Package evaluation of MendelIHT on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T19:41:25.899 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.81s ################################################################################ # 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 v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.18.0 ⌅ [67c07d97] + Automa v0.8.4 ⌅ [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 v0.2.6 [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 v0.8.6 [861a8166] + Combinatorics v1.0.2 [38540f10] + CommonSolve v0.2.4 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [f489334b] + StyledStrings v1.11.0 [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 v1.1.1+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. To see why use `status --outdated -m` Installation completed after 4.57s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 164.3s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_r1FJxO/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.0 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.118 [38e38edf] GLM v1.9.0 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.10.4 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.5.0 [2913bbd2] StatsBase v0.34.4 [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_r1FJxO/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.18.0 ⌅ [67c07d97] Automa v0.8.4 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools 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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 13.5s 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 6.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.8s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 2.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1704.6687371789758, backtracks = 0, tol = 1.6817570590457556 Iteration 2: loglikelihood = -1482.8974140099428, backtracks = 0, tol = 0.14930022976044485 Iteration 3: loglikelihood = -1431.2480214905715, backtracks = 0, tol = 0.07517171678971306 Iteration 4: loglikelihood = -1429.5071612335032, backtracks = 0, tol = 0.01254498126570633 Iteration 5: loglikelihood = -1429.484300920417, backtracks = 0, tol = 0.0014332170282752305 Iteration 6: loglikelihood = -1429.4838653138272, backtracks = 0, tol = 0.00017206531529497684 Iteration 7: loglikelihood = -1429.4838557767175, backtracks = 0, tol = 2.340104743884189e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06668901443481445 Final loglikelihood: -1429.4838557767175 SNP PVE: 0.9252119981886978 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 345 -1.02057 2 │ 681 -1.22752 3 │ 1412 -0.324446 4 │ 2815 2.07967 5 │ 3408 0.229349 6 │ 4123 1.26196 7 │ 4830 -0.712103 8 │ 8158 0.171214 9 │ 8555 -0.369557 10 │ 9236 1.64109 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.052337Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 16.7s **** 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 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 3.1s **** 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 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 = -18371.44581134031, backtracks = 0, tol = 0.6704540645996337 Iteration 2: loglikelihood = -5120.979407992772, backtracks = 0, tol = 0.09957266458116394 Iteration 3: loglikelihood = -2365.817161610109, backtracks = 0, tol = 0.09849036260889585 Iteration 4: loglikelihood = -1606.0868496883033, backtracks = 0, tol = 0.08941507477683008 Iteration 5: loglikelihood = -1471.9589379787458, backtracks = 0, tol = 0.055649379884611515 Iteration 6: loglikelihood = -1406.0981355586614, backtracks = 1, tol = 0.06516455323399024 Iteration 7: loglikelihood = -1351.5135806254775, backtracks = 0, tol = 0.06483580672045439 Iteration 8: loglikelihood = -1341.5282831941172, backtracks = 0, tol = 0.028914892486742366 Iteration 9: loglikelihood = -1335.336008267904, backtracks = 0, tol = 0.023184567457922214 Iteration 10: loglikelihood = -1331.2863636776174, backtracks = 0, tol = 0.01717599751549564 Iteration 11: loglikelihood = -1328.1855439426326, backtracks = 0, tol = 0.016272161398987375 Iteration 12: loglikelihood = -1325.891811219567, backtracks = 0, tol = 0.011564437507127 Iteration 13: loglikelihood = -1317.9812861370701, backtracks = 0, tol = 0.036835835970603456 Iteration 14: loglikelihood = -1315.5403839086518, backtracks = 0, tol = 0.010845792189572132 Iteration 15: loglikelihood = -1313.8887922126828, backtracks = 0, tol = 0.01139840018532208 Iteration 16: loglikelihood = -1312.7221428989585, backtracks = 0, tol = 0.008047210016254427 Iteration 17: loglikelihood = -1311.8267306742468, backtracks = 0, tol = 0.00842888014557184 Iteration 18: loglikelihood = -1311.149840735774, backtracks = 0, tol = 0.00610760581597492 Iteration 19: loglikelihood = -1310.6127521364483, backtracks = 0, tol = 0.006545911692440527 Iteration 20: loglikelihood = -1310.1977017433271, backtracks = 0, tol = 0.004668366056112877 Iteration 21: loglikelihood = -1306.8870289714455, backtracks = 0, tol = 0.02496628296464668 Iteration 22: loglikelihood = -1305.9125188607297, backtracks = 0, tol = 0.006898104623128805 Iteration 23: loglikelihood = -1305.4225709404222, backtracks = 0, tol = 0.005536227351412069 Iteration 24: loglikelihood = -1305.1067184294031, backtracks = 0, tol = 0.004587079450916066 Iteration 25: loglikelihood = -1304.8757227175176, backtracks = 0, tol = 0.004024099039410372 Iteration 26: loglikelihood = -1304.6986865240353, backtracks = 0, tol = 0.0037048881466773672 Iteration 27: loglikelihood = -1304.5580990926048, backtracks = 0, tol = 0.003178784905309919 Iteration 28: loglikelihood = -1304.446784305849, backtracks = 0, tol = 0.002924596406028238 Iteration 29: loglikelihood = -1304.3570335166867, backtracks = 0, tol = 0.0025401922910660885 Iteration 30: loglikelihood = -1304.2851891177763, backtracks = 0, tol = 0.0023123366719800665 Iteration 31: loglikelihood = -1304.226953408975, backtracks = 0, tol = 0.0020418893356640914 Iteration 32: loglikelihood = -1304.1800671548513, backtracks = 0, tol = 0.0018378283506441777 Iteration 33: loglikelihood = -1304.1419598085379, backtracks = 0, tol = 0.0016481878552764063 Iteration 34: loglikelihood = -1304.1111677378083, backtracks = 0, tol = 0.001467820780551465 Iteration 35: loglikelihood = -1304.0861021212622, backtracks = 0, tol = 0.0013342523250857456 Iteration 36: loglikelihood = -1304.0657981829575, backtracks = 0, tol = 0.0011769502808971486 Iteration 37: loglikelihood = -1304.049254408767, backtracks = 0, tol = 0.0010822693865946966 Iteration 38: loglikelihood = -1304.035829872492, backtracks = 0, tol = 0.0009466799607003822 Iteration 39: loglikelihood = -1304.024884902412, backtracks = 0, tol = 0.0008790977026306337 Iteration 40: loglikelihood = -1304.0159921024872, backtracks = 0, tol = 0.0007633570980279643 Iteration 41: loglikelihood = -1304.008739062206, backtracks = 0, tol = 0.000714776616421801 Iteration 42: loglikelihood = -1304.0028402685186, backtracks = 0, tol = 0.0006167608811338223 Iteration 43: loglikelihood = -1303.9980279811668, backtracks = 0, tol = 0.0005815938793547118 Iteration 44: loglikelihood = -1303.9941113337982, backtracks = 0, tol = 0.0004991200826178713 Iteration 45: loglikelihood = -1303.9909155905802, backtracks = 0, tol = 0.00047348646912501814 Iteration 46: loglikelihood = -1303.9883131406018, backtracks = 0, tol = 0.00040444909124155275 Iteration 47: loglikelihood = -1303.986189481169, backtracks = 0, tol = 0.0003856376288701383 Iteration 48: loglikelihood = -1303.984459308517, backtracks = 0, tol = 0.0003280893574030793 Iteration 49: loglikelihood = -1303.983047350634, backtracks = 0, tol = 0.00031419317316866104 Iteration 50: loglikelihood = -1303.981896603284, backtracks = 0, tol = 0.0002663847963762401 Iteration 51: loglikelihood = -1303.9809574588448, backtracks = 0, tol = 0.00025605389569418414 Iteration 52: loglikelihood = -1303.9801918386886, backtracks = 0, tol = 0.00021644677112566134 Iteration 53: loglikelihood = -1303.979566983061, backtracks = 0, tol = 0.0002087190899411583 Iteration 54: loglikelihood = -1303.9790574652561, backtracks = 0, tol = 0.00017598060316819603 Iteration 55: loglikelihood = -1303.9786416162715, backtracks = 0, tol = 0.00017016601714200607 Iteration 56: loglikelihood = -1303.9783024636508, backtracks = 0, tol = 0.0001431554000969022 Iteration 57: loglikelihood = -1303.9780256555082, backtracks = 0, tol = 0.0001387556237576148 Iteration 58: loglikelihood = -1303.9777998662476, backtracks = 0, tol = 0.00011650504847904169 Iteration 59: loglikelihood = -1303.9776155801042, backtracks = 0, tol = 0.00011315798844066313 Iteration 60: loglikelihood = -1303.977465241654, backtracks = 0, tol = 9.485205480742709e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.1s **** 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 = -1709.6190741081123, backtracks = 0, tol = 0.6713662915286428 Iteration 2: loglikelihood = -1578.2466228785127, backtracks = 0, tol = 0.13383755765458144 Iteration 3: loglikelihood = -1505.256319412567, backtracks = 0, tol = 0.09850909491992416 Iteration 4: loglikelihood = -1478.4052043608672, backtracks = 0, tol = 0.07994476711395508 Iteration 5: loglikelihood = -1473.7074859954105, backtracks = 0, tol = 0.08054754665454927 Iteration 6: loglikelihood = -1471.6829268948927, backtracks = 0, tol = 0.08147164751642437 Iteration 7: loglikelihood = -1471.488853829832, backtracks = 1, tol = 0.006783779641178564 Iteration 8: loglikelihood = -1471.4029174692464, backtracks = 1, tol = 0.004961035127671212 Iteration 9: loglikelihood = -1471.369128890389, backtracks = 1, tol = 0.003696820128353811 Iteration 10: loglikelihood = -1471.35913337184, backtracks = 1, tol = 0.0020860906410232194 Iteration 11: loglikelihood = -1471.3565366155863, backtracks = 1, tol = 0.0010421481294017705 Iteration 12: loglikelihood = -1471.3561416181196, backtracks = 2, tol = 0.0002591867884636451 Iteration 13: loglikelihood = -1471.3559182303052, backtracks = 2, tol = 0.00019506523147946793 Iteration 14: loglikelihood = -1471.3557918757901, backtracks = 2, tol = 0.0001462592473745153 Iteration 15: loglikelihood = -1471.3557203643334, backtracks = 2, tol = 0.00010967078445636223 Iteration 16: loglikelihood = -1471.3556798888442, backtracks = 2, tol = 8.22600457681738e-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 = -1878.0978452590186, backtracks = 0, tol = 0.7214586882466792 Iteration 2: loglikelihood = -1502.700594721718, backtracks = 0, tol = 0.12647816062937514 Iteration 3: loglikelihood = -1418.4439973827386, backtracks = 0, tol = 0.048784529094442454 Iteration 4: loglikelihood = -1411.8071977894183, backtracks = 0, tol = 0.03105372933913132 Iteration 5: loglikelihood = -1410.323745333874, backtracks = 0, tol = 0.02714989774163447 Iteration 6: loglikelihood = -1410.1419352571672, backtracks = 0, tol = 0.002211690634002107 Iteration 7: loglikelihood = -1410.1398788205677, backtracks = 1, tol = 0.00013676831159155288 Iteration 8: loglikelihood = -1410.139334316384, backtracks = 1, tol = 6.912075786458333e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 2.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1569.7297776720018, backtracks = 0, tol = 0.35922380465252995 Iteration 2: loglikelihood = -1438.6852224646786, backtracks = 0, tol = 0.08770853114195493 Iteration 3: loglikelihood = -1422.64977745255, backtracks = 0, tol = 0.039344847009718964 Iteration 4: loglikelihood = -1410.3916196846944, backtracks = 0, tol = 0.032926444862291425 Iteration 5: loglikelihood = -1409.6005471383648, backtracks = 1, tol = 0.003156362249785133 Iteration 6: loglikelihood = -1409.394451399407, backtracks = 1, tol = 0.001711451961704917 Iteration 7: loglikelihood = -1409.3416478891909, backtracks = 1, tol = 0.0008970155971540732 Iteration 8: loglikelihood = -1409.32826481471, backtracks = 1, tol = 0.00046035535503608426 Iteration 9: loglikelihood = -1409.324892653116, backtracks = 1, tol = 0.00023355605201322361 Iteration 10: loglikelihood = -1409.324045433828, backtracks = 1, tol = 0.00011776943186322188 Iteration 11: loglikelihood = -1409.3238328872162, backtracks = 1, tol = 5.918000710215885e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 1.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 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 8.5s **** 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 = -1503.8379335220804, backtracks = 0, tol = 0.1537960326897176 Iteration 2: loglikelihood = -1447.5377782102694, backtracks = 0, tol = 0.09584370743361675 Iteration 3: loglikelihood = -1422.5551419234744, backtracks = 0, tol = 0.17411756337425924 Iteration 4: loglikelihood = -1369.104188775723, backtracks = 0, tol = 0.06260384603344728 Iteration 5: loglikelihood = -1340.7958099659038, backtracks = 0, tol = 0.11710954231275231 Iteration 6: loglikelihood = -1320.268480545997, backtracks = 0, tol = 0.049160473673711284 Iteration 7: loglikelihood = -1317.4076219523806, backtracks = 0, tol = 0.02522609270524787 Iteration 8: loglikelihood = -1316.1536537876611, backtracks = 0, tol = 0.018369518981755515 Iteration 9: loglikelihood = -1308.5478517270917, backtracks = 0, tol = 0.05974449972342392 Iteration 10: loglikelihood = -1307.124143892031, backtracks = 1, tol = 0.012050992922186466 Iteration 11: loglikelihood = -1306.3079938597457, backtracks = 1, tol = 0.00936364440765068 Iteration 12: loglikelihood = -1306.1140719557409, backtracks = 2, tol = 0.004147914515549022 Iteration 13: loglikelihood = -1305.9541271842281, backtracks = 2, tol = 0.0038059186326998805 Iteration 14: loglikelihood = -1305.8568133771792, backtracks = 2, tol = 0.0030748606277965804 Iteration 15: loglikelihood = -1305.7999553829934, backtracks = 2, tol = 0.002486516471945681 Iteration 16: loglikelihood = -1305.7673481585691, backtracks = 2, tol = 0.0018476593968912427 Iteration 17: loglikelihood = -1305.7487975855759, backtracks = 2, tol = 0.0014552903567899506 Iteration 18: loglikelihood = -1305.7382820312876, backtracks = 2, tol = 0.0010677546014281696 Iteration 19: loglikelihood = -1305.7323331592431, backtracks = 2, tol = 0.0008302168547289317 Iteration 20: loglikelihood = -1305.7289719609303, backtracks = 2, tol = 0.0006076128338667398 Iteration 21: loglikelihood = -1305.7270744583227, backtracks = 2, tol = 0.0004700471796552094 Iteration 22: loglikelihood = -1305.7260039542214, backtracks = 2, tol = 0.00034386058625133814 Iteration 23: loglikelihood = -1305.725400277552, backtracks = 2, tol = 0.00026533179469255 Iteration 24: loglikelihood = -1305.7250599852846, backtracks = 2, tol = 0.00019412842179605613 Iteration 25: loglikelihood = -1305.7248682063248, backtracks = 2, tol = 0.00014957280163019175 Iteration 26: loglikelihood = -1305.7247601520162, backtracks = 2, tol = 0.0001094699527248348 Iteration 27: loglikelihood = -1305.7246992776272, backtracks = 2, tol = 8.426292162090305e-5 1.448112 seconds (6.81 M allocations: 115.698 MiB, 5.37% gc time, 42.06% 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 **** 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 = -1541.9001882417006, backtracks = 0, tol = 0.1537960326897176 Iteration 2: loglikelihood = -1500.995190705116, backtracks = 0, tol = 0.10153204829643232 Iteration 3: loglikelihood = -1480.795871017362, backtracks = 0, tol = 0.17186010053225495 Iteration 4: loglikelihood = -1444.7020189610548, backtracks = 0, tol = 0.11218041022480439 Iteration 5: loglikelihood = -1430.3180821252665, backtracks = 0, tol = 0.07203381682478516 Iteration 6: loglikelihood = -1411.473356431029, backtracks = 0, tol = 0.05675572830234501 Iteration 7: loglikelihood = -1392.902998239949, backtracks = 0, tol = 0.09104048175499357 Iteration 8: loglikelihood = -1378.213626740218, backtracks = 1, tol = 0.01906373272108339 Iteration 9: loglikelihood = -1368.4977141685156, backtracks = 1, tol = 0.012835119430000264 Iteration 10: loglikelihood = -1360.4893593073027, backtracks = 1, tol = 0.07059772981165606 Iteration 11: loglikelihood = -1356.4753502439862, backtracks = 0, tol = 0.06885794438945539 Iteration 12: loglikelihood = -1352.6726746424092, backtracks = 0, tol = 0.0642503660839753 Iteration 13: loglikelihood = -1349.1096542131029, backtracks = 0, tol = 0.008436479442225786 Iteration 14: loglikelihood = -1346.261661396369, backtracks = 0, tol = 0.0012424300492125068 Iteration 15: loglikelihood = -1343.684791027338, backtracks = 0, tol = 0.0007514905325111859 Iteration 16: loglikelihood = -1341.398577352121, backtracks = 0, tol = 0.0002670344052702833 Iteration 17: loglikelihood = -1339.3320003818612, backtracks = 0, tol = 0.00020881396311345593 Iteration 18: loglikelihood = -1337.4716183851654, backtracks = 0, tol = 0.00012429036925670588 Iteration 19: loglikelihood = -1335.779322422192, backtracks = 0, tol = 0.00011212159281715766 Iteration 20: loglikelihood = -1334.9361127196096, backtracks = 0, tol = 0.0635458273798428 Iteration 21: loglikelihood = -1333.314883511956, backtracks = 0, tol = 0.00816283261644978 Iteration 22: loglikelihood = -1331.8555557797063, backtracks = 0, tol = 0.05974025062279621 Iteration 23: loglikelihood = -1330.3865384695853, backtracks = 0, tol = 0.007855938505877675 Iteration 24: loglikelihood = -1329.2934364745058, backtracks = 0, tol = 0.0010433184436573991 Iteration 25: loglikelihood = -1328.2578483738744, backtracks = 0, tol = 0.0007488978935659707 Iteration 26: loglikelihood = -1327.3156200704548, backtracks = 0, tol = 0.00029968815661312296 Iteration 27: loglikelihood = -1326.4316011039189, backtracks = 0, tol = 0.0002766706570829161 Iteration 28: loglikelihood = -1325.6145763121167, backtracks = 0, tol = 0.00012906719133295728 Iteration 29: loglikelihood = -1324.847929161424, backtracks = 0, tol = 0.00013531816964798942 Iteration 30: loglikelihood = -1324.1335069142006, backtracks = 0, tol = 5.7360221300452735e-5 0.348673 seconds (1.19 M allocations: 21.795 MiB, 2.87% 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 = -3776.1248, backtracks = 0, tol = 0.09216545068444472 Iteration 2: loglikelihood = -3734.7717, backtracks = 0, tol = 0.04230695985926279 Iteration 3: loglikelihood = -3730.165, backtracks = 1, tol = 0.012358250846704506 Iteration 4: loglikelihood = -3728.87, backtracks = 1, tol = 0.007695716695746335 Iteration 5: loglikelihood = -3728.5222, backtracks = 1, tol = 0.0038340184978837843 Iteration 6: loglikelihood = -3714.329, backtracks = 1, tol = 0.06456228245754203 Iteration 7: loglikelihood = -3711.7708, backtracks = 1, tol = 0.008878151765922177 Iteration 8: loglikelihood = -3710.7756, backtracks = 1, tol = 0.005553998546734537 Iteration 9: loglikelihood = -3710.4792, backtracks = 1, tol = 0.0032220905838411724 Iteration 10: loglikelihood = -3710.4028, backtracks = 1, tol = 0.0018309820136084788 Iteration 11: loglikelihood = -3710.381, backtracks = 1, tol = 0.0009878376426275936 Iteration 12: loglikelihood = -3710.3757, backtracks = 1, tol = 0.0005045882384247207 Iteration 13: loglikelihood = -3710.3735, backtracks = 1, tol = 0.0002578634107559852 Iteration 14: loglikelihood = -3710.3733, backtracks = 1, tol = 0.00012896496072263255 Iteration 15: loglikelihood = -3710.3772, backtracks = 3, tol = 1.6304166965390273e-5 22.952029 seconds (20.30 M allocations: 788.891 MiB, 0.95% gc time, 97.96% 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 = -3659.1948, backtracks = 0, tol = 0.09216545068444472 Iteration 2: loglikelihood = -3537.9644, backtracks = 0, tol = 0.0434786403720748 Iteration 3: loglikelihood = -3309.223, backtracks = 1, tol = 0.011861834587473542 Iteration 4: loglikelihood = -3037.7322, backtracks = 1, tol = 0.006875893743960675 Iteration 5: loglikelihood = -2977.194, backtracks = 0, tol = 0.1023828583080976 Iteration 6: loglikelihood = -2754.8142, backtracks = 0, tol = 0.10301768337689916 Iteration 7: loglikelihood = -2616.0366, backtracks = 0, tol = 0.09613197836964019 Iteration 8: loglikelihood = -2537.3057, backtracks = 0, tol = 0.10092426578971476 Iteration 9: loglikelihood = -2428.9521, backtracks = 0, tol = 0.1114610434010891 Iteration 10: loglikelihood = -2359.8948, backtracks = 0, tol = 0.10971435552627187 Iteration 11: loglikelihood = -2316.7263, backtracks = 0, tol = 0.1217607402518173 Iteration 12: loglikelihood = -2275.6133, backtracks = 0, tol = 0.12359718975319682 Iteration 13: loglikelihood = -2266.9329, backtracks = 0, tol = 0.12342831232043362 Iteration 14: loglikelihood = -2201.2063, backtracks = 1, tol = 0.09446677394972458 Iteration 15: loglikelihood = -2200.5576, backtracks = 0, tol = 0.09490963704566951 Iteration 16: loglikelihood = -2185.0518, backtracks = 1, tol = 0.08445939599312023 Iteration 17: loglikelihood = -2183.3289, backtracks = 1, tol = 0.023931304229159175 Iteration 18: loglikelihood = -2182.9456, backtracks = 1, tol = 0.010756676085941446 Iteration 19: loglikelihood = -2182.8477, backtracks = 1, tol = 0.0047196590099595065 Iteration 20: loglikelihood = -2182.8147, backtracks = 1, tol = 0.002043682429234685 Iteration 21: loglikelihood = -2182.8113, backtracks = 2, tol = 0.0004459788273481533 Iteration 22: loglikelihood = -2182.8088, backtracks = 2, tol = 0.0003230027724508978 Iteration 23: loglikelihood = -2182.8086, backtracks = 3, tol = 0.00011718041626224279 Iteration 24: loglikelihood = -2182.8088, backtracks = 3, tol = 0.00010124876304084903 Iteration 25: loglikelihood = -2182.8066, backtracks = 3, tol = 8.985777462019521e-5 0.142749 seconds (1.75 M allocations: 29.090 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 28.3s **** 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 **** Initializing β to univariate regression values... 50%|█ | ETA: 0:00:05Running 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 7.866625 seconds (1.20 M allocations: 127.519 MiB, 0.30% gc time, 93.50% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 8.2s 8.590860 seconds (3.94 M allocations: 80.111 MiB, 1.58% gc time, 0.66% compilation time) 5.432331 seconds (3.92 M allocations: 89.273 MiB, 0.41% gc time) 8.391739 seconds (22.09 M allocations: 457.357 MiB, 0.63% gc time, 0.47% compilation time) 9.287723 seconds (22.05 M allocations: 462.997 MiB, 0.56% gc time) 38.755542 seconds (2.47 M allocations: 4.149 GiB, 1.01% gc time, 35.51% compilation time) 54.108486 seconds (74.21 k allocations: 187.389 MiB, 0.07% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m12.7s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 11.525 ms (77 allocations: 5.30 KiB) 5.071 μs (0 allocations: 0 bytes) 132.889 μs (4 allocations: 288 bytes) 4.843 μs (0 allocations: 0 bytes) 37.310 μs (2 allocations: 64 bytes) 40.940 μs (0 allocations: 0 bytes) 35.269 μs (0 allocations: 0 bytes) 45.639 μs (0 allocations: 0 bytes) 62.959 μs (0 allocations: 0 bytes) 27.157 ms (77 allocations: 5.30 KiB) 22.320 μs (0 allocations: 0 bytes) 162.419 μs (4 allocations: 288 bytes) 29.770 μs (0 allocations: 0 bytes) 186.588 μs (2 allocations: 64 bytes) 90.059 μs (0 allocations: 0 bytes) 146.339 μs (0 allocations: 0 bytes) 192.518 μs (0 allocations: 0 bytes) 187.368 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m55.9s **** 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 **** **** 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 0.589686 seconds (53.43 k allocations: 5.537 MiB, 43.66% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 6.3s **** 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 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 2.884161 seconds (472.91 k allocations: 177.192 MiB, 1.29% gc time, 57.35% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 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 **** Cross validating... 3%|█ | ETA: 0:03:39 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: 0:00:34 Cross validating... 22%|███████▏ | ETA: 0:00:28 Cross validating... 25%|████████▏ | ETA: 0:00:24 Cross validating... 29%|█████████▏ | ETA: 0:00:21 Cross validating... 30%|█████████▋ | ETA: 0:00:20 Cross validating... 33%|██████████▋ | ETA: 0:00:17 Cross validating... 37%|███████████▋ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 62%|███████████████████▊ | ETA: 0:00:06 Cross validating... 65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 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... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 4599.493256965029 1 3166.308945251358 2 2074.684013474336 3 1533.7728104798505 4 995.1548556214655 5 619.6406733518587 6 450.4281696674809 7 409.80250645181866 8 371.39427636834637 9 353.78123769423894 10 344.7041000301876 11 348.4307310433501 12 351.11805506696123 13 352.3338685027891 14 365.0823956648158 15 364.343719523891 16 368.89827718134757 17 361.559735013436 18 375.44370000753804 19 379.388771891854 20 366.4612554872768 Best k = 10 12.334003 seconds (11.93 M allocations: 295.088 MiB, 0.44% gc time, 58.27% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 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: 0:00:05 Crossvalidation Results: k MSE 0 4599.493256965029 1 3175.03960627535 2 2088.247728581142 3 1545.1658835547105 4 1000.2655533633197 5 629.9847780888449 6 460.1956660668053 7 418.0415676382711 8 380.4645984618602 9 362.9042951743366 10 353.4010591903454 11 362.4864155556779 12 370.9435762507105 13 377.28477065009236 14 383.7282679989095 15 392.85241184168024 16 397.31689908088987 17 398.74593713878215 18 404.8396467563946 19 415.8279133726061 20 418.3675611371226 Best k = 10 5.319992 seconds (11.24 M allocations: 232.604 MiB, 0.80% gc time, 0.72% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.5s **** 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: 0:05:07 Cross validating... 8%|██▌ | ETA: 0:01:58 Cross validating... 13%|████▏ | ETA: 0:01:11 Cross validating... 17%|█████▋ | ETA: 0:00:49 Cross validating... 22%|███████▏ | ETA: 0:00:37 Cross validating... 25%|████████▏ | ETA: 0:00:31 Cross validating... 29%|█████████▏ | ETA: 0:00:27 Cross validating... 32%|██████████▏ | ETA: 0:00:23 Cross validating... 37%|███████████▋ | ETA: 0:00:19 Cross validating... 41%|█████████████▎ | ETA: 0:00:16 Cross validating... 46%|██████████████▊ | ETA: 0:00:13 Cross validating... 51%|████████████████▎ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:07 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 1596.462736328125 1 1290.347502319336 2 974.906127319336 3 816.7674070434571 4 609.3555854492188 5 511.1869947509766 6 452.5969119567871 7 374.20385931396487 8 356.153422454834 9 333.0926874694824 10 335.7018022155762 11 337.2532813415528 12 339.57688931274413 13 340.38692846679686 14 347.8132349243164 15 342.73985000610355 16 343.7248141784668 17 343.17574047851565 18 342.47355517578126 19 357.2303805847168 20 351.32513671875 Best k = 9 13.764512 seconds (12.99 M allocations: 282.879 MiB, 0.49% gc time, 77.61% 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... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:01 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... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | 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: 0:00:02 Crossvalidation Results: k MSE 0 1596.462736328125 1 1290.7574396972657 2 974.9241682739258 3 820.4758159179688 4 611.4184518432618 5 519.7411998901367 6 457.5894229431153 7 379.62677981567384 8 361.81497274780276 9 340.0072132873535 10 346.35391708374027 11 350.59136981201175 12 355.2021211547852 13 357.8753890686035 14 365.41548489379886 15 368.7959828796387 16 374.0033988952637 17 377.22617953491215 18 375.6431907043457 19 385.5491644897461 20 373.1568849182129 Best k = 9 3.261074 seconds (11.87 M allocations: 216.180 MiB, 1.32% gc time, 1.93% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 18.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:52 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 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... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 459.9619649989844 1 397.2911578135537 2 345.8058945876883 3 313.4184975065839 4 282.6003961895162 5 256.5216580222815 6 251.35724745964453 7 245.7959826947524 8 249.487638072903 9 262.90129350851697 10 249.76122755297084 11 253.54512587252566 12 272.288882187826 13 253.831119085198 14 270.7781000652373 15 281.37681070762017 16 297.4234731590751 17 261.6479578372574 18 280.9217128775875 19 264.78747926785394 20 297.67630535462524 Best k = 7 8.788346 seconds (18.85 M allocations: 433.204 MiB, 1.17% gc time, 26.41% 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... 5%|█▌ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:05 Cross validating... 29%|█████████▏ | 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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... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 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... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 459.9619649989844 1 397.47963634784423 2 346.08951928165095 3 316.0541527156014 4 284.8648044585359 5 259.6096001672905 6 247.65267893833948 7 252.86963319203 8 255.5393014889397 9 275.7074909582401 10 275.8832481665592 11 281.83711001686873 12 296.18125470956534 13 289.4246785428759 14 298.4346860389683 15 301.79537319108465 16 309.4944761834023 17 310.6636497410543 18 314.99059872149985 19 337.06936201838033 20 347.1508374351184 Best k = 6 6.676444 seconds (19.38 M allocations: 402.148 MiB, 0.83% gc time, 0.70% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:39 Cross validating... 6%|██ | ETA: 0:00:20 Cross validating... 10%|███ | ETA: 0:00:14 Cross validating... 13%|████▏ | ETA: 0:00:11 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... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 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100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.2221489583154 1 433.6508334855139 2 401.0401793437991 3 366.5252560404061 4 347.4912102555677 5 329.5412308266108 6 325.4394775910746 7 317.2648225494793 8 318.6868103422886 9 326.152502230598 10 325.0071459681321 11 325.02341118054375 12 336.5308475231459 13 329.6339503134001 14 365.3938390623407 15 347.7518601426369 16 342.9389196740459 17 358.90196177195344 18 352.31800504430186 19 372.52313259049424 20 405.59460463629995 Best k = 7 7.183398 seconds (17.39 M allocations: 399.577 MiB, 8.53% gc time, 25.41% 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... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 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: 0:00:03 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: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 462.2221489583154 1 434.8598694178545 2 402.94035288327757 3 371.1286747985171 4 353.13033686054564 5 334.0640443846077 6 332.9081621522358 7 327.39575972205165 8 333.6327965608232 9 335.59463401013954 10 344.95048184979527 11 349.84881082164986 12 357.47550375426755 13 357.8753094724365 14 374.7006105567129 15 386.1134994346292 16 388.6740606936439 17 396.40772599180616 18 416.3343645174973 19 424.5320971346405 20 428.9460521433817 Best k = 7 5.196959 seconds (18.18 M allocations: 367.960 MiB, 1.28% gc time, 1.22% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:51 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 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... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1309.2240869844043 1 777.0719751178164 2 587.0551140811563 3 505.2790001691342 4 508.70827525577243 5 465.2619518290493 6 462.06175037929864 7 448.9613249588681 8 459.43364413392067 9 438.66190454678264 10 427.0869333525006 11 412.8178620388578 12 440.6154549018178 13 465.632249266867 14 453.1281528289188 15 438.4002621311506 16 448.87856317656303 17 445.1771287301059 18 440.4783813528833 19 443.09029365272613 20 463.7645210895654 Best k = 11 8.415739 seconds (15.79 M allocations: 354.639 MiB, 0.72% gc time, 25.57% 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: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | 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... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1309.2240869844043 1 755.1556487271864 2 567.0131308978742 3 484.70192987057226 4 597.6296059798611 5 482.2709766154412 6 465.34686795684974 7 443.8374976454652 8 456.24997971564954 9 462.3970350613212 10 460.8576352295871 11 475.50083814193374 12 471.7148929435954 13 492.3053250249742 14 509.3057101579551 15 512.3110934979577 16 528.9792294097896 17 540.0851116824913 18 552.0586179585532 19 555.9514213864783 20 560.0929583143889 Best k = 7 6.221495 seconds (14.71 M allocations: 288.759 MiB, 0.65% gc time, 0.76% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 15.1s **** 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: 0:00:51 Cross validating... 5%|█▌ | ETA: 0:00:56 Cross validating... 6%|██ | ETA: 0:00:58 Cross validating... 8%|██▌ | ETA: 0:00:59 Cross validating... 11%|███▌ | ETA: 0:00:43 Cross validating... 13%|████▏ | ETA: 0:00:38 Cross validating... 14%|████▋ | ETA: 0:00:33 Cross validating... 16%|█████▏ | ETA: 0:00:30 Cross validating... 17%|█████▋ | ETA: 0:00:33 Cross validating... 19%|██████▏ | ETA: 0:00:30 Cross validating... 21%|██████▋ | ETA: 0:00:28 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 24%|███████▋ | ETA: 0:00:27 Cross validating... 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0:00:08 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:07 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 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: 0:00:03 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: 0:00:52 Crossvalidation Results: k MSE 0 488.4430155126876 1 337.86778031964514 2 276.83315765675735 3 241.26033867636662 4 225.6400171658206 5 210.11303881116794 6 202.64956517299552 7 203.35782131545494 8 203.67401583633364 9 201.45640614957603 10 201.46769632027502 11 201.8034698739873 12 205.05794330060178 13 206.3049865370112 14 201.35081508995103 15 205.51528320684952 16 206.2739613523125 17 206.50897291953726 18 205.56938607492535 19 206.21381767056118 20 207.26329693801716 Best k = 14 52.903262 seconds (160.25 M allocations: 3.996 GiB, 0.87% gc time, 3.45% 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: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:07 Cross validating... 16%|█████▏ | ETA: 0:00:07 Cross validating... 17%|█████▋ | ETA: 0:00:07 Cross 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| ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 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: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 488.4430155126876 1 338.5292371126735 2 278.0248151181745 3 242.96455928445602 4 228.4615707442263 5 213.9959195991163 6 206.60881492946558 7 208.50912665194582 8 212.07365131692904 9 208.5777032183521 10 211.1380679441485 11 213.6201126514096 12 221.36242081076477 13 228.05763917993426 14 225.21302146135835 15 226.19404683686903 16 230.3434989255282 17 227.72564764797448 18 236.48489794640176 19 231.5526806716302 20 243.26578462072996 Best k = 6 13.161181 seconds (39.40 M allocations: 801.428 MiB, 0.67% gc time, 0.36% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m06.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:56 Cross validating... 6%|██ | ETA: 0:00:29 Cross validating... 10%|███ | ETA: 0:00:20 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: 0:00:03 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: 0:00:02 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 0 691.7500225830079 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 6.207185 seconds (18.21 M allocations: 357.466 MiB, 0.93% gc time, 38.42% 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: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 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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 3.882389 seconds (17.44 M allocations: 307.806 MiB, 1.02% gc time, 1.48% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.6s **** 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... 2%|▋ | ETA: 0:01:08 Cross validating... 3%|█ | ETA: 0:00:49 Cross validating... 4%|█▎ | ETA: 0:00:39 Cross validating... 5%|█▋ | ETA: 0:00:33 Cross validating... 6%|█▉ | ETA: 0:00:29 Cross validating... 7%|██▎ | ETA: 0:00:26 Cross validating... 8%|██▌ | ETA: 0:00:24 Cross validating... 9%|██▉ | ETA: 0:00:23 Cross validating... 10%|███▎ | ETA: 0:00:22 Cross validating... 11%|███▌ | ETA: 0:00:21 Cross validating... 12%|███▉ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 14%|████▌ | ETA: 0:00:19 Cross validating... 15%|████▊ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:17 Cross validating... 18%|█████▊ | ETA: 0:00:17 Cross validating... 19%|██████▏ | ETA: 0:00:16 Cross validating... 20%|██████▍ | ETA: 0:00:16 Cross validating... 21%|██████▊ 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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: 0:00:14 Crossvalidation Results: k MSE 1 3801.1281955156255 2 3149.8245913718247 3 2769.453676337935 4 2488.6505429388253 5 2233.040731023486 6 1971.2866926740512 7 1865.9422682261634 8 1845.629676002165 9 1824.0806604162808 10 1849.9136053758684 11 1847.1792619479425 12 1844.3915672502403 13 1833.343234075659 14 1825.3104080208063 15 1848.7759473900524 16 1845.4183420691907 17 1866.621277889265 18 1864.9714991482183 19 1874.3371974069314 20 1866.06372281971 Best k = 9 15.603700 seconds (422.42 k allocations: 249.127 MiB, 0.29% gc time, 8.86% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 19.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m48.2s **** 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: 0:00:09 Cross validating... 4%|█▎ | ETA: 0:00:09 Cross validating... 6%|█▉ | ETA: 0:00:10 Cross validating... 7%|██▎ | ETA: 0:00:10 Cross validating... 8%|██▌ | ETA: 0:00:10 Cross validating... 9%|██▉ | ETA: 0:00:11 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 12%|███▉ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 14%|████▌ | ETA: 0:00:13 Cross validating... 15%|████▊ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▌ | ETA: 0:00:15 Cross validating... 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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: 0:00:09 Cross validating... 6%|█▉ | ETA: 0:00:10 Cross validating... 7%|██▎ | ETA: 0:00:10 Cross validating... 8%|██▌ | ETA: 0:00:10 Cross validating... 9%|██▉ | ETA: 0:00:11 Cross validating... 10%|███▎ | ETA: 0:00:12 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 12%|███▉ | ETA: 0:00:13 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 14%|████▌ | ETA: 0:00:13 Cross validating... 15%|████▊ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▌ | ETA: 0:00:15 Cross validating... 18%|█████▊ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:15 Cross validating... 20%|██████▍ | ETA: 0:00:15 Cross validating... 22%|███████ | ETA: 0:00:14 Cross validating... 24%|███████▋ | ETA: 0:00:13 Cross validating... 25%|████████ | ETA: 0:00:13 Cross validating... 26%|████████▍ | ETA: 0:00:12 Cross 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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: 0:00:10 Cross validating... 8%|██▌ | ETA: 0:00:10 Cross validating... 9%|██▉ 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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 1m17.1s 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: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:1704 [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 [16] eval @ ./boot.jl:430 [inlined] [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [18] _start() @ Base ./client.jl:531 Test Summary: | Error Total Time read BGEN and VCF | 1 1 6.0s 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 1068.24s 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:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1264.11s: package tests unexpectedly errored