418.3315050219228, backtracks = 0, tol = 0.10707075072938249 Iteration 4: loglikelihood = -1411.8219428589443, backtracks = 0, tol = 0.038898114770295936 Iteration 5: loglikelihood = -1410.7307354136753, backtracks = 0, tol = 0.03138838740051226 Iteration 6: loglikelihood = -1410.653861909991, backtracks = 0, tol = 0.001736989736614678 Iteration 7: loglikelihood = -1410.6533631901768, backtracks = 1, tol = 8.130020517735094e-5 9.623231 seconds (1.11 M allocations: 122.932 MiB, 0.37% gc time, 93.40% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 10.1s 7.838027 seconds (3.94 M allocations: 80.113 MiB, 1.20% gc time, 0.67% compilation time) 5.587212 seconds (3.92 M allocations: 89.273 MiB, 0.10% gc time) 10.868414 seconds (22.33 M allocations: 469.819 MiB, 0.61% gc time, 13.28% compilation time: 70% of which was recompilation) 9.210106 seconds (22.05 M allocations: 462.989 MiB, 0.83% gc time) 39.663322 seconds (2.51 M allocations: 4.150 GiB, 1.03% gc time, 38.91% compilation time) 53.685938 seconds (74.21 k allocations: 187.391 MiB, 0.07% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m14.7s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 11.455 ms (77 allocations: 5.30 KiB) 4.970 μs (0 allocations: 0 bytes) 131.029 μs (4 allocations: 288 bytes) 5.362 μs (0 allocations: 0 bytes) 36.739 μs (2 allocations: 64 bytes) 37.659 μs (0 allocations: 0 bytes) 27.950 μs (0 allocations: 0 bytes) 38.440 μs (0 allocations: 0 bytes) 59.609 μs (0 allocations: 0 bytes) 30.663 ms (77 allocations: 5.30 KiB) 26.890 μs (0 allocations: 0 bytes) 182.318 μs (4 allocations: 288 bytes) 27.340 μs (0 allocations: 0 bytes) 177.128 μs (2 allocations: 64 bytes) 74.329 μs (0 allocations: 0 bytes) 122.878 μs (0 allocations: 0 bytes) 206.308 μs (0 allocations: 0 bytes) 188.809 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m52.8s **** 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 **** **** 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 = 0.0011189517628951667 Iteration 5: loglikelihood = -2868.0308576353746, backtracks = 0, tol = 0.00031182601179140966 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.0001039330594994784 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.10086204985851e-5 0.564712 seconds (53.53 k allocations: 5.547 MiB, 43.64% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 8.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.757664 seconds (473.30 k allocations: 177.249 MiB, 2.21% gc time, 57.25% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 3.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:40 Cross validating... 6%|██ | ETA: 0:01:48 Cross validating... 10%|███ | ETA: 0:01:11 Cross validating... 13%|████▏ | ETA: 0:00:52 Cross validating... 16%|█████▏ | ETA: 0:00:41 Cross validating... 19%|██████▏ | ETA: 0:00:33 Cross validating... 22%|███████▏ | ETA: 0:00:28 Cross validating... 25%|████████▏ | ETA: 0:00:24 Cross validating... 29%|█████████▏ | ETA: 0:00:21 Cross validating... 32%|██████████▏ | ETA: 0:00:18 Cross validating... 35%|███████████▏ | ETA: 0:00:16 Cross validating... 38%|████████████▎ | ETA: 0:00:14 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:11 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 3909.487853918581 1 2186.2914711013545 2 1667.8715480835326 3 1155.8758956710153 4 843.3440745525309 5 625.737405320407 6 435.93899249670983 7 379.07648885148797 8 339.50618854295664 9 310.52298790418683 10 313.43070456791224 11 315.6711544164776 12 318.74748513838074 13 322.3966523419555 14 324.6317673797681 15 326.10781984731625 16 327.1384470356477 17 330.08682567166375 18 328.7136317089387 19 353.45001418199763 20 368.0598489677829 Best k = 9 12.063451 seconds (12.02 M allocations: 294.916 MiB, 0.56% gc time, 59.61% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 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... 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: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 3909.487853918581 1 2186.3765161284236 2 1671.8364870315454 3 1160.9465851890773 4 849.8065942509486 5 627.8203122568246 6 441.1026997839925 7 382.5483624672768 8 342.74104759385966 9 314.53859696172043 10 323.1223184943592 11 329.1217979018659 12 338.52494258681344 13 340.47328977010403 14 354.95523567100196 15 361.22080698801045 16 362.27381925580124 17 369.20463948900954 18 365.784035234115 19 368.6468209192741 20 377.4372129461403 Best k = 9 4.967149 seconds (11.06 M allocations: 227.550 MiB, 0.78% gc time, 0.73% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.9s **** 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: 0:04:31 Cross validating... 8%|██▌ | ETA: 0:01:44 Cross validating... 13%|████▏ | ETA: 0:01:03 Cross validating... 17%|█████▋ | ETA: 0:00:44 Cross validating... 24%|███████▋ | ETA: 0:00:30 Cross validating... 29%|█████████▏ | ETA: 0:00:24 Cross validating... 33%|██████████▋ | ETA: 0:00:19 Cross validating... 38%|████████████▎ | ETA: 0:00:16 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 1533.0856029052734 1 1227.0511580810548 2 1030.888625305176 3 796.227637451172 4 647.0571466674805 5 541.4222530517577 6 462.4277743225098 7 410.07325070190427 8 383.37064874267577 9 366.2084447631836 10 368.23031732177736 11 372.9321669921875 12 377.1789580993652 13 380.6759961853028 14 399.68364147949217 15 386.91946649169927 16 389.0868358764649 17 417.1303845214844 18 389.4892632141113 19 421.0574957885742 20 435.3092005615235 Best k = 9 12.179610 seconds (13.04 M allocations: 283.296 MiB, 0.50% gc time, 77.59% 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 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 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... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1533.0856029052734 1 1227.0511580810548 2 1038.6764362182616 3 802.6765317382813 4 655.516465270996 5 546.0865552978515 6 466.67503439331057 7 417.5778338623047 8 393.3617481689454 9 375.3665063781739 10 381.5232353210449 11 393.8482819824219 12 403.71566561889654 13 413.83698205566407 14 421.02321475219725 15 433.6256749572754 16 442.35767083740234 17 455.98624679565427 18 444.6073482666016 19 464.71370336914066 20 462.371765838623 Best k = 9 3.398549 seconds (11.53 M allocations: 209.186 MiB, 1.63% gc time, 1.60% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 17.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:49 Cross validating... 6%|██ | ETA: 0:00:27 Cross validating... 10%|███ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross 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Crossvalidation Results: k MSE 0 461.8643287138184 1 375.03080799606516 2 312.87184025688066 3 292.2649043734605 4 261.3300645419216 5 250.29660182317352 6 234.3007774784245 7 225.1206590195368 8 228.8513831884001 9 230.25453763983805 10 244.84717481284957 11 236.02900974691173 12 249.6412298949253 13 255.74825743813273 14 263.064814973459 15 255.48577315020566 16 266.17620614550754 17 273.0330451253788 18 295.7990428040826 19 271.55830155179024 20 287.35922033199665 Best k = 7 8.336472 seconds (18.77 M allocations: 430.083 MiB, 0.78% gc time, 24.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 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59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | 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... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 461.8643287138184 1 374.5851766803984 2 313.3621438853337 3 293.23856879178726 4 263.02785535247284 5 252.93700040213517 6 238.6117439396768 7 230.66621020669245 8 240.46386676907883 9 247.60362737746243 10 256.8468375200623 11 261.4617189056008 12 262.87078856564403 13 267.3638839890334 14 279.5393711200134 15 295.42027795918494 16 291.8244456539086 17 297.4226387902412 18 316.1210423337878 19 306.2437792390697 20 327.2134274113715 Best k = 7 6.504259 seconds (18.86 M allocations: 386.003 MiB, 0.79% gc time, 0.72% 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: 0:00:38 Cross validating... 6%|██ | ETA: 0:00:21 Cross validating... 10%|███ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 22%|███████▏ | 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... 35%|███████████▏ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 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... 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: 0:00:06 Crossvalidation Results: k MSE 0 462.4010277617484 1 434.78680093329797 2 397.1819714631498 3 375.3707507291681 4 346.4020662775787 5 327.76471082019 6 316.22545997656107 7 320.53781663768234 8 321.9956150763411 9 324.18834724569933 10 328.6937832813521 11 329.7593231694405 12 345.05528581272085 13 347.4812878955667 14 328.52400794105915 15 336.70656641911575 16 334.82307255133094 17 338.578320133036 18 347.5166107549246 19 333.3061056693147 20 368.20440887458915 Best k = 6 7.099909 seconds (17.76 M allocations: 410.870 MiB, 8.51% gc time, 25.61% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 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: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 462.4010277617484 1 435.15087956223033 2 397.9102265567301 3 376.59155437147973 4 348.1119028763153 5 331.67219722288496 6 320.06396458786867 7 330.4439690615794 8 335.3351785709607 9 345.16721034595264 10 352.22459049091447 11 347.5956233776231 12 357.549994409629 13 367.0538725142174 14 364.2636788375411 15 373.9065282890449 16 385.12112879779767 17 378.3856648278772 18 392.1706564519029 19 397.10179072841936 20 411.7378563412519 Best k = 6 5.038503 seconds (18.35 M allocations: 370.160 MiB, 0.95% gc time, 1.24% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:50 Cross validating... 5%|█▌ | ETA: 0:00:35 Cross validating... 8%|██▌ | ETA: 0:00:23 Cross validating... 11%|███▌ | ETA: 0:00:17 Cross validating... 14%|████▋ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 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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... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 667.2188672524661 1 570.1718008679587 2 479.7959947031603 3 442.2301794293809 4 428.3662306813185 5 402.9428380675688 6 355.81366494225716 7 352.5234123539802 8 353.43014095561216 9 354.8601894868089 10 358.9008243252278 11 362.7070979802707 12 361.23446402934 13 358.4048242816674 14 372.0714013071118 15 366.42953722024276 16 394.3569117154217 17 372.6920841035684 18 391.42956361310576 19 369.7478568986421 20 366.48731515129884 Best k = 7 8.563814 seconds (18.07 M allocations: 431.372 MiB, 0.81% gc time, 24.97% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 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ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 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... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 667.2188672524661 1 554.8664074966727 2 476.95256250878174 3 443.341662457553 4 439.56798241621516 5 407.9405735014658 6 365.037531055654 7 364.3054332486075 8 366.84959879958217 9 377.0652744209792 10 383.9834666626083 11 389.4512869608344 12 395.7381682194409 13 389.51958748040784 14 404.98664474829945 15 402.1317289780699 16 410.99215346328805 17 402.30801339866963 18 414.9849251674149 19 420.9003101422009 20 434.7387750112861 Best k = 7 6.551308 seconds (17.82 M allocations: 371.957 MiB, 0.79% gc time, 0.69% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 15.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:20 Cross validating... 5%|█▌ | ETA: 0:00:57 Cross validating... 6%|██ | ETA: 0:00:58 Cross validating... 8%|██▌ | ETA: 0:00:58 Cross validating... 10%|███ | ETA: 0:00:59 Cross validating... 11%|███▌ | ETA: 0:00:58 Cross validating... 13%|████▏ | ETA: 0:00:51 Cross validating... 14%|████▋ | ETA: 0:00:51 Cross validating... 16%|█████▏ | ETA: 0:00:51 Cross validating... 17%|█████▋ | ETA: 0:00:50 Cross validating... 19%|██████▏ | ETA: 0:00:50 Cross validating... 21%|██████▋ | ETA: 0:00:49 Cross validating... 22%|███████▏ | ETA: 0:00:49 Cross validating... 24%|███████▋ | ETA: 0:00:45 Cross validating... 25%|████████▏ | ETA: 0:00:45 Cross validating... 27%|████████▋ | ETA: 0:00:42 Cross validating... 29%|█████████▏ | ETA: 0:00:42 Cross validating... 30%|█████████▋ | ETA: 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65%|████████████████████▉ | ETA: 0:00:17 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:16 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:14 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:14 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:13 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:12 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:12 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:11 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:10 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:09 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:08 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:08 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:07 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:02 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:47 Crossvalidation Results: k MSE 0 357.5822569581085 1 301.3686050585686 2 272.4791851592048 3 257.28417620602943 4 239.5493822914799 5 231.7624450931105 6 218.22301652069098 7 218.91661442870185 8 219.88759509730505 9 220.71916026705804 10 222.7622539070473 11 223.9224933976801 12 222.44287437171982 13 224.52716435469398 14 226.69849907541544 15 225.8338034962552 16 226.97749893253302 17 230.1531912447614 18 231.17719208178028 19 229.67894118959438 20 231.0569939038296 Best k = 6 48.050305 seconds (152.08 M allocations: 3.754 GiB, 0.99% gc time, 3.76% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:06 Cross validating... 5%|█▌ | ETA: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:07 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 10%|███ | ETA: 0:00:10 Cross validating... 11%|███▌ | ETA: 0:00:09 Cross validating... 13%|████▏ | ETA: 0:00:09 Cross validating... 14%|████▋ | ETA: 0:00:09 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 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0:00:06 Cross validating... 59%|██████████████████▊ | ETA: 0:00:06 Cross validating... 60%|███████████████████▎ | ETA: 0:00:05 Cross validating... 62%|███████████████████▊ | ETA: 0:00:05 Cross validating... 63%|████████████████████▍ | ETA: 0:00:05 Cross validating... 65%|████████████████████▉ | ETA: 0:00:05 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 0 357.5822569581085 1 297.96297396086385 2 272.59256054748806 3 258.5936213378802 4 241.5485767435364 5 234.1853544844757 6 220.64158963309018 7 223.54664015400527 8 224.9075211536428 9 231.0887064378226 10 235.257820318098 11 235.17375184607542 12 239.55403322701238 13 246.64233341100982 14 246.74652391085266 15 248.0984671810769 16 255.79370083297934 17 256.47510165685566 18 269.10570394909143 19 262.25010681066135 20 266.78105519938026 Best k = 6 16.804672 seconds (54.83 M allocations: 1.133 GiB, 1.02% gc time, 0.29% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m05.3s **** 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: 0:00:55 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 10%|███ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:12 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 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: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 691.7500225830079 1 622.5072396240234 2 512.5984967346192 3 404.1873347473144 4 329.1224825439453 5 269.25713952636715 6 254.24000593566893 7 224.95246855163572 8 210.14389988708496 9 203.5730756072998 10 206.3555386505127 11 208.19131018066406 12 216.8473366241455 13 229.8447658843994 14 213.42113655090333 15 214.1879868621826 16 224.7288980255127 17 218.40956840515133 18 214.59177186584472 19 217.02808283996583 20 229.5842406768799 Best k = 9 6.016647 seconds (18.20 M allocations: 357.374 MiB, 0.97% gc time, 38.52% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 691.7500225830079 1 601.5035169677735 2 491.64564691162104 3 387.2143143005371 4 320.7548650817871 5 268.1246952209473 6 254.63632737731933 7 227.02002976989746 8 212.62741166687013 9 212.0953056640625 10 212.51340118408203 11 214.56212982177735 12 220.0984645233154 13 226.74450151062013 14 231.7223010253906 15 222.91655926513673 16 236.85316429138186 17 238.8029296417236 18 236.3234663696289 19 245.07382664489745 20 246.47416119384764 Best k = 9 3.841374 seconds (17.44 M allocations: 307.807 MiB, 1.11% gc time, 1.48% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:05 Cross validating... 4%|█▎ | ETA: 0:00:36 Cross 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validating... 91%|█████████████████████████████▏ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 1 4034.034161682626 2 2888.4181515366336 3 2616.58855603052 4 2380.898750628725 5 2288.045968651424 6 2184.3576988665736 7 2123.7342558130154 8 2099.463817927264 9 2070.8666228079596 10 2042.246954845937 11 2080.711252394009 12 2086.5477457597285 13 2107.348219910023 14 2124.0039879063656 15 2143.049851004966 16 2162.437271721734 17 2200.282963452936 18 2213.477707376658 19 2206.0739834934902 20 2206.86877663143 Best k = 10 14.168366 seconds (404.67 k allocations: 220.998 MiB, 0.43% gc time, 9.72% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 18.1s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m50.4s **** 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: 0:00:08 Cross validating... 4%|█▎ | ETA: 0:00:08 Cross validating... 6%|█▉ | ETA: 0:00:09 Cross validating... 7%|██▎ | ETA: 0:00:09 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 9%|██▉ | ETA: 0:00:10 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | 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validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.991829511581 15 2189.890403738045 16 2191.1812932295775 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: 0:00:08 Cross validating... 4%|█▎ | ETA: 0:00:08 Cross validating... 6%|█▉ | ETA: 0:00:09 Cross validating... 7%|██▎ | ETA: 0:00:09 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 9%|██▉ | ETA: 0:00:10 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | ETA: 0:00:11 Cross validating... 12%|███▉ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 14%|████▌ | ETA: 0:00:12 Cross validating... 15%|████▊ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▌ | ETA: 0:00:14 Cross validating... 18%|█████▊ | ETA: 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2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.991829511581 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m15.9s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:581 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(fname::String) @ Main ./sysimg.jl:38 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(fname::String) @ Main ./sysimg.jl:38 [15] top-level scope @ none:6 Test Summary: | Error Total Time read BGEN and VCF | 1 1 7.0s 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 1057.31s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/Operations.jl:2128 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2011 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1338.66s: package tests unexpectedly errored