Package evaluation of MendelIHT on Julia 1.11.5 (32ac370b68*) started at 2025-06-29T18:02:48.657 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.63s ################################################################################ # 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 v7.19.0 ⌅ [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 v1.0.3 [38540f10] + CommonSolve v0.2.4 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [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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[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 To see why use `status --outdated -m` Installation completed after 4.66s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 113.61s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_IW57Vr/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 v0.25.120 [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 v2.5.1 [2913bbd2] StatsBase v0.34.5 [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_IW57Vr/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.19.0 ⌅ [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 14.3s 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 6.1s 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 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 2.1s 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 = -1566.213585233816, backtracks = 0, tol = 1.485987341046773 Iteration 2: loglikelihood = -1415.8470214149543, backtracks = 0, tol = 0.18760422061326762 Iteration 3: loglikelihood = -1410.652040860545, backtracks = 0, tol = 0.0221092575208584 Iteration 4: loglikelihood = -1410.6079594996731, backtracks = 0, tol = 0.0021335142583326972 Iteration 5: loglikelihood = -1410.6074689073641, backtracks = 0, tol = 0.0002422864317643774 Iteration 6: loglikelihood = -1410.6074608137924, backtracks = 0, tol = 2.792015123491862e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.056717872619628906 Final loglikelihood: -1410.6074608137924 SNP PVE: 0.9131292263273396 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1480 0.991878 2 │ 2234 1.17645 3 │ 2399 0.767983 4 │ 2683 -1.49094 5 │ 2789 1.10116 6 │ 3787 -1.46384 7 │ 5512 1.1354 8 │ 7363 0.77508 9 │ 8308 -0.62308 10 │ 8336 -0.251743 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00946765Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 21.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 3.0s **** 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 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 = -1888.1927037457433, backtracks = 0, tol = 0.280714145078066 Iteration 2: loglikelihood = -1561.3888169245754, backtracks = 0, tol = 0.06177785701713626 Iteration 3: loglikelihood = -1421.4002190887275, backtracks = 0, tol = 0.053884536603343254 Iteration 4: loglikelihood = -1360.2266172421616, backtracks = 0, tol = 0.08505695388586305 Iteration 5: loglikelihood = -1333.410051057507, backtracks = 0, tol = 0.06002116873268233 Iteration 6: loglikelihood = -1321.2908522053563, backtracks = 0, tol = 0.04251688318308212 Iteration 7: loglikelihood = -1311.4571836020527, backtracks = 0, tol = 0.0862414433470512 Iteration 8: loglikelihood = -1306.954318766259, backtracks = 0, tol = 0.019990921001374437 Iteration 9: loglikelihood = -1305.5881186928516, backtracks = 1, tol = 0.01040031718922899 Iteration 10: loglikelihood = -1304.940968913444, backtracks = 1, tol = 0.01174123687071465 Iteration 11: loglikelihood = -1304.604000440796, backtracks = 1, tol = 0.004820121431303008 Iteration 12: loglikelihood = -1304.381631851097, backtracks = 1, tol = 0.007034866732890437 Iteration 13: loglikelihood = -1304.2654824022484, backtracks = 1, tol = 0.002754678814786487 Iteration 14: loglikelihood = -1304.1842158698048, backtracks = 1, tol = 0.004328312900915577 Iteration 15: loglikelihood = -1304.1444194600263, backtracks = 1, tol = 0.0015264320054851756 Iteration 16: loglikelihood = -1304.1135353276688, backtracks = 1, tol = 0.002757928846993598 Iteration 17: loglikelihood = -1304.0959628521857, backtracks = 0, tol = 0.001597148649865347 Iteration 18: loglikelihood = -1304.086550560236, backtracks = 0, tol = 0.001226841323514468 Iteration 19: loglikelihood = -1304.0814701029858, backtracks = 0, tol = 0.0008756112781818987 Iteration 20: loglikelihood = -1304.0787667543818, backtracks = 0, tol = 0.0006533829370155863 Iteration 21: loglikelihood = -1304.0776828659293, backtracks = 1, tol = 0.00023586963040470865 Iteration 22: loglikelihood = -1304.0767312632117, backtracks = 1, tol = 0.0005034900758925054 Iteration 23: loglikelihood = -1304.0762717817986, backtracks = 0, tol = 0.00023110884476560542 Iteration 24: loglikelihood = -1304.076015521838, backtracks = 0, tol = 0.00021243787443935607 Iteration 25: loglikelihood = -1304.0758724505552, backtracks = 0, tol = 0.00012937384154084646 Iteration 26: loglikelihood = -1304.075792716762, backtracks = 0, tol = 0.00011838045761648534 Iteration 27: loglikelihood = -1304.0757482547428, backtracks = 0, tol = 7.224880310565341e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1574.8310982237028, backtracks = 0, tol = 0.28126059130257447 Iteration 2: loglikelihood = -1514.5832382887336, backtracks = 0, tol = 0.16389198436096805 Iteration 3: loglikelihood = -1495.428767252026, backtracks = 0, tol = 0.09856601335590626 Iteration 4: loglikelihood = -1492.5914625540688, backtracks = 0, tol = 0.09676846789712483 Iteration 5: loglikelihood = -1492.0623203758712, backtracks = 0, tol = 0.018393237662047302 Iteration 6: loglikelihood = -1492.0386634100482, backtracks = 1, tol = 0.002446749131086356 Iteration 7: loglikelihood = -1492.029991294893, backtracks = 1, tol = 0.0018352743705088179 Iteration 8: loglikelihood = -1492.027662850498, backtracks = 1, tol = 0.0010746662593225668 Iteration 9: loglikelihood = -1492.0270756548916, backtracks = 1, tol = 0.000521791357090261 Iteration 10: loglikelihood = -1492.0269274013738, backtracks = 1, tol = 0.00026284930535447283 Iteration 11: loglikelihood = -1492.0268899394694, backtracks = 1, tol = 0.0001312464435482369 Iteration 12: loglikelihood = -1492.0268804552131, backtracks = 1, tol = 6.601004236876026e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1808.6102939885466, backtracks = 0, tol = 0.7372399443429353 Iteration 2: loglikelihood = -1431.020074559626, backtracks = 0, tol = 0.18179079301009782 Iteration 3: loglikelihood = -1395.0931371634879, backtracks = 0, tol = 0.04071817450851689 Iteration 4: loglikelihood = -1394.449355522029, backtracks = 0, tol = 0.005006038721143925 Iteration 5: loglikelihood = -1394.446285752748, backtracks = 1, tol = 0.00017757155541014446 Iteration 6: loglikelihood = -1394.4454897335138, backtracks = 1, tol = 9.626500753682967e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.9s **** 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) = 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 = -1654.9793961626517, backtracks = 0, tol = 0.7014775281512794 Iteration 2: loglikelihood = -1420.298561181075, backtracks = 0, tol = 0.13789122605257298 Iteration 3: loglikelihood = -1399.8187699146906, backtracks = 0, tol = 0.044918582950448045 Iteration 4: loglikelihood = -1396.7720316625964, backtracks = 0, tol = 0.027096557829758783 Iteration 5: loglikelihood = -1396.3974886059664, backtracks = 0, tol = 0.028973992425890143 Iteration 6: loglikelihood = -1396.2571731204894, backtracks = 0, tol = 0.0026697804976801016 Iteration 7: loglikelihood = -1396.248532206923, backtracks = 0, tol = 0.02661282026493903 Iteration 8: loglikelihood = -1396.1789188957591, backtracks = 1, tol = 0.0008007824253381505 Iteration 9: loglikelihood = -1396.1610142904667, backtracks = 1, tol = 0.0004015698632002549 Iteration 10: loglikelihood = -1396.156422854799, backtracks = 1, tol = 0.0001993440442139547 Iteration 11: loglikelihood = -1396.155249740972, backtracks = 1, tol = 0.00010619426873845063 Iteration 12: loglikelihood = -1396.1549511680405, backtracks = 1, tol = 5.8844280133933866e-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 8.5s **** 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 = -1523.3921554765066, backtracks = 0, tol = 0.18524659945098854 Iteration 2: loglikelihood = -1462.4896352637822, backtracks = 0, tol = 0.10367881838739776 Iteration 3: loglikelihood = -1411.643919814839, backtracks = 0, tol = 0.135302079845185 Iteration 4: loglikelihood = -1387.3865420047252, backtracks = 0, tol = 0.07783808570006093 Iteration 5: loglikelihood = -1376.388992339943, backtracks = 0, tol = 0.08126185908177669 Iteration 6: loglikelihood = -1369.2763564627326, backtracks = 0, tol = 0.037042323660204345 Iteration 7: loglikelihood = -1360.1817889898316, backtracks = 1, tol = 0.07704670016296505 Iteration 8: loglikelihood = -1356.3294427821954, backtracks = 0, tol = 0.04634499975909431 Iteration 9: loglikelihood = -1355.4198130724121, backtracks = 0, tol = 0.01810756406433838 Iteration 10: loglikelihood = -1355.0852994284962, backtracks = 0, tol = 0.01067026272602671 Iteration 11: loglikelihood = -1354.9616572877744, backtracks = 0, tol = 0.006714726587903297 Iteration 12: loglikelihood = -1354.915569112466, backtracks = 0, tol = 0.003625474797787283 Iteration 13: loglikelihood = -1354.8984009455519, backtracks = 0, tol = 0.0024803391312237647 Iteration 14: loglikelihood = -1354.8920861660251, backtracks = 0, tol = 0.0013341544190910804 Iteration 15: loglikelihood = -1354.8897364935865, backtracks = 0, tol = 0.0009157196815110253 Iteration 16: loglikelihood = -1354.8888754780958, backtracks = 0, tol = 0.0004917507264509959 Iteration 17: loglikelihood = -1354.8885546438455, backtracks = 0, tol = 0.0003386897758289118 Iteration 18: loglikelihood = -1354.8884369868822, backtracks = 0, tol = 0.00018147761453270612 Iteration 19: loglikelihood = -1354.888393036329, backtracks = 0, tol = 0.000125600369966357 Iteration 20: loglikelihood = -1354.8883768797884, backtracks = 0, tol = 6.713100396993585e-5 0.985789 seconds (2.00 M allocations: 38.952 MiB, 6.40% gc time, 60.36% 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 = -1553.674580693751, backtracks = 0, tol = 0.18524659945098854 Iteration 2: loglikelihood = -1511.0409418557408, backtracks = 0, tol = 0.10367881838739776 Iteration 3: loglikelihood = -1482.155504873226, backtracks = 0, tol = 0.1198025309016644 Iteration 4: loglikelihood = -1454.4377126930465, backtracks = 0, tol = 0.07885190989659253 Iteration 5: loglikelihood = -1439.4063464455958, backtracks = 0, tol = 0.08056719553703856 Iteration 6: loglikelihood = -1426.0418674448615, backtracks = 0, tol = 0.04813835896779292 Iteration 7: loglikelihood = -1414.5710393695972, backtracks = 0, tol = 0.0907371356577546 Iteration 8: loglikelihood = -1406.7203289168376, backtracks = 0, tol = 0.08708773545852538 Iteration 9: loglikelihood = -1400.9900935851895, backtracks = 0, tol = 0.010250116366186416 Iteration 10: loglikelihood = -1396.8580628696334, backtracks = 0, tol = 0.07942952779412904 Iteration 11: loglikelihood = -1392.2042707461012, backtracks = 0, tol = 0.015048670972027908 Iteration 12: loglikelihood = -1388.7106867931088, backtracks = 0, tol = 0.0013203977437946733 Iteration 13: loglikelihood = -1385.7011673915263, backtracks = 0, tol = 0.0004267227641000673 Iteration 14: loglikelihood = -1383.1057945020243, backtracks = 0, tol = 0.0002621014356358431 Iteration 15: loglikelihood = -1380.8370719721195, backtracks = 0, tol = 0.0002122906501220033 Iteration 16: loglikelihood = -1378.845339761135, backtracks = 0, tol = 0.0001979552510390467 Iteration 17: loglikelihood = -1377.0825347729626, backtracks = 0, tol = 0.0001811088959404599 Iteration 18: loglikelihood = -1375.5147922808405, backtracks = 0, tol = 0.00016644842488761533 Iteration 19: loglikelihood = -1374.112454962759, backtracks = 0, tol = 0.00015923065491964586 Iteration 20: loglikelihood = -1372.852491790259, backtracks = 0, tol = 0.0001493337777162764 Iteration 21: loglikelihood = -1371.7153269245835, backtracks = 0, tol = 0.0001425408730655065 Iteration 22: loglikelihood = -1370.685008646391, backtracks = 0, tol = 0.00013509690305934683 Iteration 23: loglikelihood = -1369.7480230767724, backtracks = 0, tol = 0.00012894029498787445 Iteration 24: loglikelihood = -1368.8930606993138, backtracks = 0, tol = 0.00012288696862767506 Iteration 25: loglikelihood = -1368.110482301513, backtracks = 0, tol = 0.00011749845167968835 Iteration 26: loglikelihood = -1367.3920823564815, backtracks = 0, tol = 0.00011238670683963023 Iteration 27: loglikelihood = -1366.7308060193639, backtracks = 0, tol = 0.00010769912468863084 Iteration 28: loglikelihood = -1366.1205725942307, backtracks = 0, tol = 0.00010329675031306706 Iteration 29: loglikelihood = -1365.556107226609, backtracks = 0, tol = 9.920607207283025e-5 0.303823 seconds (1.10 M allocations: 20.056 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3621.7878, backtracks = 0, tol = 0.07696202595658899 Iteration 2: loglikelihood = -3588.8308, backtracks = 0, tol = 0.04015932457153194 Iteration 3: loglikelihood = -3585.5876, backtracks = 1, tol = 0.009246350384091962 Iteration 4: loglikelihood = -3558.912, backtracks = 1, tol = 0.06331226410187282 Iteration 5: loglikelihood = -3534.6316, backtracks = 0, tol = 0.08477890168631268 Iteration 6: loglikelihood = -3531.69, backtracks = 1, tol = 0.006096378722704455 Iteration 7: loglikelihood = -3530.7053, backtracks = 1, tol = 0.0037156951028487514 Iteration 8: loglikelihood = -3530.4014, backtracks = 1, tol = 0.002422577888114083 Iteration 9: loglikelihood = -3530.3093, backtracks = 1, tol = 0.0016340333217936456 Iteration 10: loglikelihood = -3519.5444, backtracks = 1, tol = 0.07261019210735735 Iteration 11: loglikelihood = -3518.5083, backtracks = 1, tol = 0.004495170566304137 Iteration 12: loglikelihood = -3518.2273, backtracks = 1, tol = 0.0020997475933178045 Iteration 13: loglikelihood = -3518.1536, backtracks = 1, tol = 0.0009975449147111533 Iteration 14: loglikelihood = -3518.1335, backtracks = 1, tol = 0.0005208212802393693 Iteration 15: loglikelihood = -3518.1272, backtracks = 1, tol = 0.0002772616822000355 Iteration 16: loglikelihood = -3518.1245, backtracks = 1, tol = 0.00016720935922887538 Iteration 17: loglikelihood = -3518.1262, backtracks = 3, tol = 2.605632423604305e-5 24.995327 seconds (20.90 M allocations: 798.975 MiB, 0.97% gc time, 97.00% 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 = -3523.056, backtracks = 0, tol = 0.07696202595658899 Iteration 2: loglikelihood = -3421.0818, backtracks = 0, tol = 0.040984203714542616 Iteration 3: loglikelihood = -3205.0193, backtracks = 1, tol = 0.009134943056355685 Iteration 4: loglikelihood = -2976.9573, backtracks = 1, tol = 0.005058466728565669 Iteration 5: loglikelihood = -2831.3108, backtracks = 0, tol = 0.08728691623876401 Iteration 6: loglikelihood = -2693.6624, backtracks = 0, tol = 0.09575049323463976 Iteration 7: loglikelihood = -2577.816, backtracks = 0, tol = 0.08524857369040849 Iteration 8: loglikelihood = -2485.488, backtracks = 0, tol = 0.08307663498129704 Iteration 9: loglikelihood = -2399.2612, backtracks = 0, tol = 0.09503284419588176 Iteration 10: loglikelihood = -2322.2253, backtracks = 0, tol = 0.09408509620342549 Iteration 11: loglikelihood = -2270.418, backtracks = 0, tol = 0.09519273627451204 Iteration 12: loglikelihood = -2226.1504, backtracks = 0, tol = 0.09431322448015035 Iteration 13: loglikelihood = -2204.1038, backtracks = 0, tol = 0.09561478896594246 Iteration 14: loglikelihood = -2182.9858, backtracks = 0, tol = 0.0948183652981608 Iteration 15: loglikelihood = -2173.6306, backtracks = 0, tol = 0.09571224661249056 Iteration 16: loglikelihood = -2167.646, backtracks = 0, tol = 0.09498173126498768 Iteration 17: loglikelihood = -2164.566, backtracks = 0, tol = 0.09281053779288391 Iteration 18: loglikelihood = -2163.411, backtracks = 0, tol = 0.09254366295409816 Iteration 19: loglikelihood = -2162.5999, backtracks = 0, tol = 0.0953856286002596 Iteration 20: loglikelihood = -2162.2634, backtracks = 0, tol = 0.09491892873939563 Iteration 21: loglikelihood = -2162.0818, backtracks = 0, tol = 0.09580857236789347 Iteration 22: loglikelihood = -2161.9648, backtracks = 0, tol = 0.09532394552527723 Iteration 23: loglikelihood = -2161.958, backtracks = 0, tol = 0.0958946689845359 Iteration 24: loglikelihood = -2161.8901, backtracks = 0, tol = 0.0954081906059939 Iteration 25: loglikelihood = -2161.0884, backtracks = 1, tol = 0.009337390153180828 Iteration 26: loglikelihood = -2160.9116, backtracks = 1, tol = 0.005059995329515553 Iteration 27: loglikelihood = -2160.868, backtracks = 1, tol = 0.0027379835016637898 Iteration 28: loglikelihood = -2160.8596, backtracks = 1, tol = 0.0014605110921158283 Iteration 29: loglikelihood = -2160.8582, backtracks = 1, tol = 0.0007600911597985902 Iteration 30: loglikelihood = -2160.8552, backtracks = 2, tol = 0.0001916476204905327 Iteration 31: loglikelihood = -2160.854, backtracks = 1, tol = 0.00028405255065202644 Iteration 32: loglikelihood = -2160.8518, backtracks = 1, tol = 0.00016952463129422138 Iteration 33: loglikelihood = -2160.851, backtracks = 2, tol = 5.0652705006369956e-5 0.279759 seconds (1.87 M allocations: 30.844 MiB, 5.15% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 29.9s **** 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 **** Initializing β to univariate regression values... 0%| | ETA: 9:18:21Running 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 10.778304 seconds (1.21 M allocations: 128.093 MiB, 0.42% gc time, 93.73% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 11.2s 9.176031 seconds (3.94 M allocations: 80.114 MiB, 0.66% gc time, 0.56% compilation time) 5.640748 seconds (3.92 M allocations: 89.275 MiB, 0.29% gc time) 9.780497 seconds (22.09 M allocations: 457.362 MiB, 0.78% gc time, 0.41% compilation time) 9.403437 seconds (22.05 M allocations: 462.994 MiB, 0.71% gc time) 38.973686 seconds (2.48 M allocations: 4.149 GiB, 0.90% gc time, 36.92% compilation time) 54.073021 seconds (74.21 k allocations: 187.398 MiB, 0.08% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m15.4s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 11.445 ms (77 allocations: 5.30 KiB) 4.997 μs (0 allocations: 0 bytes) 133.949 μs (4 allocations: 288 bytes) 5.632 μs (0 allocations: 0 bytes) 44.089 μs (2 allocations: 64 bytes) 40.669 μs (0 allocations: 0 bytes) 30.180 μs (0 allocations: 0 bytes) 30.280 μs (0 allocations: 0 bytes) 61.970 μs (0 allocations: 0 bytes) 31.046 ms (77 allocations: 5.30 KiB) 22.649 μs (0 allocations: 0 bytes) 184.048 μs (4 allocations: 288 bytes) 29.880 μs (0 allocations: 0 bytes) 222.048 μs (2 allocations: 64 bytes) 96.409 μs (0 allocations: 0 bytes) 157.838 μs (0 allocations: 0 bytes) 209.478 μs (0 allocations: 0 bytes) 183.088 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m56.1s **** 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 **** **** 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 0.590260 seconds (53.53 k allocations: 5.548 MiB, 42.67% 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 2.829355 seconds (473.29 k allocations: 177.248 MiB, 1.33% gc time, 57.82% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 3.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:41 Cross validating... 6%|██ | ETA: 0:01:49 Cross validating... 10%|███ | ETA: 0:01:11 Cross validating... 13%|████▏ | ETA: 0:00:53 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... 32%|██████████▏ | ETA: 0:00:19 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 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97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 3812.330821292835 1 3067.4289734365175 2 2395.150703275532 3 2122.2598872158237 4 1673.5791262393334 5 1292.192843672035 6 918.8842960349233 7 691.0876058842387 8 488.5962966669689 9 354.68283907783416 10 332.4884651909555 11 335.1824693974073 12 336.8348808025907 13 338.94581198932127 14 338.7824999748769 15 343.18946686367576 16 353.6647274390783 17 356.49904219486007 18 343.02560239032334 19 355.31545014147446 20 351.29135621374326 Best k = 10 12.411740 seconds (12.25 M allocations: 303.386 MiB, 0.44% gc time, 58.19% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 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... 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: 0:00:01 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... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 3812.330821292835 1 3068.5520936676858 2 2398.207938299273 3 2133.2232376733846 4 1727.1476625802752 5 1297.7533514962638 6 920.8760460294195 7 696.1950843735018 8 492.31778225856584 9 358.33110478801416 10 335.83599381833096 11 342.4885223405556 12 347.9360051814715 13 355.90786029992535 14 354.40421917923504 15 359.9346479767414 16 370.473822133319 17 383.0101298599101 18 370.0299295118451 19 385.2499462163168 20 392.3536812134988 Best k = 10 5.460717 seconds (11.34 M allocations: 234.899 MiB, 0.71% gc time, 0.69% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 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: 0:05:20 Cross validating... 8%|██▌ | ETA: 0:02:03 Cross validating... 13%|████▏ | ETA: 0:01:14 Cross validating... 17%|█████▋ | ETA: 0:00:51 Cross validating... 22%|███████▏ | ETA: 0:00:39 Cross validating... 25%|████████▏ | ETA: 0:00:33 Cross validating... 29%|█████████▏ | ETA: 0:00:28 Cross validating... 32%|██████████▏ | ETA: 0:00:24 Cross validating... 37%|███████████▋ | ETA: 0:00:20 Cross validating... 41%|█████████████▎ | ETA: 0:00:17 Cross validating... 46%|██████████████▊ | ETA: 0:00:14 Cross validating... 51%|████████████████▎ | ETA: 0:00:11 Cross validating... 56%|█████████████████▊ | ETA: 0:00:10 Cross validating... 59%|██████████████████▊ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:05 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 1534.1736259765626 1 1338.8358138427734 2 1076.5027670898437 3 883.8094380493164 4 716.1038896484375 5 531.8231918334961 6 473.4780180053711 7 386.0693975830078 8 363.4024222412109 9 345.86187857055666 10 349.82352371215825 11 352.32402505493167 12 354.9933956298828 13 365.1153628234863 14 357.3312015075684 15 375.5406383666992 16 376.7457078552246 17 377.5170079345703 18 383.3516274719238 19 365.49834878540037 20 368.4868383483887 Best k = 9 14.262459 seconds (12.90 M allocations: 278.975 MiB, 0.48% gc time, 78.06% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | 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... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | 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... 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 1534.1736259765626 1 1343.8243012695311 2 1081.705096801758 3 888.1462337646484 4 720.8328638305663 5 536.3564529418945 6 480.7743207092285 7 392.54249862670895 8 370.71040618896484 9 355.31991650390626 10 365.0807710876465 11 371.0712183227539 12 377.4934324645996 13 381.3933801574707 14 388.74663574218744 15 399.286630859375 16 410.00875799560544 17 419.0920640258789 18 414.29404492187496 19 416.3692508544922 20 420.69170953369144 Best k = 9 3.397457 seconds (12.20 M allocations: 221.458 MiB, 1.29% gc time, 2.38% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.3s **** 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: 0:00:49 Cross validating... 5%|█▌ | ETA: 0:00:34 Cross validating... 8%|██▌ | ETA: 0:00:22 Cross validating... 11%|███▌ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross 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100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 466.7390143237617 1 435.66017392223193 2 380.8640316647269 3 346.6995537686065 4 324.78066987391287 5 289.3058089293385 6 262.8502236557908 7 243.926991209199 8 220.41646007322936 9 218.44549836745992 10 224.6690476223077 11 228.50598650261347 12 225.17090782916262 13 224.38726632392837 14 242.96910141207883 15 231.05201745438933 16 261.047554716782 17 234.50886303229333 18 252.46528909099993 19 261.8894122879227 20 251.14464706964293 Best k = 9 8.463635 seconds (17.78 M allocations: 408.364 MiB, 1.01% gc time, 24.58% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 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: 0:00:05 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... 24%|███████▋ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:05 Cross validating... 29%|█████████▏ | ETA: 0:00:05 Cross validating... 30%|█████████▋ | ETA: 0:00:05 Cross validating... 32%|██████████▏ | ETA: 0:00:05 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 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0:00:06 Crossvalidation Results: k MSE 0 466.7390143237617 1 436.76106299148887 2 383.14457856780615 3 348.7336634349804 4 326.94734630323853 5 292.8560228714278 6 266.15886551184917 7 247.48853078985218 8 224.19909281696118 9 225.2643246025636 10 235.17196850999244 11 232.16224663701428 12 245.78967133947359 13 242.13849440096004 14 242.93322409836708 15 257.3776557132567 16 259.4261677901905 17 263.3578325484242 18 272.35647950547866 19 280.76659328010396 20 277.75635400653545 Best k = 8 6.804336 seconds (18.87 M allocations: 387.147 MiB, 0.77% gc time, 0.61% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.7s **** 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: 0:00:39 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... 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... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 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... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 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 0 463.14841004928644 1 434.22388097573423 2 405.10800310885975 3 375.8828731780299 4 352.2362407860853 5 341.8943671250582 6 339.8988186874242 7 335.4886576241573 8 340.0847686909134 9 338.0029072108102 10 338.2558431546704 11 353.40444834323705 12 370.21530342777135 13 349.457881222352 14 344.79213730792446 15 377.1820889092502 16 365.6402586578612 17 383.9230167785136 18 379.0530179150534 19 428.4592810275975 20 396.8998106438107 Best k = 7 7.101093 seconds (17.30 M allocations: 398.380 MiB, 9.04% gc time, 25.74% 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: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 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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 0 463.14841004928644 1 434.3802105615297 2 405.34156519707034 3 376.3287103495372 4 353.9053710158588 5 344.89433362086663 6 343.54322492743955 7 345.4071347803893 8 358.3154031868371 9 357.14257385647045 10 368.48645047864426 11 399.41616953959317 12 407.9165436795026 13 401.3497550975883 14 418.2229982800369 15 416.26168306120314 16 429.0831303555883 17 452.73750059986486 18 454.8376775063949 19 464.32503620815453 20 466.693802850494 Best k = 6 5.232249 seconds (18.21 M allocations: 368.259 MiB, 0.83% gc time, 1.14% 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: 0:00:52 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | 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... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | 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... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | 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... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 859.431314615756 1 813.6501155705361 2 757.0755130020661 3 662.9299523903983 4 533.5926290020395 5 487.23950675600133 6 428.5856366766773 7 399.0609413612927 8 360.1063760039719 9 345.79251951871186 10 347.45671319487906 11 348.51272019572286 12 349.29027261829935 13 362.9084269059482 14 353.425335964898 15 360.36996782674544 16 364.3086923490408 17 374.8292568072234 18 370.36819302565584 19 379.17508892539587 20 367.5149308298752 Best k = 9 8.657949 seconds (16.96 M allocations: 398.661 MiB, 0.95% gc time, 25.27% 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: 0:00:05 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... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 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79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 859.431314615756 1 799.7010903518538 2 739.8873964169909 3 652.2551778402332 4 540.5855070468374 5 500.504983675934 6 435.5131656332849 7 402.21077193871963 8 367.37403452857836 9 348.7649181946735 10 362.78801226031163 11 368.2157155884791 12 372.8069394336735 13 369.9406811254399 14 382.0872889453907 15 376.5086287187565 16 388.7865803260814 17 407.3769380033321 18 405.59744266417243 19 400.19834417551624 20 413.51874778642525 Best k = 9 6.308467 seconds (15.45 M allocations: 308.667 MiB, 0.71% gc time, 0.76% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 15.4s **** 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... 3%|█ | ETA: 0:01:18 Cross validating... 6%|██ | ETA: 0:00:53 Cross validating... 10%|███ | ETA: 0:00:36 Cross validating... 11%|███▌ | ETA: 0:00:39 Cross validating... 13%|████▏ | ETA: 0:00:41 Cross validating... 14%|████▋ | ETA: 0:00:42 Cross validating... 16%|█████▏ | ETA: 0:00:42 Cross validating... 19%|██████▏ | ETA: 0:00:38 Cross validating... 21%|██████▋ | ETA: 0:00:34 Cross validating... 22%|███████▏ | ETA: 0:00:35 Cross validating... 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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... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:44 Crossvalidation Results: k MSE 0 366.7918770496879 1 334.11966551307796 2 302.49705173122334 3 271.89602505464774 4 258.9954221128076 5 237.54452270577542 6 216.2641365143541 7 204.68581594174455 8 204.76512813754448 9 196.591711333663 10 198.03264730632125 11 196.35718917905214 12 197.21462520494174 13 198.82316473547624 14 199.77331192895815 15 199.83016658815743 16 201.3989603025494 17 200.90041115917805 18 201.49654257134793 19 201.45544471950316 20 204.0114265329142 Best k = 11 45.337313 seconds (153.91 M allocations: 3.850 GiB, 0.99% gc time, 3.79% 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... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 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62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 366.7918770496879 1 332.5962447445092 2 301.5430441627941 3 273.0637490342639 4 268.5054032468137 5 241.2733398429468 6 221.49511759706343 7 208.04154858006748 8 209.74457771936383 9 211.91290698537304 10 207.671729613665 11 207.7222296410368 12 210.3368966734423 13 215.4326709604473 14 216.78371362850606 15 223.54516508624033 16 220.65493659398197 17 224.67250011147297 18 224.02459533883075 19 225.95011666689254 20 227.97977662014756 Best k = 10 10.590761 seconds (33.13 M allocations: 673.539 MiB, 0.78% gc time, 0.40% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 56.3s **** 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: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross 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validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 691.7500225830079 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 5.760598 seconds (18.20 M allocations: 357.309 MiB, 1.65% gc time, 37.47% 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... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 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 3.873361 seconds (17.44 M allocations: 307.807 MiB, 1.03% gc time, 1.52% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:04 Cross validating... 4%|█▎ | ETA: 0:00:35 Cross validating... 6%|█▉ | ETA: 0:00:26 Cross validating... 8%|██▌ | ETA: 0:00:22 Cross validating... 9%|██▉ | ETA: 0:00:20 Cross validating... 10%|███▎ | ETA: 0:00:19 Cross validating... 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Pass Total Time wrapper univariate | 20 20 1m36.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:07 Cross validating... 4%|█▎ | ETA: 0:00:07 Cross validating... 6%|█▉ | ETA: 0:00:08 Cross validating... 7%|██▎ | ETA: 0:00:08 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 9%|██▉ | ETA: 0:00:09 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: 0:00:14 Cross validating... 19%|██████▏ | ETA: 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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... 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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 **** 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: 0:00:09 Cross validating... 7%|██▎ | ETA: 0:00:10 Cross validating... 8%|██▌ | ETA: 0:00:10 Cross validating... 9%|██▉ | ETA: 0:00:10 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 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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 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m14.6s 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 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 1050.91s 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:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1198.59s: package tests unexpectedly errored