Package evaluation of MendelIHT on Julia 1.12.0-DEV.1805 (a080deafdd*) started at 2025-03-24T23:08:28.003 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.74s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.12/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.18.0 ⌅ [67c07d97] + Automa v0.8.4 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.6 [336ed68f] + CSV v0.10.15 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.6 [861a8166] + Combinatorics v1.0.2 [38540f10] + CommonSolve v0.2.4 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[8e850b90] + libblastrampoline_jll v5.11.2+0 [8e850ede] + nghttp2_jll v1.63.0+1 [3f19e933] + p7zip_jll v17.5.0+1 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.57s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 78.01s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_UTxwtV/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.0 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.118 [38e38edf] GLM v1.9.0 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.10.2 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.5.0 [2913bbd2] StatsBase v0.34.4 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.11.0 [44cfe95a] Pkg v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_UTxwtV/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.18.0 ⌅ [67c07d97] Automa v0.8.4 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools 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Testing Running tests... Precompiling packages... Info Given MendelIHT was explicitly requested, output will be shown live  [ Info: Compiling VCF parser... 202166.1 ms ✓ MendelIHT 1 dependency successfully precompiled in 208 seconds. 165 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ [Output was shown above] └ WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_atx_additive_meanimpute!(Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_atx_additive_meanimpute_rem!(Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _turbo_!(Base.Val{var"#UNROLL#"}, Base.Val{var"#OPS#"}, Base.Val{var"#ARF#"}, Base.Val{var"#AM#"}, Base.Val{var"#LPSYM#"}, Base.Val{Tuple{var"#LB#", var"#V#"}}, Vararg{Any, var"#num#vargs#"}) where {var"#UNROLL#", var"#OPS#", var"#ARF#", var"#AM#", var"#LPSYM#", var"#LB#", var"#V#", var"#num#vargs#"} at /home/pkgeval/.julia/packages/LoopVectorization/tIJUA/src/reconstruct_loopset.jl ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_AtX_additive_meanimpute!(Any, Any, Any, Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_AtX_additive_meanimpute_rem!(Any, Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl 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{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 12.3s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 5.2s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 2.1s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 2.7s Test Summary: | Pass Total Time maf_weights | 6 6 2.0s WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_ax_additive_meanimpute!(Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl **** 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 = -1547.9540007628302, backtracks = 0, tol = 1.3421023642866439 Iteration 2: loglikelihood = -1451.1775561368013, backtracks = 0, tol = 0.16563749526971547 Iteration 3: loglikelihood = -1447.3554541819442, backtracks = 0, tol = 0.057844154451036786 Iteration 4: loglikelihood = -1447.1688742263852, backtracks = 0, tol = 0.004829827971338992 Iteration 5: loglikelihood = -1447.166131881983, backtracks = 0, tol = 0.0006220651553237781 Iteration 6: loglikelihood = -1447.166074489442, backtracks = 0, tol = 7.58197543576239e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.052188873291015625 Final loglikelihood: -1447.166074489442 SNP PVE: 0.9104361693560576 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 829 -1.05842 2 │ 1049 0.478487 3 │ 1842 0.583995 4 │ 3195 -1.58331 5 │ 5280 -1.0825 6 │ 5343 1.48527 7 │ 6574 -1.02459 8 │ 6665 0.572937 9 │ 6705 1.40777 10 │ 9511 0.132127 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.143095Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 15.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -357.05406929589384, backtracks = 0, tol = 0.8380082173781972 Iteration 2: loglikelihood = -253.69247673658248, backtracks = 0, tol = 0.38139022833574177 Iteration 3: loglikelihood = -242.78890265594725, backtracks = 0, tol = 0.21772646553308606 Iteration 4: loglikelihood = -211.3640910919962, backtracks = 0, tol = 0.18632794312765352 Iteration 5: loglikelihood = -206.07758041780974, backtracks = 1, tol = 0.051383518206643046 Iteration 6: loglikelihood = -204.018617087407, backtracks = 3, tol = 0.020052933740041072 Iteration 7: loglikelihood = -202.12440666162166, backtracks = 3, tol = 0.022394307327778626 Iteration 8: loglikelihood = -200.51339216597611, backtracks = 3, tol = 0.021600855513207017 Iteration 9: loglikelihood = -199.1607521139652, backtracks = 3, tol = 0.020205916063858787 Iteration 10: loglikelihood = -198.03368293305746, backtracks = 3, tol = 0.018747980180644195 Iteration 11: loglikelihood = -197.1010787346633, backtracks = 3, tol = 0.01730311555883611 Iteration 12: loglikelihood = -199.1081399043643, backtracks = 3, tol = 0.10742989707378812 Iteration 13: loglikelihood = -196.35077450026276, backtracks = 0, tol = 0.10574886891481221 Iteration 14: loglikelihood = -195.5179886251886, backtracks = 1, tol = 0.016488769010944707 Iteration 15: loglikelihood = -195.26353610431914, backtracks = 3, tol = 0.005398010607219295 Iteration 16: loglikelihood = -194.94618143558304, backtracks = 3, tol = 0.008296620982687967 Iteration 17: loglikelihood = -198.1603861597454, backtracks = 3, tol = 0.1191184942601117 Iteration 18: loglikelihood = -196.08507656080548, backtracks = 0, tol = 0.04091866505365408 Iteration 19: loglikelihood = -194.68771845520706, backtracks = 2, tol = 0.08627046961582337 Iteration 20: loglikelihood = -194.18573370488792, backtracks = 1, tol = 0.012532615214018756 Iteration 21: loglikelihood = -194.04409249060237, backtracks = 2, tol = 0.0045289192218591345 Iteration 22: loglikelihood = -193.89081161879778, backtracks = 2, tol = 0.005408550068552711 Iteration 23: loglikelihood = -197.78991514558754, backtracks = 3, tol = 0.12418846818411548 Iteration 24: loglikelihood = -195.3458651891717, backtracks = 0, tol = 0.04474686356665713 Iteration 25: loglikelihood = -193.85329270192864, backtracks = 1, tol = 0.11642705219079118 Iteration 26: loglikelihood = -193.5872888252266, backtracks = 1, tol = 0.005994529796500222 Iteration 27: loglikelihood = -193.49244103087173, backtracks = 1, tol = 0.003977497505879251 Iteration 28: loglikelihood = -193.43959542357507, backtracks = 2, tol = 0.00330084983993103 Iteration 29: loglikelihood = -197.2834449493823, backtracks = 3, tol = 0.14332949891400917 Iteration 30: loglikelihood = -191.1561814374434, backtracks = 0, tol = 0.14271551862933007 Iteration 31: loglikelihood = -190.2589777412173, backtracks = 1, tol = 0.018296148237923138 Iteration 32: loglikelihood = -189.9878891870221, backtracks = 1, tol = 0.010701165536450384 Iteration 33: loglikelihood = -189.867470684632, backtracks = 1, tol = 0.007473112269951343 Iteration 34: loglikelihood = -193.0058316555954, backtracks = 3, tol = 0.1141647124557401 Iteration 35: loglikelihood = -191.61778833782117, backtracks = 0, tol = 0.033257092226161265 Iteration 36: loglikelihood = -190.26592749131268, backtracks = 0, tol = 0.12758732776034531 Iteration 37: loglikelihood = -189.83372327320802, backtracks = 1, tol = 0.008553392013129577 Iteration 38: loglikelihood = -189.70612855593623, backtracks = 1, tol = 0.0044027459232161385 Iteration 39: loglikelihood = -189.65408637483733, backtracks = 1, tol = 0.003586549894028387 Iteration 40: loglikelihood = -189.6305816735391, backtracks = 3, tol = 0.0019965524261909384 Iteration 41: loglikelihood = -200.89359611814402, backtracks = 3, tol = 0.14583347899126511 Iteration 42: loglikelihood = -193.27097139861027, backtracks = 0, tol = 0.14535809468532176 Iteration 43: loglikelihood = -192.2935217503592, backtracks = 1, tol = 0.015904619777886927 Iteration 44: loglikelihood = -192.0507085557377, backtracks = 1, tol = 0.008141180826631752 Iteration 45: loglikelihood = -191.98876965234143, backtracks = 1, tol = 0.0042025046810855214 Iteration 46: loglikelihood = -191.9726936044892, backtracks = 1, tol = 0.0021655324830217207 Iteration 47: loglikelihood = -191.96846706923031, backtracks = 1, tol = 0.0011055332529237927 Iteration 48: loglikelihood = -191.96734266484526, backtracks = 1, tol = 0.0005555964548322557 Iteration 49: loglikelihood = -191.9670386960076, backtracks = 1, tol = 0.0002733997501911196 Iteration 50: loglikelihood = -191.96695335555074, backtracks = 1, tol = 0.00013154922168130258 Iteration 51: loglikelihood = -191.96692620413978, backtracks = 1, tol = 7.105685194739283e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 2.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -4622.551604054822, backtracks = 0, tol = 0.5193249584056574 Iteration 2: loglikelihood = -2370.2288702568135, backtracks = 0, tol = 0.08516290153602937 Iteration 3: loglikelihood = -1628.2779805230734, backtracks = 0, tol = 0.08510667286475938 Iteration 4: loglikelihood = -1454.7696920028593, backtracks = 0, tol = 0.0668742044459884 Iteration 5: loglikelihood = -1431.3125991102183, backtracks = 0, tol = 0.03096243493721412 Iteration 6: loglikelihood = -1370.9661279340523, backtracks = 0, tol = 0.16122934512236825 Iteration 7: loglikelihood = -1349.3630129217245, backtracks = 0, tol = 0.04940467706625358 Iteration 8: loglikelihood = -1343.7926998077623, backtracks = 1, tol = 0.01978148870667957 Iteration 9: loglikelihood = -1340.6877984318428, backtracks = 1, tol = 0.020786586019244175 Iteration 10: loglikelihood = -1339.5385760132565, backtracks = 0, tol = 0.012002264400159814 Iteration 11: loglikelihood = -1338.7087512939925, backtracks = 0, tol = 0.008770666883607416 Iteration 12: loglikelihood = -1338.0471200271809, backtracks = 0, tol = 0.009202490961716712 Iteration 13: loglikelihood = -1337.5611919264059, backtracks = 0, tol = 0.0068315254211271815 Iteration 14: loglikelihood = -1337.1677722756895, backtracks = 0, tol = 0.008861085901302218 Iteration 15: loglikelihood = -1336.8784420289094, backtracks = 0, tol = 0.005365773829878683 Iteration 16: loglikelihood = -1336.6426487706751, backtracks = 0, tol = 0.00830889055512656 Iteration 17: loglikelihood = -1336.4693830843828, backtracks = 0, tol = 0.0042155895178531706 Iteration 18: loglikelihood = -1336.3281681965102, backtracks = 0, tol = 0.0075333067894796865 Iteration 19: loglikelihood = -1336.224603535248, backtracks = 0, tol = 0.0032987942132679192 Iteration 20: loglikelihood = -1336.16161033523, backtracks = 1, tol = 0.003285417825487917 Iteration 21: loglikelihood = -1336.12157407111, backtracks = 0, tol = 0.0023316827511620777 Iteration 22: loglikelihood = -1336.0879763748148, backtracks = 0, tol = 0.0019661902500722776 Iteration 23: loglikelihood = -1336.0599480123442, backtracks = 0, tol = 0.0019281952172840674 Iteration 24: loglikelihood = -1336.036237277979, backtracks = 0, tol = 0.001644775736410173 Iteration 25: loglikelihood = -1336.0162812038793, backtracks = 0, tol = 0.0016084936088701395 Iteration 26: loglikelihood = -1335.999299059606, backtracks = 0, tol = 0.0013870891445086474 Iteration 27: loglikelihood = -1335.984911704244, backtracks = 0, tol = 0.0013509629964146399 Iteration 28: loglikelihood = -1335.9726138951476, backtracks = 0, tol = 0.0011769438265490225 Iteration 29: loglikelihood = -1335.962142829153, backtracks = 0, tol = 0.0011408861764204189 Iteration 30: loglikelihood = -1335.9531620910782, backtracks = 0, tol = 0.0010033406429694226 Iteration 31: loglikelihood = -1335.945485612643, backtracks = 0, tol = 0.00096779505251894 Iteration 32: loglikelihood = -1335.9388843297286, backtracks = 0, tol = 0.0008584948021478311 Iteration 33: loglikelihood = -1335.9332244266582, backtracks = 0, tol = 0.0008240138136469228 Iteration 34: loglikelihood = -1335.928347142337, backtracks = 0, tol = 0.0007395998080766954 Iteration 35: loglikelihood = -1335.9241551175528, backtracks = 0, tol = 0.0007037755007892871 Iteration 36: loglikelihood = -1335.920536737996, backtracks = 0, tol = 0.0006442338335140557 Iteration 37: loglikelihood = -1335.917420552438, backtracks = 0, tol = 0.0006026602190576049 Iteration 38: loglikelihood = -1335.9147271789939, backtracks = 0, tol = 0.0005611132586091041 Iteration 39: loglikelihood = -1335.912403836131, backtracks = 0, tol = 0.0005172238966553744 Iteration 40: loglikelihood = -1335.91039352758, backtracks = 0, tol = 0.0004886749726617941 Iteration 41: loglikelihood = -1335.9086570682018, backtracks = 0, tol = 0.00044474502639401894 Iteration 42: loglikelihood = -1335.907153211537, backtracks = 0, tol = 0.0004255549697691602 Iteration 43: loglikelihood = -1335.9058527541674, backtracks = 0, tol = 0.0003830472048758651 Iteration 44: loglikelihood = -1335.9047256505712, backtracks = 0, tol = 0.0003705621886663819 Iteration 45: loglikelihood = -1335.903750070842, backtracks = 0, tol = 0.0003303719111973459 Iteration 46: loglikelihood = -1335.9029040073738, backtracks = 0, tol = 0.00032265639796489416 Iteration 47: loglikelihood = -1335.9021711032428, backtracks = 0, tol = 0.0002852854857237575 Iteration 48: loglikelihood = -1335.9015351628182, backtracks = 0, tol = 0.0002809291851961884 Iteration 49: loglikelihood = -1335.900983906807, backtracks = 0, tol = 0.0002466099336957463 Iteration 50: loglikelihood = -1335.9005053691124, backtracks = 0, tol = 0.0002445874466862209 Iteration 51: loglikelihood = -1335.9000903174838, backtracks = 0, tol = 0.0002133706637379263 Iteration 52: loglikelihood = -1335.8997298806676, backtracks = 0, tol = 0.0002129389659883374 Iteration 53: loglikelihood = -1335.8994171087504, backtracks = 0, tol = 0.00018475647947788264 Iteration 54: loglikelihood = -1335.8991454056625, backtracks = 0, tol = 0.000185379779107836 Iteration 55: loglikelihood = -1335.8989095342881, backtracks = 0, tol = 0.000160088577839107 Iteration 56: loglikelihood = -1335.8987045779063, backtracks = 0, tol = 0.0001613830913912738 Iteration 57: loglikelihood = -1335.8985265867852, backtracks = 0, tol = 0.00013879626202567663 Iteration 58: loglikelihood = -1335.8983718880488, backtracks = 0, tol = 0.0001404895534315826 Iteration 59: loglikelihood = -1335.8982375008227, backtracks = 0, tol = 0.00012039772484316897 Iteration 60: loglikelihood = -1335.8981206762705, backtracks = 0, tol = 0.0001222987324082352 Iteration 61: loglikelihood = -1335.8980191634064, backtracks = 0, tol = 0.00010448470546575675 Iteration 62: loglikelihood = -1335.8979309016433, backtracks = 0, tol = 0.00010646163676328278 Iteration 63: loglikelihood = -1335.8978541903375, backtracks = 0, tol = 9.071013698488432e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1611.7783710331794, backtracks = 0, tol = 0.5429122138665803 Iteration 2: loglikelihood = -1536.9312097411641, backtracks = 0, tol = 0.10187751309718637 Iteration 3: loglikelihood = -1495.0098337304687, backtracks = 0, tol = 0.08620053005081553 Iteration 4: loglikelihood = -1478.4687849391826, backtracks = 0, tol = 0.0698954717687513 Iteration 5: loglikelihood = -1477.6178270047783, backtracks = 0, tol = 0.08832996333986172 Iteration 6: loglikelihood = -1476.9860351233385, backtracks = 0, tol = 0.017706363179325054 Iteration 7: loglikelihood = -1475.7074521415939, backtracks = 0, tol = 0.09018398387523986 Iteration 8: loglikelihood = -1475.4315473197653, backtracks = 0, tol = 0.012444601490430508 Iteration 9: loglikelihood = -1475.424740471993, backtracks = 0, tol = 0.002044726511979215 Iteration 10: loglikelihood = -1475.4236376209185, backtracks = 0, tol = 0.0007992423003561796 Iteration 11: loglikelihood = -1475.423384263289, backtracks = 0, tol = 0.000421461264415647 Iteration 12: loglikelihood = -1475.4233236544014, backtracks = 0, tol = 0.00018435453054499535 Iteration 13: loglikelihood = -1475.4233088468536, backtracks = 0, tol = 0.0001035488255678887 Iteration 14: loglikelihood = -1475.4233061166951, backtracks = 1, tol = 2.4104326507533065e-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 = -1791.4054754184197, backtracks = 0, tol = 0.7651202266997176 Iteration 2: loglikelihood = -1466.99920792822, backtracks = 0, tol = 0.11941760158182639 Iteration 3: loglikelihood = -1396.3191899206088, backtracks = 0, tol = 0.042024925559588464 Iteration 4: loglikelihood = -1395.9617005519253, backtracks = 0, tol = 0.02752658424571503 Iteration 5: loglikelihood = -1394.478346648922, backtracks = 0, tol = 0.027347642890703575 Iteration 6: loglikelihood = -1394.385294688835, backtracks = 1, tol = 0.0009998518731319595 Iteration 7: loglikelihood = -1394.3613362175631, backtracks = 1, tol = 0.00048547293065730613 Iteration 8: loglikelihood = -1394.3552028303336, backtracks = 1, tol = 0.00023052785008909006 Iteration 9: loglikelihood = -1394.3536403927133, backtracks = 1, tol = 0.0001154455382915593 Iteration 10: loglikelihood = -1394.3532439636274, backtracks = 1, tol = 5.838779259952757e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1611.632176233673, backtracks = 0, tol = 0.3375724056034735 Iteration 2: loglikelihood = -1415.8426114717993, backtracks = 0, tol = 0.10409987430476894 Iteration 3: loglikelihood = -1396.3719253383906, backtracks = 0, tol = 0.04550457622140698 Iteration 4: loglikelihood = -1395.1718734002761, backtracks = 0, tol = 0.0286531930592344 Iteration 5: loglikelihood = -1394.9870644942407, backtracks = 0, tol = 0.003599533084337625 Iteration 6: loglikelihood = -1394.984667739521, backtracks = 0, tol = 0.00025652209968976466 Iteration 7: loglikelihood = -1394.9846174555, backtracks = 0, tol = 4.2638343424332606e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 8.6s **** 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 = -1447.5789574503433, backtracks = 0, tol = 0.15441238483117034 Iteration 2: loglikelihood = -1399.355999477294, backtracks = 0, tol = 0.08725884003857431 Iteration 3: loglikelihood = -1365.3409154079527, backtracks = 0, tol = 0.12025006350452283 Iteration 4: loglikelihood = -1345.2525089494695, backtracks = 0, tol = 0.07976810346379103 Iteration 5: loglikelihood = -1338.5789907897026, backtracks = 0, tol = 0.04060355642737055 Iteration 6: loglikelihood = -1336.1610143544078, backtracks = 0, tol = 0.024063694960897053 Iteration 7: loglikelihood = -1326.3084325310415, backtracks = 0, tol = 0.08090689718376033 Iteration 8: loglikelihood = -1320.3396929754429, backtracks = 0, tol = 0.05566148923690884 Iteration 9: loglikelihood = -1319.5244581841798, backtracks = 0, tol = 0.01765330801019035 Iteration 10: loglikelihood = -1319.3229465158763, backtracks = 1, tol = 0.003415821015271152 Iteration 11: loglikelihood = -1319.2427833410197, backtracks = 2, tol = 0.0037470405968866986 Iteration 12: loglikelihood = -1319.1926550586552, backtracks = 2, tol = 0.002842542098562441 Iteration 13: loglikelihood = -1319.1640026549976, backtracks = 2, tol = 0.002180706503050221 Iteration 14: loglikelihood = -1319.147726036495, backtracks = 2, tol = 0.0016545655797777748 Iteration 15: loglikelihood = -1319.1385127841047, backtracks = 2, tol = 0.0012495740649273452 Iteration 16: loglikelihood = -1319.1333088207223, backtracks = 2, tol = 0.0009410943027258452 Iteration 17: loglikelihood = -1319.1303733200373, backtracks = 2, tol = 0.0007076674700901586 Iteration 18: loglikelihood = -1319.1287188390495, backtracks = 2, tol = 0.0005316493477674374 Iteration 19: loglikelihood = -1319.1277868817667, backtracks = 2, tol = 0.00039918807992880915 Iteration 20: loglikelihood = -1319.1272621205683, backtracks = 2, tol = 0.0002996233271230745 Iteration 21: loglikelihood = -1319.1269667216764, backtracks = 2, tol = 0.0002248396625719121 Iteration 22: loglikelihood = -1319.1268004680674, backtracks = 2, tol = 0.00016869510013510554 Iteration 23: loglikelihood = -1319.1267069120731, backtracks = 2, tol = 0.00012655675008519355 Iteration 24: loglikelihood = -1319.1266542707276, backtracks = 2, tol = 9.493697169383122e-5 1.495802 seconds (9.68 M allocations: 159.476 MiB, 4.53% gc time, 29.50% compilation time: 5% of which was recompilation) **** 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 = -1491.4931596939348, backtracks = 0, tol = 0.15441238483117034 Iteration 2: loglikelihood = -1449.4655691062048, backtracks = 0, tol = 0.09353927450472077 Iteration 3: loglikelihood = -1426.3707479014981, backtracks = 0, tol = 0.08336351184738945 Iteration 4: loglikelihood = -1408.2354721927716, backtracks = 0, tol = 0.07691763190917299 Iteration 5: loglikelihood = -1392.6988132670997, backtracks = 0, tol = 0.07731327490994581 Iteration 6: loglikelihood = -1381.1931777593195, backtracks = 0, tol = 0.07909678032865937 Iteration 7: loglikelihood = -1378.650230754686, backtracks = 0, tol = 0.09601393211569997 Iteration 8: loglikelihood = -1369.1721702098714, backtracks = 0, tol = 0.0959340727779124 Iteration 9: loglikelihood = -1364.920223973337, backtracks = 0, tol = 0.08448690501855663 Iteration 10: loglikelihood = -1359.4805557215784, backtracks = 0, tol = 0.08350160924881314 Iteration 11: loglikelihood = -1356.555696128509, backtracks = 0, tol = 0.08950169263889404 Iteration 12: loglikelihood = -1353.1719523417376, backtracks = 0, tol = 0.012845891197235877 Iteration 13: loglikelihood = -1350.537331847447, backtracks = 0, tol = 0.0019611510644698665 Iteration 14: loglikelihood = -1348.2158668225802, backtracks = 0, tol = 0.0005718984842511531 Iteration 15: loglikelihood = -1346.0856873598107, backtracks = 0, tol = 0.0920864702621175 Iteration 16: loglikelihood = -1344.2353559546775, backtracks = 0, tol = 0.010937149954630958 Iteration 17: loglikelihood = -1342.6359088877166, backtracks = 0, tol = 0.0017933706831382292 Iteration 18: loglikelihood = -1341.8579488029425, backtracks = 0, tol = 0.08992785964357985 Iteration 19: loglikelihood = -1340.130647761573, backtracks = 0, tol = 0.013800705188509888 Iteration 20: loglikelihood = -1338.935764205941, backtracks = 0, tol = 0.0026480661464003156 Iteration 21: loglikelihood = -1337.8365152377773, backtracks = 0, tol = 0.0007558694445993598 Iteration 22: loglikelihood = -1336.7170527328694, backtracks = 0, tol = 0.08622809989091866 Iteration 23: loglikelihood = -1335.801121508948, backtracks = 0, tol = 0.0070308080131545 Iteration 24: loglikelihood = -1334.9871968371542, backtracks = 0, tol = 0.001893716245869713 Iteration 25: loglikelihood = -1334.919091216284, backtracks = 0, tol = 0.0901241052191894 Iteration 26: loglikelihood = -1333.761053972739, backtracks = 0, tol = 0.014342140881486769 Iteration 27: loglikelihood = -1333.0919588941272, backtracks = 0, tol = 0.002707396049261618 Iteration 28: loglikelihood = -1332.464328418, backtracks = 0, tol = 0.0007709640183583546 Iteration 29: loglikelihood = -1331.7451555090097, backtracks = 0, tol = 0.07793389331012761 Iteration 30: loglikelihood = -1331.2182429435636, backtracks = 0, tol = 0.006526701874634441 Iteration 31: loglikelihood = -1330.7352180643502, backtracks = 0, tol = 0.0020781387238349575 Iteration 32: loglikelihood = -1329.9507413445863, backtracks = 1, tol = 0.00031361005782955774 Iteration 33: loglikelihood = -1329.6011044319464, backtracks = 1, tol = 0.00042123568025733934 Iteration 34: loglikelihood = -1329.3257904517577, backtracks = 1, tol = 0.00025351918056277953 Iteration 35: loglikelihood = -1329.0037931906375, backtracks = 1, tol = 0.00012255608629851224 Iteration 36: loglikelihood = -1328.4725232471255, backtracks = 1, tol = 6.105110268455397e-5 0.376908 seconds (1.37 M allocations: 25.269 MiB, 3.07% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3506.2805, backtracks = 0, tol = 0.07114212309064426 Iteration 2: loglikelihood = -3477.4172, backtracks = 0, tol = 0.040320354459993074 Iteration 3: loglikelihood = -3473.4905, backtracks = 1, tol = 0.008066199104643073 Iteration 4: loglikelihood = -3456.4119, backtracks = 1, tol = 0.05752723174575591 Iteration 5: loglikelihood = -3452.4177, backtracks = 0, tol = 0.0773409448678385 Iteration 6: loglikelihood = -3450.764, backtracks = 1, tol = 0.005579807163727965 Iteration 7: loglikelihood = -3450.257, backtracks = 1, tol = 0.0035650010738749243 Iteration 8: loglikelihood = -3450.1152, backtracks = 1, tol = 0.001995666287847714 Iteration 9: loglikelihood = -3450.076, backtracks = 1, tol = 0.001048029847935261 Iteration 10: loglikelihood = -3450.0632, backtracks = 1, tol = 0.0005405199514280843 Iteration 11: loglikelihood = -3450.0603, backtracks = 1, tol = 0.0002740360573224074 Iteration 12: loglikelihood = -3450.0647, backtracks = 3, tol = 3.975107121503362e-5 22.631482 seconds (15.99 M allocations: 623.433 MiB, 0.95% gc time, 97.67% compilation time: <1% of which was recompilation) **** 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 = -3424.5703, backtracks = 0, tol = 0.07114212309064426 Iteration 2: loglikelihood = -3340.9922, backtracks = 0, tol = 0.0410518842087458 Iteration 3: loglikelihood = -3186.9365, backtracks = 1, tol = 0.008061528430224804 Iteration 4: loglikelihood = -3005.7905, backtracks = 1, tol = 0.006773299197128777 Iteration 5: loglikelihood = -2975.0298, backtracks = 0, tol = 0.09536835862769241 Iteration 6: loglikelihood = -2804.6252, backtracks = 0, tol = 0.09595788948858786 Iteration 7: loglikelihood = -2721.333, backtracks = 0, tol = 0.08523004058080341 Iteration 8: loglikelihood = -2620.4773, backtracks = 0, tol = 0.09189734646242749 Iteration 9: loglikelihood = -2508.8203, backtracks = 0, tol = 0.09141113662869733 Iteration 10: loglikelihood = -2442.569, backtracks = 0, tol = 0.08876197783007425 Iteration 11: loglikelihood = -2375.24, backtracks = 0, tol = 0.08882891639578169 Iteration 12: loglikelihood = -2322.2947, backtracks = 0, tol = 0.10572699762524392 Iteration 13: loglikelihood = -2286.2366, backtracks = 0, tol = 0.10516136591966564 Iteration 14: loglikelihood = -2247.837, backtracks = 0, tol = 0.10185066587064831 Iteration 15: loglikelihood = -2232.3293, backtracks = 0, tol = 0.10081044016000698 Iteration 16: loglikelihood = -2220.2856, backtracks = 0, tol = 0.11334279101288215 Iteration 17: loglikelihood = -2203.087, backtracks = 0, tol = 0.0945919187735551 Iteration 18: loglikelihood = -2195.1882, backtracks = 0, tol = 0.08837604318159471 Iteration 19: loglikelihood = -2192.3665, backtracks = 0, tol = 0.08641380530939462 Iteration 20: loglikelihood = -2191.0125, backtracks = 0, tol = 0.09695305091996922 Iteration 21: loglikelihood = -2188.5007, backtracks = 0, tol = 0.09134204240490891 Iteration 22: loglikelihood = -2188.1162, backtracks = 1, tol = 0.006284962700234494 Iteration 23: loglikelihood = -2188.0205, backtracks = 1, tol = 0.0034459244566502436 Iteration 24: loglikelihood = -2187.9976, backtracks = 1, tol = 0.0018971470639110681 Iteration 25: loglikelihood = -2187.9875, backtracks = 1, tol = 0.0010347496241210191 Iteration 26: loglikelihood = -2187.985, backtracks = 2, tol = 0.0002808163373376223 Iteration 27: loglikelihood = -2187.9807, backtracks = 2, tol = 0.00021751985144780763 Iteration 28: loglikelihood = -2187.9797, backtracks = 2, tol = 0.0001681660077717912 Iteration 29: loglikelihood = -2187.9797, backtracks = 2, tol = 0.0001298910366202905 Iteration 30: loglikelihood = -2187.9766, backtracks = 3, tol = 5.014442631206379e-5 0.236178 seconds (1.77 M allocations: 29.475 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 27.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2973.20721158067, backtracks = 0, tol = 0.9753037901485436 Iteration 2: loglikelihood = -1640.6694321323835, backtracks = 0, tol = 0.2999151154493682 Iteration 3: loglikelihood = -1418.3315050219228, backtracks = 0, tol = 0.10707075072938249 Iteration 4: loglikelihood = -1411.8219428589443, backtracks = 0, tol = 0.038898114770295936 Iteration 5: loglikelihood = -1410.7307354136753, backtracks = 0, tol = 0.03138838740051226 Iteration 6: loglikelihood = -1410.653861909991, backtracks = 0, tol = 0.001736989736614678 Iteration 7: loglikelihood = -1410.6533631901768, backtracks = 1, tol = 8.130020517735094e-5 7.136532 seconds (1.10 M allocations: 124.044 MiB, 0.61% gc time, 83.03% compilation time: 31% of which was recompilation) Test Summary: | Pass Total Time initialze beta | 1 1 7.6s 9.367252 seconds (3.68 M allocations: 76.383 MiB, 0.43% gc time, 0.48% compilation time) 5.558880 seconds (3.66 M allocations: 85.290 MiB, 0.09% gc time) 8.848106 seconds (20.52 M allocations: 433.414 MiB, 1.09% gc time, 0.59% compilation time) 8.489523 seconds (20.48 M allocations: 439.212 MiB, 0.99% gc time) WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_AX_additive!(Any, Any, Any, Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_AX_additive_rem!(Any, Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_AtX_additive!(Any, Any, Any, Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_AtX_additive_rem!(Any, Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl 50.227184 seconds (3.82 M allocations: 4.218 GiB, 0.77% gc time, 20.20% compilation time: <1% of which was recompilation) 74.930624 seconds (73.74 k allocations: 187.302 MiB, 0.18% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m55.4s Test Summary: | Pass Total Time update_support! | 10 10 0.5s WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_AX_additive_meanimpute!(Any, Any, Any, Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _snparray_AX_additive_meanimpute_rem!(Any, Any, Any, Any, Any, Any, Any) at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/linalg_direct.jl 9.388 ms (77 allocations: 4.67 KiB) 4.983 μs (0 allocations: 0 bytes) 149.259 μs (4 allocations: 288 bytes) 14.720 μs (0 allocations: 0 bytes) 49.619 μs (2 allocations: 64 bytes) 32.170 μs (0 allocations: 0 bytes) 41.219 μs (0 allocations: 0 bytes) 40.219 μs (0 allocations: 0 bytes) 71.640 μs (0 allocations: 0 bytes) 31.019 ms (77 allocations: 4.67 KiB) 26.980 μs (0 allocations: 0 bytes) 170.549 μs (4 allocations: 288 bytes) 75.620 μs (0 allocations: 0 bytes) 257.108 μs (2 allocations: 64 bytes) 109.639 μs (0 allocations: 0 bytes) 213.788 μs (0 allocations: 0 bytes) 207.718 μs (0 allocations: 0 bytes) 243.228 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m20.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.14802242082004133 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077987 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 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 1.560478 seconds (57.25 k allocations: 5.692 MiB, 12.75% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 7.1s **** 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 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 = 0.02433527426328489 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741211 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484518 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 4.072935 seconds (354.55 k allocations: 170.202 MiB, 0.88% gc time, 30.10% compilation time: 13% of which was recompilation) Test Summary: | Pass Total Time initialze beta | 5 5 4.6s **** 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: 0:03:31 Cross validating... 13%|████▏ | ETA: 0:00:52 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... 30%|█████████▋ | ETA: 0:00:19 Cross validating... 33%|██████████▋ | ETA: 0:00:17 Cross validating... 37%|███████████▋ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:13 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 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97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 3996.414206264225 1 3543.3663350940383 2 2878.747550319169 3 2274.2587414495274 4 2034.6732985845997 5 1601.9842141897063 6 662.7777085663204 7 532.8093444530984 8 431.8593740525811 9 359.3245003780236 10 452.09975664231627 11 436.1930375138735 12 418.75910300790156 13 370.9239033763339 14 392.6675298640798 15 373.3702979743874 16 461.9706583691019 17 423.95676619965474 18 406.32992735213077 19 414.0503140704071 20 450.12981498071315 Best k = 9 12.635230 seconds (12.10 M allocations: 305.124 MiB, 0.40% gc time, 57.11% compilation time: <1% of which was recompilation) **** 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: 0:00:03 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 3996.414206264225 1 3543.901593182526 2 2881.535800373663 3 2287.0325171858303 4 2056.583216331004 5 1626.5488613333687 6 704.0289055819421 7 602.398680989378 8 529.3011222715757 9 505.2649808717043 10 471.7314027734145 11 462.2931867905869 12 442.2512554869037 13 440.5036381252381 14 418.9332982311475 15 426.6938873206815 16 432.86800782748526 17 435.5677214012709 18 442.51380931649913 19 464.9890459697593 20 450.22638909097736 Best k = 14 5.787321 seconds (11.78 M allocations: 252.262 MiB, 0.75% gc time, 0.97% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 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: 0:04:27 Cross validating... 8%|██▌ | ETA: 0:01:43 Cross validating... 13%|████▏ | ETA: 0:01:02 Cross validating... 17%|█████▋ | ETA: 0:00:43 Cross validating... 21%|██████▋ | ETA: 0:00:35 Cross validating... 25%|████████▏ | ETA: 0:00:27 Cross validating... 30%|█████████▋ | ETA: 0:00:22 Cross validating... 35%|███████████▏ | ETA: 0:00:18 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 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 1698.1347595214843 1 1385.2070435791015 2 1047.8572725219728 3 825.0151403198242 4 657.2116749267578 5 574.532574584961 6 459.6061855163574 7 405.5582631835938 8 373.6008379516602 9 360.0970147705078 10 362.0683962402344 11 365.7319743347168 12 367.6964764099121 13 370.9316201782227 14 372.3816258544922 15 376.84046383667 16 379.9947436828613 17 389.65871395874024 18 399.46709759521485 19 380.5070198364258 20 381.3895534973145 Best k = 9 13.008036 seconds (12.07 M allocations: 265.561 MiB, 0.50% gc time, 73.85% compilation time: <1% of which was recompilation) **** 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... 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... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:01 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | 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: 0:00:02 Crossvalidation Results: k MSE 0 1698.1347595214843 1 1387.149668334961 2 1049.5477445068361 3 826.1753112792969 4 663.5466638793945 5 581.1662437133789 6 464.153011138916 7 416.2810054626465 8 383.49840914916996 9 369.0559821166992 10 375.05782177734375 11 384.06131814575195 12 394.0617152709961 13 399.20536117553706 14 405.2975439758301 15 419.98401373291017 16 428.0471104125977 17 419.6607846374512 18 425.81062762451177 19 430.1941192016602 20 436.0541896057129 Best k = 9 3.580730 seconds (10.82 M allocations: 199.123 MiB, 1.55% gc time, 0.64% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 17.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:26 Cross validating... 10%|███ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:13 Cross validating... 17%|█████▋ | ETA: 0:00:11 Cross validating... 21%|██████▋ | ETA: 0:00:10 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross 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ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 465.1483638428958 1 405.4491993422 2 375.89787633096194 3 341.9736009505083 4 310.0702788424338 5 288.9305869578813 6 282.0117404371995 7 277.8111952907532 8 267.78836981887093 9 256.58973268501967 10 267.0677797960583 11 263.59583936022614 12 264.6645736577394 13 269.8460585371932 14 292.4051454689094 15 290.3758345359227 16 288.87076960787994 17 327.09610382865236 18 321.0108003230579 19 312.4836362611084 20 301.7333904495533 Best k = 9 8.224777 seconds (17.58 M allocations: 416.651 MiB, 0.95% gc time, 24.25% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 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... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | 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: 0:00:02 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 0 465.1483638428958 1 405.9962504329401 2 376.39177059472786 3 336.4029012738232 4 311.23863467980107 5 291.1306311041848 6 284.9577827018841 7 289.2414296306796 8 281.8579028867227 9 289.55041482179314 10 287.31205803797246 11 287.7977027249946 12 294.60446569242794 13 307.5520470261212 14 313.53288953271385 15 323.9118646043668 16 323.46540753397284 17 330.24147540613336 18 347.7252237239444 19 354.2016814652761 20 367.73727864078535 Best k = 8 6.472107 seconds (17.54 M allocations: 364.255 MiB, 1.25% gc time, 0.72% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.2s **** 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: 0:00:38 Cross validating... 6%|██ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 14%|████▋ | ETA: 0:00:10 Cross validating... 17%|█████▋ | ETA: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 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: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 465.03316049968174 1 442.27658014761926 2 417.8404875596693 3 395.4336207729219 4 369.6851363384614 5 343.69978502356923 6 329.14286338806295 7 332.43094856637174 8 331.5502951255628 9 333.7024596750574 10 335.6701005505276 11 337.3573030558342 12 351.771060127377 13 334.2424480874906 14 358.2641573232337 15 344.2540197584533 16 351.51513405344747 17 365.77539159164155 18 379.5855952488997 19 346.2384524249862 20 354.7027609345389 Best k = 6 7.868129 seconds (16.28 M allocations: 385.078 MiB, 10.80% gc time, 26.27% compilation time: <1% of which was recompilation) **** 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: 0:00:04 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: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 465.03316049968174 1 443.07541465072205 2 420.2502452054233 3 396.28760050064784 4 374.5637047600693 5 348.9346652244337 6 334.89107709553895 7 344.26937695344446 8 342.7742611134717 9 350.4099824294027 10 358.0770439677569 11 360.28893003244383 12 375.24922799254824 13 365.5783221396914 14 381.4481496629137 15 392.30340601696753 16 384.6471350225143 17 407.5557751372503 18 422.7575249340744 19 410.46741724725996 20 443.5255636345794 Best k = 6 5.407501 seconds (17.20 M allocations: 354.003 MiB, 1.31% gc time, 0.44% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 14.2s **** 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: 0:00:52 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: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 899.3537552594189 1 684.978628141541 2 578.2894246017314 3 511.77061007077833 4 466.67028020766185 5 441.9093341888885 6 426.7628268971488 7 424.82374650928284 8 399.80332913174743 9 396.4129701160165 10 402.2797475808275 11 401.40766238592187 12 392.39658765973405 13 391.52150681129604 14 395.82218361406893 15 387.64290385360835 16 410.9628270648467 17 416.88166558813884 18 413.696699199795 19 406.9382284449943 20 411.087571225613 Best k = 15 8.310671 seconds (15.09 M allocations: 358.032 MiB, 0.85% gc time, 24.74% 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 Cross validating... 32%|██████████▏ | ETA: 0:00:04 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: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 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: 0:00:02 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: 0:00:00 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 0 899.3537552594189 1 671.1813060166627 2 565.9774576503987 3 506.13632900741504 4 465.38333813784976 5 446.99716960499813 6 434.0015571166316 7 418.06098313310156 8 409.0462279103427 9 417.2864384736662 10 406.5513116436397 11 398.78178666847504 12 410.27025366594347 13 407.5527815776725 14 411.3145830145407 15 413.01362532536564 16 422.6642902060972 17 444.6502450461917 18 447.82727482822054 19 450.4319400804969 20 447.1282171598364 Best k = 11 5.759569 seconds (13.79 M allocations: 274.314 MiB, 0.69% gc time, 0.80% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 5%|█▌ | ETA: 0:00:57 Cross validating... 6%|██ | ETA: 0:00:54 Cross validating... 10%|███ | ETA: 0:00:43 Cross validating... 11%|███▌ | ETA: 0:00:43 Cross validating... 13%|████▏ | ETA: 0:00:38 Cross validating... 14%|████▋ | ETA: 0:00:39 Cross validating... 16%|█████▏ | ETA: 0:00:40 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 19%|██████▏ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:41 Cross validating... 22%|███████▏ | ETA: 0:00:41 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84%|██████████████████████████▉ | ETA: 0:00:07 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:40 Crossvalidation Results: k MSE 0 387.66708503425286 1 312.5499476037717 2 275.0500200427349 3 253.63547856111222 4 245.74823063864355 5 229.29845291806276 6 223.87476458856548 7 221.24993428046287 8 222.89605488216108 9 225.1245021836729 10 226.28606543957312 11 226.79230820317233 12 224.01913759802284 13 230.1806457521584 14 223.60237052782657 15 227.18845336692578 16 229.10001998305938 17 227.11690169157671 18 227.1754192487035 19 231.50470962076196 20 230.04644182521264 Best k = 7 41.173148 seconds (134.38 M allocations: 3.436 GiB, 1.10% gc time, 3.61% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:04 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: 0:00:07 Cross validating... 14%|████▋ | ETA: 0:00:07 Cross validating... 16%|█████▏ | ETA: 0:00:08 Cross validating... 17%|█████▋ | ETA: 0:00:08 Cross 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83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 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: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 387.66708503425286 1 312.9767699050762 2 275.5687469603573 3 255.06697039742517 4 247.09045965816068 5 231.95115047631484 6 226.49721984335704 7 225.0568310590512 8 230.45796949904172 9 234.53618592077476 10 237.70229366703035 11 239.9128796581573 12 235.2636846658621 13 250.57531843519916 14 254.99575939758103 15 254.31648351732707 16 263.8295594102326 17 265.64668899943655 18 267.3361123373618 19 273.6056423966107 20 280.6426240999061 Best k = 7 12.237843 seconds (35.66 M allocations: 735.862 MiB, 0.90% gc time, 0.37% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 53.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:54 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%|██████▏ | 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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: 0:00:05 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 6.258017 seconds (17.16 M allocations: 341.399 MiB, 0.95% gc time, 34.38% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 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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 4.323169 seconds (16.42 M allocations: 292.591 MiB, 1.04% gc time, 0.86% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 11.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:51 Cross validating... 3%|█ | ETA: 0:01:28 Cross validating... 4%|█▎ | ETA: 0:01:16 Cross validating... 5%|█▋ | ETA: 0:01:09 Cross validating... 6%|█▉ | ETA: 0:01:04 Cross validating... 7%|██▎ | ETA: 0:01:00 Cross validating... 8%|██▌ | ETA: 0:00:58 Cross validating... 9%|██▉ | ETA: 0:00:59 Cross validating... 10%|███▎ | ETA: 0:01:00 Cross validating... 11%|███▌ | ETA: 0:01:00 Cross validating... 12%|███▉ | ETA: 0:01:01 Cross validating... 13%|████▏ | ETA: 0:01:01 Cross validating... 14%|████▌ | ETA: 0:01:01 Cross validating... 15%|████▊ | ETA: 0:01:01 Cross validating... 16%|█████▏ | ETA: 0:01:01 Cross validating... 17%|█████▌ | ETA: 0:01:01 Cross validating... 18%|█████▊ | ETA: 0:01:01 Cross validating... 19%|██████▏ | ETA: 0:01:00 Cross validating... 20%|██████▍ | ETA: 0:01:00 Cross validating... 21%|██████▊ | ETA: 0:00:58 Cross validating... 22%|███████ | ETA: 0:00:57 Cross validating... 23%|███████▍ | ETA: 0:00:55 Cross validating... 24%|███████▋ | ETA: 0:00:54 Cross validating... 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| ETA: 0:00:06 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:05 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:04 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:03 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:03 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:02 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:01:10 Crossvalidation Results: k MSE 1 5421.613536586756 2 4418.786040277044 3 3695.6114365392295 4 3424.4913228206206 5 3111.4513476571337 6 2873.5799106074683 7 2855.647750490599 8 2791.523431566735 9 2737.4500849140522 10 2785.765380044314 11 2805.686777777115 12 2815.701065233074 13 2841.483950400976 14 2884.5184164822413 15 2870.57754527897 16 2877.5771586327955 17 2916.0653964627295 18 2941.222935181333 19 2979.4935209348387 20 2997.561638088278 Best k = 9 72.340285 seconds (370.75 k allocations: 236.740 MiB, 0.10% gc time, 1.87% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 1m17.3s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m39.8s **** 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: 0:00:45 Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 4%|█▎ | ETA: 0:00:48 Cross validating... 5%|█▋ | ETA: 0:00:47 Cross validating... 6%|█▉ | ETA: 0:00:54 Cross validating... 7%|██▎ | ETA: 0:00:55 Cross validating... 8%|██▌ | ETA: 0:00:55 Cross validating... 9%|██▉ | ETA: 0:01:00 Cross validating... 10%|███▎ | ETA: 0:01:03 Cross validating... 11%|███▌ | ETA: 0:01:07 Cross validating... 12%|███▉ | 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validating... 98%|███████████████████████████████▍| ETA: 0:00:02 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:01:46 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.397342870813 3 2305.6176519676274 4 2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.2671874606517 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: 0:00:46 Cross validating... 3%|█ | ETA: 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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: 0:00:49 Cross validating... 3%|█ | ETA: 0:00:47 Cross validating... 4%|█▎ | ETA: 0:00:50 Cross validating... 5%|█▋ | ETA: 0:00:49 Cross validating... 6%|█▉ | ETA: 0:00:55 Cross validating... 7%|██▎ | ETA: 0:00:56 Cross validating... 8%|██▌ | ETA: 0:00:56 Cross validating... 9%|██▉ | ETA: 0:01:00 Cross validating... 10%|███▎ | ETA: 0:01:04 Cross validating... 11%|███▌ | ETA: 0:01:07 Cross validating... 12%|███▉ | ETA: 0:01:10 Cross validating... 13%|████▏ | ETA: 0:01:11 Cross validating... 14%|████▌ | ETA: 0:01:12 Cross validating... 15%|████▊ | ETA: 0:01:14 Cross validating... 16%|█████▏ | ETA: 0:01:19 Cross validating... 17%|█████▌ | ETA: 0:01:20 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 2105.1311995023634 11 2132.407165368786 12 2138.2671874606517 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 5m46.9s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [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:611 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:301 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:301 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:485 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:295 [18] _start() @ Base ./client.jl:558 Test Summary: | Error Total Time read BGEN and VCF | 1 1 6.5s 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 1706.43s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2359 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2214 [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/v1.12/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/v1.12/Pkg/src/API.jl:159 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:146 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:300 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:329 [12] _start() @ Base ./client.jl:558 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1817.42s: package tests unexpectedly errored