Package evaluation to test MendelIHT on Julia 1.14.0-DEV.3155 (07edee4e4c*) started at 2026-09-11T01:54:34.168 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.32s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.30.1 [67c07d97] + Automa v1.2.0 ⌅ [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 v0.10.17 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.9 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.14 [f70d9fcc] + CommonWorldInvalidations v1.2.2 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.2.0 [a10d1c49] + DBInterface v2.7.0 [9a962f9c] + 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[efcefdf7] + PCRE2_jll v10.48.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.70.0+0 [3f19e933] + p7zip_jll v17.8.2+0 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 To see why use `status --outdated -m` Installation completed after 5.06s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.4 s ✓ BGEN 5.6 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. NOTE: This behavior may have differed in Julia versions prior to 1.12. Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 19.2 s ✓ MendelIHT 3 dependencies successfully precompiled in 30 seconds. 173 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 48.42s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_MjO1cG/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.17 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.9.0 [2913bbd2] StatsBase v0.34.13 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libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/RTt4y/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ 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 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 11.8s Test Summary: | Pass Total Time deviance | 1 1 0.3s Test Summary: | Pass Total Time update_μ! | 4 4 1.2s Test Summary: | Pass Total Time _choose! | 7 7 6.9s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 0.9s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 1.7s **** 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 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 = -1542.7177279105078, backtracks = 0, tol = 1.6572336580042424 Iteration 2: loglikelihood = -1421.8038287482693, backtracks = 0, tol = 0.1277894705790521 Iteration 3: loglikelihood = -1416.4511893835036, backtracks = 0, tol = 0.020212341883799535 Iteration 4: loglikelihood = -1416.3600727758267, backtracks = 0, tol = 0.003134695490038151 Iteration 5: loglikelihood = -1416.3581031537678, backtracks = 0, tol = 0.0005198992540682628 Iteration 6: loglikelihood = -1416.3580564409167, backtracks = 0, tol = 7.927703270185993e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.048477888107299805 Final loglikelihood: -1416.3580564409167 SNP PVE: 0.8838749095487708 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 569 -0.272729 2 │ 960 -0.486865 3 │ 2366 1.48882 4 │ 2488 -0.437533 5 │ 2893 -0.155944 6 │ 4484 0.520766 7 │ 5356 -0.649428 8 │ 6127 -0.278075 9 │ 6664 1.82224 10 │ 8705 0.481032 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.00693545Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 22.0s **** 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 = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-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 = -242436.69732583285, backtracks = 0, tol = 0.9210096889509576 Iteration 2: loglikelihood = -93316.71015894711, backtracks = 0, tol = 0.05629750088897708 Iteration 3: loglikelihood = -35111.26896938307, backtracks = 0, tol = 0.0641760774731819 Iteration 4: loglikelihood = -13080.941123986444, backtracks = 0, tol = 0.07145691802847967 Iteration 5: loglikelihood = -5059.363799038053, backtracks = 0, tol = 0.07760745322400102 Iteration 6: loglikelihood = -2298.844648673693, backtracks = 0, tol = 0.08043361168908993 Iteration 7: loglikelihood = -1575.4923545046113, backtracks = 0, tol = 0.07289905821313317 Iteration 8: loglikelihood = -1448.2859097538724, backtracks = 0, tol = 0.04908383757170851 Iteration 9: loglikelihood = -1438.0255095409393, backtracks = 0, tol = 0.018333321976645216 Iteration 10: loglikelihood = -1368.0233620070298, backtracks = 0, tol = 0.07286094770691115 Iteration 11: loglikelihood = -1361.288800914068, backtracks = 0, tol = 0.024547738934204824 Iteration 12: loglikelihood = -1357.895782528926, backtracks = 0, tol = 0.015286927894744931 Iteration 13: loglikelihood = -1356.0627277023927, backtracks = 0, tol = 0.013034772452802202 Iteration 14: loglikelihood = -1354.7164286712919, backtracks = 0, tol = 0.009429458816103279 Iteration 15: loglikelihood = -1353.7529688811169, backtracks = 0, tol = 0.008787151481783008 Iteration 16: loglikelihood = -1352.9967914996882, backtracks = 0, tol = 0.007030628049451281 Iteration 17: loglikelihood = -1352.4172546271498, backtracks = 0, tol = 0.006366165199953381 Iteration 18: loglikelihood = -1351.9506743449704, backtracks = 0, tol = 0.005510282199843097 Iteration 19: loglikelihood = -1351.5828660859086, backtracks = 0, tol = 0.004783780128130387 Iteration 20: loglikelihood = -1351.283338711701, backtracks = 0, tol = 0.004409361396793851 Iteration 21: loglikelihood = -1351.0440807366685, backtracks = 0, tol = 0.0036722051949664267 Iteration 22: loglikelihood = -1350.8482786309105, backtracks = 0, tol = 0.003561859905124193 Iteration 23: loglikelihood = -1350.690888705248, backtracks = 0, tol = 0.002856618651810125 Iteration 24: loglikelihood = -1350.561904847318, backtracks = 0, tol = 0.0028887495640953164 Iteration 25: loglikelihood = -1350.4579412939188, backtracks = 0, tol = 0.0022412557543550616 Iteration 26: loglikelihood = -1350.37279285655, backtracks = 0, tol = 0.0023454342349602496 Iteration 27: loglikelihood = -1350.3041050216552, backtracks = 0, tol = 0.001768318933380197 Iteration 28: loglikelihood = -1350.247945232662, backtracks = 0, tol = 0.001903440243159883 Iteration 29: loglikelihood = -1350.2026510706683, backtracks = 0, tol = 0.0014003344590163714 Iteration 30: loglikelihood = -1350.1657029629407, backtracks = 0, tol = 0.0015427862138886073 Iteration 31: loglikelihood = -1350.1359247924172, backtracks = 0, tol = 0.0011405525327896336 Iteration 32: loglikelihood = -1350.1116942983087, backtracks = 0, tol = 0.0012484308948266924 Iteration 33: loglikelihood = -1350.0921841684685, backtracks = 0, tol = 0.0009267103785660072 Iteration 34: loglikelihood = -1350.0763481006181, backtracks = 0, tol = 0.0010084945937318057 Iteration 35: loglikelihood = -1350.0636097251422, backtracks = 0, tol = 0.0007511767046971503 Iteration 36: loglikelihood = -1350.0532941866145, backtracks = 0, tol = 0.0008133149262863375 Iteration 37: loglikelihood = -1350.0450043683484, backtracks = 0, tol = 0.0006075775207392731 Iteration 38: loglikelihood = -1350.038305325389, backtracks = 0, tol = 0.0006549110630559922 Iteration 39: loglikelihood = -1350.0329264608633, backtracks = 0, tol = 0.0004904919473458646 Iteration 40: loglikelihood = -1350.0285877541537, backtracks = 0, tol = 0.0005266513245292155 Iteration 41: loglikelihood = -1350.0251067088377, backtracks = 0, tol = 0.0003953166488971524 Iteration 42: loglikelihood = -1350.0223032505928, backtracks = 0, tol = 0.0004230232851221692 Iteration 43: loglikelihood = -1350.0200554224632, backtracks = 0, tol = 0.00031816243083184745 Iteration 44: loglikelihood = -1350.018247546766, backtracks = 0, tol = 0.0003394574754690651 Iteration 45: loglikelihood = -1350.016798766223, backtracks = 0, tol = 0.00025576513116028026 Iteration 46: loglikelihood = -1350.015634840861, backtracks = 0, tol = 0.000272181849219466 Iteration 47: loglikelihood = -1350.014702520907, backtracks = 0, tol = 0.0002054040621761251 Iteration 48: loglikelihood = -1350.0139541985754, backtracks = 0, tol = 0.0002180968949681514 Iteration 49: loglikelihood = -1350.0133550013436, backtracks = 0, tol = 0.00016482635787614297 Iteration 50: loglikelihood = -1350.0128744200563, backtracks = 0, tol = 0.00017466707212827326 Iteration 51: loglikelihood = -1350.012489722633, backtracks = 0, tol = 0.0001321775003329614 Iteration 52: loglikelihood = -1350.0121813679887, backtracks = 0, tol = 0.00013982659943611678 Iteration 53: loglikelihood = -1350.0119345940122, backtracks = 0, tol = 0.00010593868420000752 Iteration 54: loglikelihood = -1350.01173689005, backtracks = 0, tol = 0.00011189838173336705 Iteration 55: loglikelihood = -1350.0115786992003, backtracks = 0, tol = 8.487144408043321e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1767.9288731267493, backtracks = 0, tol = 0.9676318404313524 Iteration 2: loglikelihood = -1666.5124260878395, backtracks = 0, tol = 0.060422999478903706 Iteration 3: loglikelihood = -1593.1489471663003, backtracks = 0, tol = 0.06332208923613758 Iteration 4: loglikelihood = -1521.3681254675387, backtracks = 0, tol = 0.0723474395424319 Iteration 5: loglikelihood = -1473.3438471170548, backtracks = 0, tol = 0.0892483406629619 Iteration 6: loglikelihood = -1448.988948416502, backtracks = 0, tol = 0.08484924250863737 Iteration 7: loglikelihood = -1441.4471387936187, backtracks = 0, tol = 0.05901838114638755 Iteration 8: loglikelihood = -1438.1846604536993, backtracks = 0, tol = 0.06352292424335741 Iteration 9: loglikelihood = -1437.247808514967, backtracks = 0, tol = 0.08879584396030402 Iteration 10: loglikelihood = -1436.3427146640133, backtracks = 0, tol = 0.017412133553558425 Iteration 11: loglikelihood = -1436.3002733628143, backtracks = 0, tol = 0.004731107209500556 Iteration 12: loglikelihood = -1434.4577497158568, backtracks = 0, tol = 0.07191670823925168 Iteration 13: loglikelihood = -1434.2251287420893, backtracks = 0, tol = 0.014776547324164982 Iteration 14: loglikelihood = -1434.2135525978506, backtracks = 0, tol = 0.002861327534602457 Iteration 15: loglikelihood = -1433.7002415331053, backtracks = 0, tol = 0.08356603084086711 Iteration 16: loglikelihood = -1433.5952609952772, backtracks = 0, tol = 0.010150010745961372 Iteration 17: loglikelihood = -1433.5904227577998, backtracks = 0, tol = 0.0016220162854312368 Iteration 18: loglikelihood = -1433.5897438634272, backtracks = 0, tol = 0.0006050736548037738 Iteration 19: loglikelihood = -1433.5896272537739, backtracks = 0, tol = 0.0002873476219810107 Iteration 20: loglikelihood = -1433.589604967771, backtracks = 0, tol = 0.00011161987125844628 Iteration 21: loglikelihood = -1433.5896009895685, backtracks = 0, tol = 5.555391107896148e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.1s **** 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 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 = -1849.9179051308972, backtracks = 0, tol = 0.7548329971284409 Iteration 2: loglikelihood = -1467.9325461857986, backtracks = 0, tol = 0.11897953638124978 Iteration 3: loglikelihood = -1400.2359211262647, backtracks = 0, tol = 0.05259794923489448 Iteration 4: loglikelihood = -1394.883403404668, backtracks = 0, tol = 0.028580435886930367 Iteration 5: loglikelihood = -1394.358420738401, backtracks = 0, tol = 0.003842996204434357 Iteration 6: loglikelihood = -1392.7806520613265, backtracks = 0, tol = 0.026889638035010564 Iteration 7: loglikelihood = -1392.2535604586724, backtracks = 0, tol = 0.004016099603835676 Iteration 8: loglikelihood = -1392.2362377685338, backtracks = 0, tol = 0.001024886342626908 Iteration 9: loglikelihood = -1392.235429345594, backtracks = 0, tol = 0.00016356481234592368 Iteration 10: loglikelihood = -1392.235387804936, backtracks = 0, tol = 4.897707552893866e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.4s **** 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 **** 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 = -1637.476866424426, backtracks = 0, tol = 0.3704606756329658 Iteration 2: loglikelihood = -1421.8449238564217, backtracks = 0, tol = 0.08067014841222887 Iteration 3: loglikelihood = -1398.6358466976621, backtracks = 0, tol = 0.03826191957905029 Iteration 4: loglikelihood = -1394.6584070072972, backtracks = 0, tol = 0.030880649750482443 Iteration 5: loglikelihood = -1393.9895373302745, backtracks = 0, tol = 0.004966546347640097 Iteration 6: loglikelihood = -1393.9780290106605, backtracks = 1, tol = 0.0005666946253792925 Iteration 7: loglikelihood = -1393.9748049035334, backtracks = 1, tol = 0.0002884107667084429 Iteration 8: loglikelihood = -1393.9739416607347, backtracks = 1, tol = 0.0001387043349829793 Iteration 9: loglikelihood = -1393.9737196407623, backtracks = 1, tol = 6.566775825405913e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** 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 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 = -1473.1241001452804, backtracks = 0, tol = 0.11162633196865432 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175712 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195713 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165582 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.008924704068495177 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039412, backtracks = 0, tol = 0.09056900655606137 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168892 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711446 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300694 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864148 Iteration 17: loglikelihood = -1394.9773102201912, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-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 = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747526, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088284 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.003052291101552644 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.002193157681835551 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910676 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469133 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111326 Iteration 13: loglikelihood = -1434.0179556115856, backtracks = 2, tol = 0.0006363671566384205 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.021056460842673336 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540959 Iteration 16: loglikelihood = -1433.5408744767517, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831415 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338233 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431646 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.0004062814588068666 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.00030341799187724174 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291083832 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532828, backtracks = 2, tol = 0.0250802150540324 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200223 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.02001511172794573 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.513945055356, backtracks = 2, tol = 0.003906515984506249 Iteration 34: loglikelihood = -1429.469197232521, backtracks = 2, tol = 0.003683664863256532 Iteration 35: loglikelihood = -1428.86075262229, backtracks = 2, tol = 0.08711763846658718 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943248 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111564 Iteration 39: loglikelihood = -1428.4620745885084, backtracks = 2, tol = 0.002595137111913267 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148499 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840858 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998762 Iteration 44: loglikelihood = -1428.4181556141764, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660976293 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.415350523391, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973649723 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 7.9s **** 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 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 = -1464.2596043714927, backtracks = 0, tol = 0.21458524300125223 Iteration 2: loglikelihood = -1417.84765563651, backtracks = 0, tol = 0.08108510237330512 Iteration 3: loglikelihood = -1386.9703828772354, backtracks = 0, tol = 0.08137899344463913 Iteration 4: loglikelihood = -1373.4911215737998, backtracks = 0, tol = 0.04404415567782946 Iteration 5: loglikelihood = -1353.447287350201, backtracks = 0, tol = 0.08211841473280945 Iteration 6: loglikelihood = -1348.5430767410796, backtracks = 1, tol = 0.03480167661586759 Iteration 7: loglikelihood = -1343.8597816256954, backtracks = 1, tol = 0.06293909919176868 Iteration 8: loglikelihood = -1341.5235471797218, backtracks = 0, tol = 0.031087370701963147 Iteration 9: loglikelihood = -1340.9369154982417, backtracks = 0, tol = 0.011022633432283626 Iteration 10: loglikelihood = -1338.4644737224257, backtracks = 0, tol = 0.06921832768554924 Iteration 11: loglikelihood = -1337.692866976421, backtracks = 0, tol = 0.019385179081857547 Iteration 12: loglikelihood = -1337.5492542511222, backtracks = 0, tol = 0.0067616699750936045 Iteration 13: loglikelihood = -1337.5056024282114, backtracks = 0, tol = 0.004324952669824362 Iteration 14: loglikelihood = -1337.4905307311644, backtracks = 0, tol = 0.002432703311521004 Iteration 15: loglikelihood = -1337.4848534124571, backtracks = 0, tol = 0.0013505682639600991 Iteration 16: loglikelihood = -1337.4827023734458, backtracks = 0, tol = 0.0009217882569588679 Iteration 17: loglikelihood = -1337.481879119841, backtracks = 0, tol = 0.00049099905824945 Iteration 18: loglikelihood = -1337.481564430218, backtracks = 0, tol = 0.0003525277151834626 Iteration 19: loglikelihood = -1337.4814437494342, backtracks = 0, tol = 0.00018506652319775485 Iteration 20: loglikelihood = -1337.481397516271, backtracks = 0, tol = 0.0001352722072951604 Iteration 21: loglikelihood = -1337.4813797638226, backtracks = 0, tol = 7.056903325258292e-5 0.981225 seconds (2.52 M allocations: 49.341 MiB, 9.92% gc time, 56.27% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1518.6222386432373, backtracks = 0, tol = 0.21458524300125223 Iteration 2: loglikelihood = -1483.642197239866, backtracks = 0, tol = 0.08284282022128986 Iteration 3: loglikelihood = -1459.7954374317717, backtracks = 0, tol = 0.07787514502827426 Iteration 4: loglikelihood = -1442.1701079448915, backtracks = 0, tol = 0.09399639928352956 Iteration 5: loglikelihood = -1428.8330250479087, backtracks = 0, tol = 0.06362843939679438 Iteration 6: loglikelihood = -1415.8942592224491, backtracks = 0, tol = 0.06688492928486925 Iteration 7: loglikelihood = -1407.0259037033723, backtracks = 0, tol = 0.0349856672829743 Iteration 8: loglikelihood = -1400.360149197917, backtracks = 0, tol = 0.018592631023689216 Iteration 9: loglikelihood = -1395.3234673487038, backtracks = 0, tol = 0.010497008092763029 Iteration 10: loglikelihood = -1389.6292082421342, backtracks = 0, tol = 0.06286688617639591 Iteration 11: loglikelihood = -1384.694645203097, backtracks = 0, tol = 0.06700522855898644 Iteration 12: loglikelihood = -1381.188771959453, backtracks = 0, tol = 0.006433266370489052 Iteration 13: loglikelihood = -1378.2871114786108, backtracks = 0, tol = 0.005453894067228227 Iteration 14: loglikelihood = -1375.6379502780235, backtracks = 0, tol = 0.003633522684408418 Iteration 15: loglikelihood = -1373.390502732532, backtracks = 0, tol = 0.003806133906709306 Iteration 16: loglikelihood = -1371.3180755947467, backtracks = 0, tol = 0.0026016879825479402 Iteration 17: loglikelihood = -1369.5376532864373, backtracks = 0, tol = 0.0027773501297586904 Iteration 18: loglikelihood = -1367.8866104793553, backtracks = 0, tol = 0.002038302715792549 Iteration 19: loglikelihood = -1366.4499655631887, backtracks = 0, tol = 0.0020465783136853 Iteration 20: loglikelihood = -1365.1103676604585, backtracks = 0, tol = 0.001649165079022174 Iteration 21: loglikelihood = -1363.9311033195283, backtracks = 0, tol = 0.001527424844121135 Iteration 22: loglikelihood = -1362.8262358375875, backtracks = 0, tol = 0.0013681292504975453 Iteration 23: loglikelihood = -1361.8436529811336, backtracks = 0, tol = 0.0011526617253455205 Iteration 24: loglikelihood = -1361.2774684201866, backtracks = 0, tol = 0.07096131782251906 Iteration 25: loglikelihood = -1360.2988481827465, backtracks = 0, tol = 0.006832590697011061 Iteration 26: loglikelihood = -1359.4880200525497, backtracks = 0, tol = 0.00154498201423038 Iteration 27: loglikelihood = -1358.235001050264, backtracks = 1, tol = 0.0005147183740518148 Iteration 28: loglikelihood = -1358.2046163124396, backtracks = 1, tol = 0.07121808574747697 Iteration 29: loglikelihood = -1357.6612176550411, backtracks = 0, tol = 0.07657174923216194 Iteration 30: loglikelihood = -1356.8357397055295, backtracks = 0, tol = 0.0055255835136867205 Iteration 31: loglikelihood = -1356.2501576915618, backtracks = 0, tol = 0.0015305427131640202 Iteration 32: loglikelihood = -1355.6810011909106, backtracks = 0, tol = 0.0007237152609434965 Iteration 33: loglikelihood = -1355.1620763560493, backtracks = 0, tol = 0.0004721434226128597 Iteration 34: loglikelihood = -1354.665686478614, backtracks = 0, tol = 0.0005985625324203971 Iteration 35: loglikelihood = -1354.2071834561655, backtracks = 0, tol = 0.000311527480573771 Iteration 36: loglikelihood = -1353.4582268206857, backtracks = 1, tol = 0.0002239138826945011 Iteration 37: loglikelihood = -1352.9418798578902, backtracks = 1, tol = 0.00018014071939988932 Iteration 38: loglikelihood = -1352.7615416914655, backtracks = 2, tol = 0.00010231185475014968 Iteration 39: loglikelihood = -1354.0434138521496, backtracks = 3, tol = 4.804313822614636e-5 0.390747 seconds (1.56 M allocations: 28.759 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 = -3649.939, backtracks = 0, tol = 0.08033215726312759 Iteration 2: loglikelihood = -3613.9744, backtracks = 0, tol = 0.038129613960030125 Iteration 3: loglikelihood = -3609.98, backtracks = 1, tol = 0.011192526636531525 Iteration 4: loglikelihood = -3591.4385, backtracks = 1, tol = 0.05756330806228948 Iteration 5: loglikelihood = -3581.1042, backtracks = 0, tol = 0.07615236641486728 Iteration 6: loglikelihood = -3560.9993, backtracks = 0, tol = 0.08685707024620387 Iteration 7: loglikelihood = -3557.0798, backtracks = 0, tol = 0.013623428910665739 Iteration 8: loglikelihood = -3556.8948, backtracks = 0, tol = 0.0024856531044909866 Iteration 9: loglikelihood = -3546.013, backtracks = 0, tol = 0.07381805604818623 Iteration 10: loglikelihood = -3545.0579, backtracks = 0, tol = 0.006861523069984624 Iteration 11: loglikelihood = -3544.978, backtracks = 0, tol = 0.00274739034414419 Iteration 12: loglikelihood = -3544.968, backtracks = 1, tol = 0.0003516894437369522 Iteration 13: loglikelihood = -3544.9631, backtracks = 1, tol = 0.00032586576853022996 Iteration 14: loglikelihood = -3544.9631, backtracks = 1, tol = 0.0002507736835663082 Iteration 15: loglikelihood = -3544.963, backtracks = 1, tol = 0.00011837548715794992 Iteration 16: loglikelihood = -3544.9653, backtracks = 3, tol = 1.5890451900785427e-5 18.532266 seconds (14.98 M allocations: 694.441 MiB, 1.15% gc time, 96.91% 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 = -3550.0876, backtracks = 0, tol = 0.08033215726312759 Iteration 2: loglikelihood = -3444.001, backtracks = 0, tol = 0.03905955195206775 Iteration 3: loglikelihood = -3248.8677, backtracks = 1, tol = 0.010948425322384835 Iteration 4: loglikelihood = -3029.2986, backtracks = 1, tol = 0.0061972365016582515 Iteration 5: loglikelihood = -2979.5403, backtracks = 0, tol = 0.08784184442406891 Iteration 6: loglikelihood = -2793.5234, backtracks = 0, tol = 0.10162320143960425 Iteration 7: loglikelihood = -2648.2686, backtracks = 0, tol = 0.09246047297465056 Iteration 8: loglikelihood = -2543.7761, backtracks = 0, tol = 0.08784469986601494 Iteration 9: loglikelihood = -2438.549, backtracks = 0, tol = 0.08782413214088791 Iteration 10: loglikelihood = -2348.4136, backtracks = 0, tol = 0.09146670818802263 Iteration 11: loglikelihood = -2283.564, backtracks = 0, tol = 0.08766753020895714 Iteration 12: loglikelihood = -2232.2913, backtracks = 0, tol = 0.08077913536322506 Iteration 13: loglikelihood = -2206.7568, backtracks = 0, tol = 0.08089257651590905 Iteration 14: loglikelihood = -2183.4045, backtracks = 0, tol = 0.08375013561264494 Iteration 15: loglikelihood = -2176.0356, backtracks = 0, tol = 0.08317720042419612 Iteration 16: loglikelihood = -2166.316, backtracks = 0, tol = 0.08523930844066344 Iteration 17: loglikelihood = -2166.1191, backtracks = 0, tol = 0.08457804889360206 Iteration 18: loglikelihood = -2162.2217, backtracks = 1, tol = 0.009521413880768704 Iteration 19: loglikelihood = -2160.0352, backtracks = 0, tol = 0.08582363657276276 Iteration 20: loglikelihood = -2159.2688, backtracks = 1, tol = 0.008741363403406017 Iteration 21: loglikelihood = -2159.0884, backtracks = 1, tol = 0.004347903608380808 Iteration 22: loglikelihood = -2159.0444, backtracks = 1, tol = 0.002140523816400965 Iteration 23: loglikelihood = -2159.0364, backtracks = 1, tol = 0.0010459294551647663 Iteration 24: loglikelihood = -2159.0322, backtracks = 1, tol = 0.0005086127981474036 Iteration 25: loglikelihood = -2159.0298, backtracks = 2, tol = 0.0001341294400712278 Iteration 26: loglikelihood = -2159.0261, backtracks = 2, tol = 0.00010689958580267703 Iteration 27: loglikelihood = -2159.0232, backtracks = 3, tol = 4.2072224805982836e-5 0.238570 seconds (1.60 M allocations: 26.581 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 22.7s **** 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 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 = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307224 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.2870682551290383 Iteration 3: loglikelihood = -1460.3823326395222, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.074435032946, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461055, backtracks = 0, tol = 8.427264473930937e-5 4.198534 seconds (956.62 k allocations: 129.033 MiB, 0.74% gc time, 92.22% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.6s 7.050863 seconds (4.01 M allocations: 82.752 MiB, 0.41% gc time, 1.09% compilation time) 4.061482 seconds (3.98 M allocations: 91.817 MiB, 0.94% gc time) 9.999186 seconds (20.65 M allocations: 454.910 MiB, 1.03% gc time, 17.83% compilation time: 56% of which was recompilation) 8.106892 seconds (20.19 M allocations: 434.834 MiB, 0.94% gc time) 29.420020 seconds (3.44 M allocations: 4.231 GiB, 7.80% gc time, 27.60% compilation time) 41.668275 seconds (82.96 k allocations: 183.862 MiB, 0.22% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 1m57.0s Test Summary: | Pass Total Time update_support! | 10 10 0.4s 14.990 ms (89 allocations: 5.20 KiB) 4.406 μs (0 allocations: 0 bytes) 95.809 μs (4 allocations: 288 bytes) 547.262 ns (0 allocations: 0 bytes) 33.570 μs (2 allocations: 64 bytes) 20.590 μs (0 allocations: 0 bytes) 4.010 μs (0 allocations: 0 bytes) 3.567 μs (0 allocations: 0 bytes) 73.449 μs (0 allocations: 0 bytes) 38.500 ms (89 allocations: 5.20 KiB) 18.110 μs (0 allocations: 0 bytes) 128.658 μs (4 allocations: 288 bytes) 2.726 μs (0 allocations: 0 bytes) 143.509 μs (2 allocations: 64 bytes) 41.610 μs (0 allocations: 0 bytes) 23.380 μs (0 allocations: 0 bytes) 23.330 μs (0 allocations: 0 bytes) 170.439 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 1m51.4s **** 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 **** **** 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 = -2900.918630019449, backtracks = 0, tol = 0.14802242082004138 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.03512679046077988 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.005569349616332472 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 = 0.00010393305949948345 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049858006e-5 0.427887 seconds (46.00 k allocations: 5.429 MiB, 63.63% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 10.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 1.514814 seconds (235.70 k allocations: 166.227 MiB, 59.78% compilation time) Test Summary: | Pass Total Time initialze beta | 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:02:51 Cross validating... 16%|█████▏ | ETA: 0:00:34 Cross validating... 25%|████████▏ | ETA: 0:00:20 Cross validating... 29%|█████████▏ | ETA: 0:00:18 Cross validating... 32%|██████████▏ | ETA: 0:00:16 Cross validating... 35%|███████████▏ | ETA: 0:00:14 Cross validating... 38%|████████████▎ | ETA: 0:00:12 Cross validating... 41%|█████████████▎ | ETA: 0:00:11 Cross validating... 44%|██████████████▎ | ETA: 0:00:10 Cross validating... 48%|███████████████▎ | ETA: 0:00:09 Cross validating... 51%|████████████████▎ | ETA: 0:00:08 Cross validating... 54%|█████████████████▎ | ETA: 0:00:07 Cross validating... 57%|██████████████████▎ | ETA: 0:00:06 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 63%|████████████████████▍ | ETA: 0:00:05 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:04 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 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: 0:00:10 Crossvalidation Results: k MSE 0 2869.4777971207263 1 1641.009660940345 2 856.9321835839582 3 713.612104919237 4 636.8627515580463 5 547.1084625004487 6 458.0041523621388 7 388.5740672345176 8 362.72231508318174 9 340.59233101886724 10 341.8800469219589 11 335.9371583448305 12 343.10853199445876 13 343.2773303217681 14 345.4189909848106 15 345.60824913522157 16 355.9287534028912 17 350.4088120471154 18 365.2532534718591 19 383.13655198221755 20 353.660108781962 Best k = 11 10.529436 seconds (11.41 M allocations: 306.218 MiB, 1.99% gc time, 56.88% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 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 2869.4777971207263 1 1645.580820708971 2 860.9556343844889 3 720.6121969355345 4 645.0587964332587 5 555.9047563115083 6 466.74089247605326 7 395.1149489438775 8 369.55569572402237 9 347.5961737775875 10 352.92917687338 11 347.8876875563378 12 360.18226092538214 13 361.9977023571514 14 370.31032497398684 15 372.9619636337042 16 393.4372545947716 17 387.31383219539566 18 404.7216674115438 19 396.3591828121348 20 393.5696459630534 Best k = 9 4.703107 seconds (10.65 M allocations: 223.841 MiB, 1.52% gc time, 1.52% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 15.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:04:54 Cross validating... 8%|██▌ | ETA: 0:01:53 Cross validating... 13%|████▏ | ETA: 0:01:08 Cross validating... 17%|█████▋ | ETA: 0:00:47 Cross validating... 21%|██████▋ | ETA: 0:00:39 Cross validating... 24%|███████▋ | ETA: 0:00:33 Cross validating... 27%|████████▋ | ETA: 0:00:28 Cross validating... 30%|█████████▋ | ETA: 0:00:24 Cross validating... 33%|██████████▋ | ETA: 0:00:21 Cross validating... 37%|███████████▋ | ETA: 0:00:19 Cross validating... 41%|█████████████▎ | ETA: 0:00:16 Cross validating... 46%|██████████████▊ | ETA: 0:00:13 Cross validating... 51%|████████████████▎ | ETA: 0:00:11 Cross validating... 56%|█████████████████▊ | ETA: 0:00:09 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... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 1733.1070307617188 1 1374.8867873535157 2 1066.2089713745117 3 732.359967163086 4 625.2496818237305 5 498.9552260131836 6 413.9643477478028 7 364.1910092163086 8 332.64009243774416 9 320.7796267089844 10 323.7079246520997 11 325.0887985229492 12 324.1950888366699 13 326.2127540588379 14 329.8769241333008 15 334.4002237243653 16 326.8977723388672 17 331.45938735961914 18 339.1127738342285 19 352.7330293273926 20 353.2296211853028 Best k = 9 14.111486 seconds (12.48 M allocations: 322.067 MiB, 1.12% gc time, 77.04% 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 **** Cross validating... 5%|█▌ | 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... 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ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1733.1070307617188 1 1374.8867467041018 2 1068.3828522338868 3 732.359967163086 4 627.2144082641602 5 501.38838800048836 6 415.02280969238285 7 367.9345037841797 8 337.542929473877 9 326.10684637451175 10 334.0809582824707 11 336.5655139465332 12 340.87970758056645 13 344.0641144104004 14 345.02674468994144 15 343.9175270996094 16 345.82567379760746 17 360.05011520385744 18 364.29927618408203 19 378.8954315490723 20 381.45844348144533 Best k = 9 3.413591 seconds (10.56 M allocations: 193.539 MiB, 3.01% gc time, 1.41% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 18.9s **** 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: 0:00:41 Cross validating... 6%|██ | ETA: 0:00:22 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 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: 0:00:02 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... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.150077192804 1 389.85841621689025 2 377.2548045672056 3 364.0515210827542 4 348.1261197742897 5 337.76002454219577 6 334.260250951778 7 334.5226075914149 8 338.01632587180694 9 339.73234288480353 10 341.7898322960524 11 343.66941541970016 12 346.89772304605805 13 369.40602860264244 14 353.4678322965606 15 354.65103098346833 16 379.8490445661424 17 389.84932339879185 18 364.75111982984146 19 394.76585413353473 20 378.056493026013 Best k = 6 7.350696 seconds (17.33 M allocations: 410.600 MiB, 1.57% gc time, 25.93% 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: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 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: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | 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: 0:00:02 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: 0:00:02 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 0 462.150077192804 1 390.05038292990076 2 378.27963387525597 3 365.0284489206634 4 349.72722189179785 5 348.0551588822873 6 337.69398332828456 7 343.2434162761019 8 355.0701222434022 9 371.98319128417955 10 365.95772518572903 11 367.68167410040695 12 394.45431281796454 13 390.96456942529164 14 412.8282194503242 15 416.14373978210693 16 427.09280207355357 17 453.6632549540283 18 436.22800598377626 19 440.9458558305686 20 471.75333568523774 Best k = 6 5.495205 seconds (17.86 M allocations: 374.093 MiB, 1.58% gc time, 1.38% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.2s **** 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: 0:00:21 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: 0:00:09 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | 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... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 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: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.8145670252276 1 432.65847598118955 2 413.08911100087175 3 391.75214505296356 4 363.1533649733675 5 340.02531155137245 6 328.2981058567575 7 312.6599330495018 8 310.8739079538893 9 312.7519929220908 10 326.67212908412796 11 327.6272586289683 12 324.0320775006951 13 340.5862316650354 14 321.16175619096913 15 315.39767604065895 16 323.13929108420723 17 345.6980490068934 18 353.4026967815332 19 370.559417396825 20 359.99712216994976 Best k = 8 7.746267 seconds (16.91 M allocations: 412.688 MiB, 1.42% gc time, 29.92% 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... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | 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... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 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... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.8145670252276 1 432.68286119371373 2 414.42324559254394 3 393.3462687232894 4 373.98842327119473 5 349.101546465213 6 331.77521325861 7 330.3572570962109 8 316.89184457695274 9 320.6940299646862 10 351.7633437064328 11 351.3307875714064 12 351.43230826592196 13 358.40378034090384 14 354.01608102809803 15 355.7121786525441 16 371.2488562063364 17 376.62032778463794 18 378.822109051593 19 415.7825474367446 20 414.41738950369415 Best k = 8 5.928666 seconds (18.06 M allocations: 375.261 MiB, 2.02% gc time, 0.88% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic 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: 0:00:42 Cross validating... 6%|██ | ETA: 0:00:23 Cross validating... 10%|███ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 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: 0:00:02 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 1097.6770294722119 1 544.5261733560035 2 465.63609190282455 3 464.0116628859708 4 463.95010689909884 5 450.9553030571225 6 440.1755457600848 7 447.76077969211747 8 444.95284947468576 9 456.24592300726545 10 449.9741129711134 11 462.3318296342543 12 454.3969387561876 13 453.1850791878355 14 450.32709420361584 15 450.99678308489024 16 450.08696390615387 17 452.41145030264954 18 456.65179454291183 19 459.56948921608193 20 465.23057025874 Best k = 6 7.238078 seconds (14.42 M allocations: 328.470 MiB, 1.17% gc time, 25.81% 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... 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: 0:00:03 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: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 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: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1097.6770294722119 1 528.881261895638 2 451.896762792467 3 466.56252308056344 4 463.9073762001533 5 473.5223710907315 6 467.8365226753324 7 518.8237367721405 8 513.3810371011326 9 511.0176538375444 10 501.45310466171395 11 511.2766168586035 12 508.54416342662535 13 507.9292522433509 14 503.8041197686068 15 504.0507216825323 16 509.406415715551 17 509.5269093338317 18 516.7804215032833 19 523.131477780727 20 529.4037216235986 Best k = 2 5.355798 seconds (13.69 M allocations: 271.452 MiB, 1.08% gc time, 0.50% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson 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: 0:00:44 Cross validating... 5%|█▌ | ETA: 0:00:47 Cross validating... 6%|██ | ETA: 0:00:38 Cross validating... 8%|██▌ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:22 Cross validating... 14%|████▋ | ETA: 0:00:20 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 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Time: 0:00:36 Crossvalidation Results: k MSE 0 446.1812531111277 1 285.98831110848295 2 255.46358270072193 3 253.89129785485792 4 249.2733863881606 5 246.63844618738472 6 247.723974020153 7 248.15093510697162 8 250.35469914708628 9 250.77406760450177 10 251.0531968931356 11 252.246262074019 12 255.60101641673606 13 257.012162464537 14 255.50705581065884 15 253.18552496847872 16 259.8109227162626 17 260.81842279513324 18 254.37539360973935 19 262.3399330781202 20 257.01390989150065 Best k = 5 37.001037 seconds (117.68 M allocations: 3.074 GiB, 3.36% gc time, 4.27% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 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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 0 446.1812531111277 1 287.4286537329057 2 258.5553372822104 3 257.1807996809672 4 253.0099319499014 5 256.5454443266587 6 257.5506023387559 7 261.86030628117794 8 262.96588165623956 9 267.9017679702381 10 270.3959518808162 11 274.38637789611045 12 281.18101510823556 13 286.03829346385913 14 290.2066530121847 15 287.68603065975196 16 302.911081356253 17 301.93923670122257 18 293.0260501577936 19 310.75796719031837 20 302.8803076681253 Best k = 4 11.540845 seconds (34.05 M allocations: 678.778 MiB, 1.49% gc time, 0.64% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 48.9s **** 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: 0:00:27 Cross validating... 10%|███ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 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: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | 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... 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 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 5.682672 seconds (17.23 M allocations: 344.125 MiB, 2.66% gc time, 37.59% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 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: 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86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 3.346095 seconds (16.27 M allocations: 288.806 MiB, 2.17% gc time, 1.31% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.3s **** 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... 2%|▋ | ETA: 0:01:07 Cross validating... 3%|█ | ETA: 0:00:50 Cross validating... 4%|█▎ | ETA: 0:00:42 Cross validating... 5%|█▋ | ETA: 0:00:36 Cross validating... 6%|█▉ | ETA: 0:00:33 Cross validating... 7%|██▎ | ETA: 0:00:30 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 9%|██▉ | ETA: 0:00:27 Cross validating... 10%|███▎ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:25 Cross validating... 12%|███▉ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:23 Cross validating... 14%|████▌ | ETA: 0:00:22 Cross validating... 15%|████▊ | ETA: 0:00:21 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▌ | ETA: 0:00:20 Cross validating... 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0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 4027.6240957235186 2 3487.036710253512 3 2721.429165584429 4 2221.9435153171717 5 1873.2681882128318 6 1847.0941661698573 7 1846.300344833734 8 1851.0378612026389 9 1836.6478379733162 10 1857.0437078974849 11 1878.7865980742952 12 1873.87656736246 13 1877.5426615117483 14 1898.178924382489 15 1875.9562997407181 16 1894.0292137310694 17 1906.6226394923779 18 1926.1265153961435 19 1889.4375371982592 20 1886.1132398357356 Best k = 9 19.268458 seconds (358.48 k allocations: 311.353 MiB, 0.43% gc time, 7.00% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.7s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m36.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | 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ETA: 0:00:02 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: 0:00:23 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 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | 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2222.025304867614 5 2075.167038458837 6 2067.794898972384 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.1311995023634 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross 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97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:22 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 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.1812932295775 17 2209.4669750564367 18 2221.2595493644303 19 2238.742594576326 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m22.4s 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:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/BjTS1/src/decompression.jl:199 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Core.TypeEgal{Float64}, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Core.TypeEgal{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2252 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.0s RNG of the outermost testset: Xoshiro(0x283517dc52057f65, 0xa108729e3746430d, 0x29c47ac5c4f14d9d, 0x40bd5681684a2d00, 0xa152331daa96079d) 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 956.46s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.14/Pkg/src/Operations.jl:3298 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1062.49s: package tests unexpectedly errored