Package evaluation to test MendelIHT on Julia 1.11.7 (58327cce5e*) started at 2025-10-29T04:24:49.250 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.64s ################################################################################ # 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 v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.15 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.6 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.58s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 59.88s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_3MX7tQ/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [38e38edf] GLM v1.9.0 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.7 [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_3MX7tQ/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 [67c07d97] Automa v1.1.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools 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Testing Running tests... Precompiling MendelIHT... 273163.8 ms ✓ MendelIHT 1 dependency successfully precompiled in 279 seconds. 166 already precompiled. ┌ 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 1.6s Test Summary: | Pass Total Time _choose! | 7 7 8.7s 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 2.1s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1684.7429652002284, backtracks = 0, tol = 1.866018565483602 Iteration 2: loglikelihood = -1419.0283068561457, backtracks = 0, tol = 0.19516909306718858 Iteration 3: loglikelihood = -1406.8177799089367, backtracks = 0, tol = 0.02399288572853595 Iteration 4: loglikelihood = -1406.690810003218, backtracks = 0, tol = 0.003366423511308532 Iteration 5: loglikelihood = -1406.6885220682811, backtracks = 0, tol = 0.00047225546505648853 Iteration 6: loglikelihood = -1406.688477325433, backtracks = 0, tol = 6.054990329246243e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05584907531738281 Final loglikelihood: -1406.688477325433 SNP PVE: 0.9448672007468594 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 670 -0.643732 2 │ 2778 1.96196 3 │ 4405 1.49521 4 │ 5049 -0.760758 5 │ 6145 -1.59246 6 │ 6450 1.1145 7 │ 6482 -0.564472 8 │ 7628 -0.135404 9 │ 8330 -1.28207 10 │ 8803 1.95821 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.00555895Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 21.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -357.05406929589384, backtracks = 0, tol = 0.8380082173781972 Iteration 2: loglikelihood = -253.69247673658248, backtracks = 0, tol = 0.38139022833574177 Iteration 3: loglikelihood = -242.78890265594725, backtracks = 0, tol = 0.21772646553308606 Iteration 4: loglikelihood = -211.3640910919962, backtracks = 0, tol = 0.18632794312765352 Iteration 5: loglikelihood = -206.07758041780974, backtracks = 1, tol = 0.051383518206643046 Iteration 6: loglikelihood = -204.018617087407, backtracks = 3, tol = 0.020052933740041072 Iteration 7: loglikelihood = -202.12440666162166, backtracks = 3, tol = 0.022394307327778626 Iteration 8: loglikelihood = -200.51339216597611, backtracks = 3, tol = 0.021600855513207017 Iteration 9: loglikelihood = -199.1607521139652, backtracks = 3, tol = 0.020205916063858787 Iteration 10: loglikelihood = -198.03368293305746, backtracks = 3, tol = 0.018747980180644195 Iteration 11: loglikelihood = -197.1010787346633, backtracks = 3, tol = 0.01730311555883611 Iteration 12: loglikelihood = -199.1081399043643, backtracks = 3, tol = 0.10742989707378812 Iteration 13: loglikelihood = -196.35077450026276, backtracks = 0, tol = 0.10574886891481221 Iteration 14: loglikelihood = -195.5179886251886, backtracks = 1, tol = 0.016488769010944707 Iteration 15: loglikelihood = -195.26353610431914, backtracks = 3, tol = 0.005398010607219295 Iteration 16: loglikelihood = -194.94618143558304, backtracks = 3, tol = 0.008296620982687967 Iteration 17: loglikelihood = -198.1603861597454, backtracks = 3, tol = 0.1191184942601117 Iteration 18: loglikelihood = -196.08507656080548, backtracks = 0, tol = 0.04091866505365408 Iteration 19: loglikelihood = -194.68771845520706, backtracks = 2, tol = 0.08627046961582337 Iteration 20: loglikelihood = -194.18573370488792, backtracks = 1, tol = 0.012532615214018756 Iteration 21: loglikelihood = -194.04409249060237, backtracks = 2, tol = 0.0045289192218591345 Iteration 22: loglikelihood = -193.89081161879778, backtracks = 2, tol = 0.005408550068552711 Iteration 23: loglikelihood = -197.78991514558754, backtracks = 3, tol = 0.12418846818411548 Iteration 24: loglikelihood = -195.3458651891717, backtracks = 0, tol = 0.04474686356665713 Iteration 25: loglikelihood = -193.85329270192864, backtracks = 1, tol = 0.11642705219079118 Iteration 26: loglikelihood = -193.5872888252266, backtracks = 1, tol = 0.005994529796500222 Iteration 27: loglikelihood = -193.49244103087173, backtracks = 1, tol = 0.003977497505879251 Iteration 28: loglikelihood = -193.43959542357507, backtracks = 2, tol = 0.00330084983993103 Iteration 29: loglikelihood = -197.2834449493823, backtracks = 3, tol = 0.14332949891400917 Iteration 30: loglikelihood = -191.1561814374434, backtracks = 0, tol = 0.14271551862933007 Iteration 31: loglikelihood = -190.2589777412173, backtracks = 1, tol = 0.018296148237923138 Iteration 32: loglikelihood = -189.9878891870221, backtracks = 1, tol = 0.010701165536450384 Iteration 33: loglikelihood = -189.867470684632, backtracks = 1, tol = 0.007473112269951343 Iteration 34: loglikelihood = -193.0058316555954, backtracks = 3, tol = 0.1141647124557401 Iteration 35: loglikelihood = -191.61778833782117, backtracks = 0, tol = 0.033257092226161265 Iteration 36: loglikelihood = -190.26592749131268, backtracks = 0, tol = 0.12758732776034531 Iteration 37: loglikelihood = -189.83372327320802, backtracks = 1, tol = 0.008553392013129577 Iteration 38: loglikelihood = -189.70612855593623, backtracks = 1, tol = 0.0044027459232161385 Iteration 39: loglikelihood = -189.65408637483733, backtracks = 1, tol = 0.003586549894028387 Iteration 40: loglikelihood = -189.6305816735391, backtracks = 3, tol = 0.0019965524261909384 Iteration 41: loglikelihood = -200.89359611814402, backtracks = 3, tol = 0.14583347899126511 Iteration 42: loglikelihood = -193.27097139861027, backtracks = 0, tol = 0.14535809468532176 Iteration 43: loglikelihood = -192.2935217503592, backtracks = 1, tol = 0.015904619777886927 Iteration 44: loglikelihood = -192.0507085557377, backtracks = 1, tol = 0.008141180826631752 Iteration 45: loglikelihood = -191.98876965234143, backtracks = 1, tol = 0.0042025046810855214 Iteration 46: loglikelihood = -191.9726936044892, backtracks = 1, tol = 0.0021655324830217207 Iteration 47: loglikelihood = -191.96846706923031, backtracks = 1, tol = 0.0011055332529237927 Iteration 48: loglikelihood = -191.96734266484526, backtracks = 1, tol = 0.0005555964548322557 Iteration 49: loglikelihood = -191.9670386960076, backtracks = 1, tol = 0.0002733997501911196 Iteration 50: loglikelihood = -191.96695335555074, backtracks = 1, tol = 0.00013154922168130258 Iteration 51: loglikelihood = -191.96692620413978, backtracks = 1, tol = 7.105685194739283e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 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 = -4275.403008890986, backtracks = 0, tol = 0.41161586835788533 Iteration 2: loglikelihood = -2234.302065814908, backtracks = 0, tol = 0.0722483513477127 Iteration 3: loglikelihood = -1614.255935241979, backtracks = 0, tol = 0.0651271262487458 Iteration 4: loglikelihood = -1497.8989230183624, backtracks = 0, tol = 0.04552863216542381 Iteration 5: loglikelihood = -1368.657900946008, backtracks = 0, tol = 0.1832560247324041 Iteration 6: loglikelihood = -1335.8711183668265, backtracks = 0, tol = 0.09059820734896676 Iteration 7: loglikelihood = -1333.0387855432884, backtracks = 0, tol = 0.06363173194923182 Iteration 8: loglikelihood = -1327.66241762206, backtracks = 0, tol = 0.01891140413567421 Iteration 9: loglikelihood = -1318.9387909779111, backtracks = 0, tol = 0.046463730510911794 Iteration 10: loglikelihood = -1316.646859170738, backtracks = 0, tol = 0.01879915083502677 Iteration 11: loglikelihood = -1315.904401422666, backtracks = 0, tol = 0.007197907470874681 Iteration 12: loglikelihood = -1315.457975379942, backtracks = 0, tol = 0.009315647199920053 Iteration 13: loglikelihood = -1315.1624389241106, backtracks = 0, tol = 0.004400769548905705 Iteration 14: loglikelihood = -1314.9634631293488, backtracks = 0, tol = 0.006199754256069378 Iteration 15: loglikelihood = -1314.824487800825, backtracks = 0, tol = 0.002991535231373067 Iteration 16: loglikelihood = -1314.727829302536, backtracks = 0, tol = 0.004233935719859464 Iteration 17: loglikelihood = -1314.6592220216678, backtracks = 0, tol = 0.00209432340908124 Iteration 18: loglikelihood = -1314.6107720212042, backtracks = 0, tol = 0.0029453536372593676 Iteration 19: loglikelihood = -1314.576120163694, backtracks = 0, tol = 0.001485282762640767 Iteration 20: loglikelihood = -1314.5514381809694, backtracks = 0, tol = 0.0020745425741632894 Iteration 21: loglikelihood = -1314.5337096276758, backtracks = 0, tol = 0.0010607899933645596 Iteration 22: loglikelihood = -1314.5210147036594, backtracks = 0, tol = 0.001473439678929657 Iteration 23: loglikelihood = -1314.5118720977036, backtracks = 0, tol = 0.0007608851547117975 Iteration 24: loglikelihood = -1314.5053026781322, backtracks = 0, tol = 0.0010524811366135216 Iteration 25: loglikelihood = -1314.500563408806, backtracks = 0, tol = 0.0005473096780235243 Iteration 26: loglikelihood = -1314.4971500778565, backtracks = 0, tol = 0.0007547568205560042 Iteration 27: loglikelihood = -1314.494684821206, backtracks = 0, tol = 0.00039444085027061317 Iteration 28: loglikelihood = -1314.492906443865, backtracks = 0, tol = 0.000542748809825358 Iteration 29: loglikelihood = -1314.4916210098052, backtracks = 0, tol = 0.00028465184540581515 Iteration 30: loglikelihood = -1314.4906926924882, backtracks = 0, tol = 0.00039105680900854037 Iteration 31: loglikelihood = -1314.4900213251435, backtracks = 0, tol = 0.000205617604868424 Iteration 32: loglikelihood = -1314.4895360940277, backtracks = 0, tol = 0.0002821545271528542 Iteration 33: loglikelihood = -1314.4891850355289, backtracks = 0, tol = 0.00014862907191837542 Iteration 34: loglikelihood = -1314.4889311660304, backtracks = 0, tol = 0.0002037838285560458 Iteration 35: loglikelihood = -1314.4887474446818, backtracks = 0, tol = 0.00010748850942066392 Iteration 36: loglikelihood = -1314.4886145328194, backtracks = 0, tol = 0.00014728783787757444 Iteration 37: loglikelihood = -1314.488518327969, backtracks = 0, tol = 7.776360965433181e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.7s **** 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 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 = -1680.9420367657042, backtracks = 0, tol = 0.410602083254514 Iteration 2: loglikelihood = -1553.103154518339, backtracks = 0, tol = 0.20988817113102548 Iteration 3: loglikelihood = -1510.3441394039664, backtracks = 0, tol = 0.13651234511265095 Iteration 4: loglikelihood = -1498.0557039781568, backtracks = 0, tol = 0.10915234116586202 Iteration 5: loglikelihood = -1494.3193271659436, backtracks = 0, tol = 0.03766510180677433 Iteration 6: loglikelihood = -1494.1432189168816, backtracks = 1, tol = 0.0050552883956897846 Iteration 7: loglikelihood = -1493.6930289843672, backtracks = 1, tol = 0.054892828153045685 Iteration 8: loglikelihood = -1491.6594279639519, backtracks = 0, tol = 0.07180194425345753 Iteration 9: loglikelihood = -1491.0658989584604, backtracks = 0, tol = 0.10755715407477212 Iteration 10: loglikelihood = -1490.2261095311796, backtracks = 0, tol = 0.025962591574962272 Iteration 11: loglikelihood = -1490.1852447869533, backtracks = 0, tol = 0.005241675464696053 Iteration 12: loglikelihood = -1490.1809871191576, backtracks = 0, tol = 0.001432829168629101 Iteration 13: loglikelihood = -1490.1801236311287, backtracks = 0, tol = 0.0008444910538012301 Iteration 14: loglikelihood = -1490.1799246869477, backtracks = 0, tol = 0.00032680415276261813 Iteration 15: loglikelihood = -1490.179875978008, backtracks = 0, tol = 0.00019451608763794035 Iteration 16: loglikelihood = -1490.1798637671932, backtracks = 0, tol = 9.506238648438865e-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 = -1695.786531676285, backtracks = 0, tol = 0.770251801492155 Iteration 2: loglikelihood = -1441.1628534545425, backtracks = 0, tol = 0.09754198324472294 Iteration 3: loglikelihood = -1393.0255982779263, backtracks = 0, tol = 0.04151528695376498 Iteration 4: loglikelihood = -1392.2243678137063, backtracks = 0, tol = 0.006246525481941219 Iteration 5: loglikelihood = -1392.2108037129835, backtracks = 0, tol = 0.0006529556271793977 Iteration 6: loglikelihood = -1391.9624882801966, backtracks = 0, tol = 0.024824017836357903 Iteration 7: loglikelihood = -1391.872743908544, backtracks = 0, tol = 0.001522561894494304 Iteration 8: loglikelihood = -1391.592023832292, backtracks = 0, tol = 0.025494384567696423 Iteration 9: loglikelihood = -1391.512213701479, backtracks = 1, tol = 0.0008615474356082337 Iteration 10: loglikelihood = -1391.491698922932, backtracks = 1, tol = 0.0004443712485643523 Iteration 11: loglikelihood = -1391.4864502299333, backtracks = 1, tol = 0.0002251117997585404 Iteration 12: loglikelihood = -1391.4851124915874, backtracks = 1, tol = 0.00011237541752577184 Iteration 13: loglikelihood = -1391.4847725632928, backtracks = 1, tol = 5.95732751991527e-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 = -1516.7763720482283, backtracks = 0, tol = 0.30866319760634814 Iteration 2: loglikelihood = -1408.056143817539, backtracks = 0, tol = 0.07514419061885448 Iteration 3: loglikelihood = -1392.3608565558243, backtracks = 0, tol = 0.03624849305177423 Iteration 4: loglikelihood = -1392.1746294682289, backtracks = 0, tol = 0.0024687565290353987 Iteration 5: loglikelihood = -1392.1723612834235, backtracks = 0, tol = 0.00032150450561573517 Iteration 6: loglikelihood = -1392.1723181633229, backtracks = 0, tol = 4.91342053799149e-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 8.3s **** 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 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 = -1414.2717621496115, backtracks = 0, tol = 0.18529781178876634 Iteration 2: loglikelihood = -1390.0442112491817, backtracks = 0, tol = 0.08175656978714495 Iteration 3: loglikelihood = -1364.8840800512282, backtracks = 0, tol = 0.09438196032053192 Iteration 4: loglikelihood = -1360.2206783123186, backtracks = 0, tol = 0.04369972158737926 Iteration 5: loglikelihood = -1358.7831818397883, backtracks = 0, tol = 0.027477927702835202 Iteration 6: loglikelihood = -1358.257420899521, backtracks = 0, tol = 0.013525076174980657 Iteration 7: loglikelihood = -1358.032712882101, backtracks = 0, tol = 0.011894668636221122 Iteration 8: loglikelihood = -1357.9332382737098, backtracks = 0, tol = 0.005714840783544124 Iteration 9: loglikelihood = -1354.4204049763516, backtracks = 0, tol = 0.07035007936787563 Iteration 10: loglikelihood = -1353.0548163625901, backtracks = 0, tol = 0.026727603097009056 Iteration 11: loglikelihood = -1352.8787046041793, backtracks = 0, tol = 0.00811813519342544 Iteration 12: loglikelihood = -1352.8439706369459, backtracks = 0, tol = 0.004108279194646208 Iteration 13: loglikelihood = -1352.8353635392612, backtracks = 0, tol = 0.002250275749059265 Iteration 14: loglikelihood = -1352.833033641863, backtracks = 0, tol = 0.0009734807902254453 Iteration 15: loglikelihood = -1352.8323872377205, backtracks = 0, tol = 0.000631612964554493 Iteration 16: loglikelihood = -1352.832205821428, backtracks = 0, tol = 0.0002649821469188515 Iteration 17: loglikelihood = -1352.8321547733208, backtracks = 0, tol = 0.00017775658252110413 Iteration 18: loglikelihood = -1352.832140379549, backtracks = 0, tol = 7.417685227978028e-5 1.088888 seconds (2.01 M allocations: 38.827 MiB, 6.95% gc time, 63.67% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1489.204842941446, backtracks = 0, tol = 0.18529781178876634 Iteration 2: loglikelihood = -1463.4763970564363, backtracks = 0, tol = 0.08175656978714495 Iteration 3: loglikelihood = -1442.0624176465892, backtracks = 0, tol = 0.09051784546830174 Iteration 4: loglikelihood = -1429.726346198367, backtracks = 0, tol = 0.07399397043787975 Iteration 5: loglikelihood = -1424.5563286667277, backtracks = 0, tol = 0.0786125405565513 Iteration 6: loglikelihood = -1415.8860511707378, backtracks = 0, tol = 0.06961035602236224 Iteration 7: loglikelihood = -1407.3216187569851, backtracks = 0, tol = 0.04912996150660994 Iteration 8: loglikelihood = -1399.767036117486, backtracks = 0, tol = 0.06502713354483618 Iteration 9: loglikelihood = -1395.3474379200575, backtracks = 0, tol = 0.02884652580778352 Iteration 10: loglikelihood = -1391.7268284183167, backtracks = 0, tol = 0.006672959461870997 Iteration 11: loglikelihood = -1388.703828485168, backtracks = 0, tol = 0.0025243741507890625 Iteration 12: loglikelihood = -1386.0276129079539, backtracks = 0, tol = 0.0011113750689639068 Iteration 13: loglikelihood = -1383.7068773838732, backtracks = 0, tol = 0.0005093614322233937 Iteration 14: loglikelihood = -1380.0779021792032, backtracks = 1, tol = 0.0001362902846630394 Iteration 15: loglikelihood = -1379.9453740568779, backtracks = 0, tol = 0.0707809589880296 Iteration 16: loglikelihood = -1376.5965392247006, backtracks = 0, tol = 0.06953826110462445 Iteration 17: loglikelihood = -1375.1355997085222, backtracks = 0, tol = 0.004543122423597148 Iteration 18: loglikelihood = -1373.9064530104924, backtracks = 0, tol = 0.0006375303924211645 Iteration 19: loglikelihood = -1372.9301344672097, backtracks = 0, tol = 0.06786554371699483 Iteration 20: loglikelihood = -1371.8084436431154, backtracks = 0, tol = 0.004913207523463253 Iteration 21: loglikelihood = -1370.8835660122622, backtracks = 0, tol = 0.0004519607425399629 Iteration 22: loglikelihood = -1369.8249278505255, backtracks = 0, tol = 0.06655483274985056 Iteration 23: loglikelihood = -1368.986618567781, backtracks = 0, tol = 0.006479857714226083 Iteration 24: loglikelihood = -1368.2338679930265, backtracks = 0, tol = 0.0028059364717456007 Iteration 25: loglikelihood = -1367.569303729337, backtracks = 0, tol = 0.0011574555692896484 Iteration 26: loglikelihood = -1366.9317532466619, backtracks = 0, tol = 0.0006853580729532245 Iteration 27: loglikelihood = -1366.345240441503, backtracks = 0, tol = 0.00033062734072506703 Iteration 28: loglikelihood = -1365.652794817181, backtracks = 1, tol = 0.0001207174141479245 Iteration 29: loglikelihood = -1364.7650237907942, backtracks = 1, tol = 0.0001157184617618768 Iteration 30: loglikelihood = -1364.003548664416, backtracks = 1, tol = 0.00014239575197100613 Iteration 31: loglikelihood = -1363.3009143072682, backtracks = 1, tol = 0.0001504922876083921 Iteration 32: loglikelihood = -1362.6812621187794, backtracks = 1, tol = 0.00015077722709012857 Iteration 33: loglikelihood = -1362.1320547427117, backtracks = 1, tol = 0.00014432581435395046 Iteration 34: loglikelihood = -1361.6259944613792, backtracks = 1, tol = 0.00013493360275359305 Iteration 35: loglikelihood = -1361.1691535812358, backtracks = 1, tol = 0.0001265363805557921 Iteration 36: loglikelihood = -1360.7550336925442, backtracks = 1, tol = 0.00011810551317321162 Iteration 37: loglikelihood = -1360.3775584916484, backtracks = 1, tol = 0.00011006389382828325 Iteration 38: loglikelihood = -1360.0315957750056, backtracks = 1, tol = 0.0001026846960309509 Iteration 39: loglikelihood = -1359.7130009764173, backtracks = 1, tol = 9.606415298253188e-5 0.432778 seconds (1.67 M allocations: 30.807 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 = -3464.3657, backtracks = 0, tol = 0.08630711366181172 Iteration 2: loglikelihood = -3435.8816, backtracks = 0, tol = 0.038073909667976434 Iteration 3: loglikelihood = -3433.577, backtracks = 1, tol = 0.008914916529054854 Iteration 4: loglikelihood = -3432.9578, backtracks = 1, tol = 0.00541591949891037 Iteration 5: loglikelihood = -3432.798, backtracks = 1, tol = 0.0027240839477345362 Iteration 6: loglikelihood = -3432.7566, backtracks = 1, tol = 0.0014033868900006751 Iteration 7: loglikelihood = -3432.7476, backtracks = 1, tol = 0.000700391821746299 Iteration 8: loglikelihood = -3432.7432, backtracks = 1, tol = 0.000351543640618502 Iteration 9: loglikelihood = -3432.7456, backtracks = 3, tol = 4.376756145129615e-5 22.898986 seconds (17.32 M allocations: 739.680 MiB, 1.02% gc time, 98.04% 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 = -3384.4045, backtracks = 0, tol = 0.08630711366181172 Iteration 2: loglikelihood = -3301.749, backtracks = 0, tol = 0.03873954100294891 Iteration 3: loglikelihood = -3125.7832, backtracks = 1, tol = 0.008703514350014242 Iteration 4: loglikelihood = -3063.7114, backtracks = 0, tol = 0.09261667642158534 Iteration 5: loglikelihood = -2914.4927, backtracks = 0, tol = 0.0901060332782599 Iteration 6: loglikelihood = -2809.8423, backtracks = 0, tol = 0.08365754850557874 Iteration 7: loglikelihood = -2717.8303, backtracks = 0, tol = 0.07912579525909187 Iteration 8: loglikelihood = -2623.239, backtracks = 0, tol = 0.005115919744308162 Iteration 9: loglikelihood = -2532.3804, backtracks = 0, tol = 0.08296572658407428 Iteration 10: loglikelihood = -2448.2336, backtracks = 0, tol = 0.08308957248872736 Iteration 11: loglikelihood = -2373.363, backtracks = 0, tol = 0.008829741436440042 Iteration 12: loglikelihood = -2312.6672, backtracks = 0, tol = 0.08557865147713638 Iteration 13: loglikelihood = -2266.477, backtracks = 0, tol = 0.08980350067001501 Iteration 14: loglikelihood = -2228.065, backtracks = 0, tol = 0.09013821717972281 Iteration 15: loglikelihood = -2209.7915, backtracks = 0, tol = 0.09273614065034891 Iteration 16: loglikelihood = -2195.1409, backtracks = 0, tol = 0.09731082664084183 Iteration 17: loglikelihood = -2184.0793, backtracks = 0, tol = 0.11247500018507223 Iteration 18: loglikelihood = -2178.4087, backtracks = 0, tol = 0.11294157952213026 Iteration 19: loglikelihood = -2170.3723, backtracks = 1, tol = 0.02154590776512334 Iteration 20: loglikelihood = -2168.6, backtracks = 1, tol = 0.008614767906657366 Iteration 21: loglikelihood = -2168.1548, backtracks = 1, tol = 0.003445708862883824 Iteration 22: loglikelihood = -2168.0361, backtracks = 1, tol = 0.0013938916057933384 Iteration 23: loglikelihood = -2168.0, backtracks = 1, tol = 0.0005799610563793091 Iteration 24: loglikelihood = -2167.9873, backtracks = 1, tol = 0.0002512174400274342 Iteration 25: loglikelihood = -2167.983, backtracks = 1, tol = 0.00011328689784627522 Iteration 26: loglikelihood = -2167.9817, backtracks = 1, tol = 6.457748652102751e-5 0.203134 seconds (1.43 M allocations: 23.630 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 28.0s **** 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 **** Initializing β to univariate regression values... 0%| | ETA: 8:10:09Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2973.20721158067, backtracks = 0, tol = 0.9753037901485436 Iteration 2: loglikelihood = -1640.6694321323835, backtracks = 0, tol = 0.2999151154493682 Iteration 3: loglikelihood = -1418.3315050219228, backtracks = 0, tol = 0.10707075072938249 Iteration 4: loglikelihood = -1411.8219428589443, backtracks = 0, tol = 0.038898114770295936 Iteration 5: loglikelihood = -1410.7307354136753, backtracks = 0, tol = 0.03138838740051226 Iteration 6: loglikelihood = -1410.653861909991, backtracks = 0, tol = 0.001736989736614678 Iteration 7: loglikelihood = -1410.6533631901768, backtracks = 1, tol = 8.130020517735094e-5 9.403843 seconds (1.12 M allocations: 123.364 MiB, 0.52% gc time, 92.68% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 9.9s 8.483675 seconds (3.94 M allocations: 80.116 MiB, 0.56% gc time, 0.57% compilation time) 5.049989 seconds (3.92 M allocations: 89.276 MiB, 1.03% gc time) 10.871058 seconds (22.33 M allocations: 469.832 MiB, 0.74% gc time, 12.30% compilation time: 75% of which was recompilation) 9.189029 seconds (22.05 M allocations: 462.996 MiB, 0.60% gc time) 39.548751 seconds (2.51 M allocations: 4.150 GiB, 0.91% gc time, 39.06% compilation time) 52.386822 seconds (74.21 k allocations: 187.410 MiB, 0.04% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m13.6s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 11.053 ms (77 allocations: 5.30 KiB) 4.930 μs (0 allocations: 0 bytes) 158.928 μs (4 allocations: 288 bytes) 5.450 μs (0 allocations: 0 bytes) 42.510 μs (2 allocations: 64 bytes) 40.780 μs (0 allocations: 0 bytes) 27.650 μs (0 allocations: 0 bytes) 40.330 μs (0 allocations: 0 bytes) 60.549 μs (0 allocations: 0 bytes) 30.805 ms (77 allocations: 5.30 KiB) 21.590 μs (0 allocations: 0 bytes) 178.529 μs (4 allocations: 288 bytes) 23.139 μs (0 allocations: 0 bytes) 214.578 μs (2 allocations: 64 bytes) 89.469 μs (0 allocations: 0 bytes) 124.549 μs (0 allocations: 0 bytes) 179.409 μs (0 allocations: 0 bytes) 191.768 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m54.0s **** 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 **** **** 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 0.567971 seconds (53.53 k allocations: 5.547 MiB, 44.72% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 8.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.855709 seconds (473.30 k allocations: 177.247 MiB, 2.83% gc time, 56.08% 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: 0:03:36 Cross validating... 6%|██ | ETA: 0:01:46 Cross validating... 10%|███ | ETA: 0:01:10 Cross validating... 13%|████▏ | ETA: 0:00:51 Cross validating... 16%|█████▏ | ETA: 0:00:40 Cross validating... 19%|██████▏ | ETA: 0:00:33 Cross validating... 22%|███████▏ | ETA: 0:00:28 Cross validating... 25%|████████▏ | ETA: 0:00:24 Cross validating... 29%|█████████▏ | ETA: 0:00:21 Cross validating... 32%|██████████▏ | ETA: 0:00:18 Cross validating... 35%|███████████▏ | ETA: 0:00:16 Cross validating... 38%|████████████▎ | ETA: 0:00:14 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:11 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 5909.599340208142 1 4662.530385354342 2 3288.8210016829385 3 2389.026229976257 4 1802.7673370138186 5 1177.7686402963122 6 748.9641060751089 7 574.8732350126842 8 438.94004035838816 9 334.31677989831985 10 336.1969877098853 11 339.86127623161894 12 338.2809109083177 13 342.9796924700054 14 342.9667561944586 15 349.155769923692 16 349.86752443291874 17 349.1634646320558 18 355.69936052591567 19 368.10966962970065 20 362.1777659297102 Best k = 9 12.065981 seconds (12.23 M allocations: 301.716 MiB, 0.37% gc time, 58.55% 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: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 17%|█████▋ | 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... 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... 68%|█████████████████████▉ | 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... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 5909.599340208142 1 4681.479220965957 2 3298.221836647907 3 2408.1175462740543 4 1817.842256503276 5 1196.7254417576844 6 761.0403448524912 7 585.5220189630468 8 449.1285088342297 9 340.7995001800889 10 347.4166096327407 11 356.15241308080044 12 357.9179609019735 13 367.5900654320375 14 367.3901194939881 15 379.9030143655889 16 384.9266371068391 17 382.794654353432 18 394.3917969201399 19 395.10382414561246 20 400.09771922884806 Best k = 9 5.247135 seconds (11.43 M allocations: 236.619 MiB, 0.75% gc time, 0.73% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.2s **** 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... 3%|█ | ETA: 0:04:59 Cross validating... 8%|██▌ | ETA: 0:01:55 Cross validating... 13%|████▏ | ETA: 0:01:09 Cross validating... 17%|█████▋ | ETA: 0:00:48 Cross validating... 22%|███████▏ | ETA: 0:00:36 Cross validating... 27%|████████▋ | ETA: 0:00:28 Cross validating... 32%|██████████▏ | ETA: 0:00:23 Cross validating... 35%|███████████▏ | ETA: 0:00:20 Cross validating... 40%|████████████▊ | ETA: 0:00:16 Cross validating... 44%|██████████████▎ | ETA: 0:00:14 Cross validating... 49%|███████████████▊ | ETA: 0:00:11 Cross validating... 54%|█████████████████▎ | ETA: 0:00:10 Cross validating... 59%|██████████████████▊ | ETA: 0:00:08 Cross validating... 62%|███████████████████▊ | ETA: 0:00:07 Cross validating... 65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 1559.0756439208985 1 1197.981892578125 2 975.6913804321289 3 816.3458664550781 4 643.7947208251953 5 500.05256945800784 6 430.70582241821285 7 380.81423599243163 8 351.89737603759767 9 336.13039193725587 10 338.9995740356445 11 342.5478004760742 12 346.2815972595215 13 345.65902169799807 14 352.5396260070801 15 368.7970400085449 16 355.81435653686526 17 364.5419102172852 18 356.31585668945314 19 400.5457583618164 20 376.482140838623 Best k = 9 13.249044 seconds (12.79 M allocations: 277.965 MiB, 0.48% gc time, 78.31% 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... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | 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... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 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 1559.0756439208985 1 1197.981892578125 2 976.6139306030273 3 823.162525024414 4 650.531516418457 5 501.79854083251956 6 434.82993835449224 7 383.99952069091796 8 355.22224130249026 9 339.72196591186525 10 350.4399043884277 11 358.4844251708984 12 365.580662109375 13 371.65658602905273 14 385.91380050659177 15 386.64714596557616 16 392.38017980957034 17 399.8210157775879 18 403.07142480468747 19 401.9979222717285 20 416.11148260498044 Best k = 9 3.151500 seconds (11.91 M allocations: 216.779 MiB, 1.35% gc time, 1.84% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 18.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:49 Cross validating... 5%|█▌ | ETA: 0:00:35 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | 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... 59%|██████████████████▊ | 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... 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... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | 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... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.8244884231103 1 408.4061007984102 2 382.9127919794399 3 319.3040370361541 4 296.28266663010925 5 259.9353590105614 6 223.7787851945139 7 218.61327335989176 8 202.08271712762894 9 188.79944075177113 10 178.70166358243353 11 183.41193713765375 12 205.95903276194238 13 191.92222488988955 14 214.58979002961206 15 194.91043343407978 16 190.79242936692071 17 209.06777987994138 18 213.20300233860246 19 223.96470510368377 20 189.81689058912764 Best k = 10 8.465138 seconds (18.91 M allocations: 438.420 MiB, 1.18% gc time, 25.21% 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... 19%|██████▏ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:05 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: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 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 0 462.8244884231103 1 409.8160648997442 2 387.71731269896134 3 326.0078242876293 4 302.24847545189306 5 266.71906908535107 6 228.68863599404105 7 224.29183172523153 8 206.31561154418577 9 196.19610161820594 10 191.20405313052237 11 203.18226288863482 12 214.24149139559697 13 209.50266161983222 14 218.8651380290314 15 216.29968661521633 16 229.9531787479056 17 227.57016680553863 18 231.53922655867694 19 229.51382571499897 20 232.23472293127278 Best k = 10 6.490269 seconds (19.30 M allocations: 397.258 MiB, 0.81% gc time, 0.68% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic 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: 0:00:39 Cross validating... 6%|██ | ETA: 0:00:21 Cross validating... 10%|███ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 16%|█████▏ | ETA: 0:00:10 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 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... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.30341272824086 1 414.4852085021029 2 394.3148479780541 3 375.00997935791816 4 348.2611357563311 5 318.69342086677943 6 304.2660277000931 7 306.2096868738898 8 309.36002265999485 9 312.77854543528207 10 317.33497470603874 11 330.809039580903 12 317.9103170005424 13 322.30014165382886 14 331.48338558688675 15 353.29260556872237 16 338.7389533272196 17 367.3870160680908 18 334.27682380585327 19 361.38675221090637 20 348.7411081734918 Best k = 6 7.054560 seconds (17.25 M allocations: 395.983 MiB, 8.78% gc time, 26.34% 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: 0:00:04 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: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 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 0 463.30341272824086 1 415.28363762637275 2 395.44739882988716 3 376.84615684464774 4 351.115601936296 5 322.681445313839 6 308.9465658898548 7 314.9051823982581 8 324.2728738281941 9 335.9879428020282 10 339.27377772285627 11 349.5783261869538 12 357.1111146448965 13 365.6987897367619 14 371.1130874366241 15 367.99350855442526 16 378.40079651127854 17 411.2854612820698 18 383.25657425469615 19 402.7923607590933 20 420.4415923227108 Best k = 6 4.897554 seconds (17.94 M allocations: 362.545 MiB, 1.21% gc time, 1.27% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:51 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▋ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross 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validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1390.9287934036936 1 1114.5568246700802 2 866.5009566337325 3 693.1793554024879 4 554.5192922020613 5 485.0086178328352 6 404.6876751202375 7 362.88387167446433 8 386.998911662424 9 369.1934344252653 10 372.32522159121703 11 378.93432819810386 12 368.99915034460196 13 378.57280876459487 14 399.81430681927543 15 398.16653531929796 16 412.7784652438671 17 400.0565202849116 18 410.6901635722901 19 419.3053260411282 20 416.85788492571066 Best k = 7 8.364285 seconds (16.70 M allocations: 379.093 MiB, 0.88% gc time, 25.94% 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... 22%|███████▏ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 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: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1390.9287934036936 1 1036.4815322073675 2 782.3053093504498 3 650.8520218228145 4 546.1934872300315 5 453.005347668431 6 402.6388095415498 7 365.23640376442836 8 365.5525135241796 9 367.878907116655 10 375.35778014894044 11 385.68766095598926 12 392.7624676678302 13 404.6969285039493 14 401.51321183180517 15 403.8475360547998 16 411.172502922043 17 420.650248087647 18 415.69871974326605 19 415.3265471901401 20 410.1522553427402 Best k = 7 6.111605 seconds (15.15 M allocations: 300.569 MiB, 0.65% gc time, 0.72% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.9s **** 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: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:41 Cross validating... 8%|██▌ | ETA: 0:00:45 Cross validating... 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0:00:49 Crossvalidation Results: k MSE 0 496.5871678300109 1 414.2219560901864 2 326.2275732507559 3 293.81744930147926 4 256.5047924736623 5 226.60963383545857 6 198.69705485848706 7 190.91722682113976 8 191.14933605451694 9 191.14601155291803 10 192.71745520329327 11 193.4363907984896 12 195.6959663554464 13 195.3801978714156 14 192.84284237877858 15 196.26974993914632 16 194.23757438802022 17 196.0542257405715 18 199.8230102320689 19 198.61032236267084 20 199.82761104221404 Best k = 7 49.702131 seconds (156.08 M allocations: 3.844 GiB, 0.93% gc time, 3.54% 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: 0:00:06 Cross validating... 11%|███▌ | ETA: 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 496.5871678300109 1 411.07029537372443 2 325.1611673934554 3 296.20464859000157 4 253.33868076867859 5 229.6348482769302 6 202.37255357199524 7 194.48937855092942 8 196.3119941433119 9 200.68671158390376 10 201.62245346019853 11 204.19972752980664 12 208.6202354410396 13 209.38236538577667 14 215.57299078632332 15 208.6915506969167 16 234.33358691988337 17 221.08636683695846 18 236.20615507200898 19 233.2951518201982 20 239.25636914145784 Best k = 7 13.381310 seconds (40.76 M allocations: 838.211 MiB, 1.00% gc time, 0.41% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m03.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:54 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 10%|███ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:12 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 691.7500225830079 1 622.5072396240234 2 512.5984967346192 3 404.1873347473144 4 329.1224825439453 5 269.25713952636715 6 254.24000593566893 7 224.95246855163572 8 210.14389988708496 9 203.5730756072998 10 206.3555386505127 11 208.19131018066406 12 216.8473366241455 13 229.8447658843994 14 213.42113655090333 15 214.1879868621826 16 224.7288980255127 17 218.40956840515133 18 214.59177186584472 19 217.02808283996583 20 229.5842406768799 Best k = 9 6.010001 seconds (18.20 M allocations: 357.300 MiB, 0.91% gc time, 38.45% 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: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 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 3.873554 seconds (17.44 M allocations: 307.809 MiB, 1.08% gc time, 1.51% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:01 Cross validating... 4%|█▎ | ETA: 0:00:34 Cross validating... 6%|█▉ | ETA: 0:00:24 Cross validating... 7%|██▎ | ETA: 0:00:22 Cross validating... 8%|██▌ | ETA: 0:00:20 Cross validating... 9%|██▉ | ETA: 0:00:19 Cross validating... 10%|███▎ | ETA: 0:00:19 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 12%|███▉ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:16 Cross validating... 17%|█████▌ | ETA: 0:00:15 Cross validating... 18%|█████▊ | ETA: 0:00:15 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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 2644.455056746173 2 2504.383751988822 3 2326.114872825764 4 2266.6656647060427 5 2181.809973898756 6 2122.7299614931817 7 2136.4786016545604 8 2137.5121069222855 9 2163.7842425597355 10 2177.9611436121486 11 2188.2886342023107 12 2183.170156406141 13 2201.1949030880164 14 2208.7969449727507 15 2266.9785927888033 16 2249.932955610955 17 2287.1843550112226 18 2292.6350605464486 19 2333.519468949066 20 2304.5049130497846 Best k = 6 14.821231 seconds (421.92 k allocations: 263.245 MiB, 0.32% gc time, 8.99% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 18.6s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m52.5s **** 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... 2%|▋ | ETA: 0:00:08 Cross validating... 4%|█▎ | ETA: 0:00:08 Cross validating... 6%|█▉ | ETA: 0:00:09 Cross validating... 7%|██▎ | ETA: 0:00:09 Cross validating... 8%|██▌ | ETA: 0:00:09 Cross validating... 9%|██▉ | ETA: 0:00:10 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | ETA: 0:00:11 Cross validating... 12%|███▉ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross validating... 14%|████▌ | ETA: 0:00:13 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: 0:00:14 Cross validating... 20%|██████▍ | ETA: 0:00:14 Cross validating... 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98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.991829511581 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:08 Cross validating... 4%|█▎ | ETA: 0:00:08 Cross 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2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.991829511581 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%|██▉ | ETA: 0:00:10 Cross validating... 10%|███▎ | ETA: 0:00:11 Cross validating... 11%|███▌ | ETA: 0:00:11 Cross validating... 12%|███▉ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:12 Cross 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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 1m15.6s 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 1352.79s 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 1447.41s: package tests unexpectedly errored