Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1826 (44c835795b*) started at 2026-03-02T20:52:48.923 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.25s ################################################################################ # 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 v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+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 v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+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 5.98s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4402.5 ms ✓ BGEN 7073.6 ms ✓ 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`. 24694.1 ms ✓ MendelIHT 3 dependencies successfully precompiled in 39 seconds. 171 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 63.0s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_Wo1oVP/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.1 [2913bbd2] StatsBase v0.34.10 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v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ 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 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 21.1s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 11.0s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.7s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** 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 = -1788.699814419482, backtracks = 0, tol = 2.1369580898599763 Iteration 2: loglikelihood = -1484.6883309504155, backtracks = 0, tol = 0.13820904826766553 Iteration 3: loglikelihood = -1411.6021838563402, backtracks = 0, tol = 0.05757362479187517 Iteration 4: loglikelihood = -1406.920643552068, backtracks = 0, tol = 0.04117216151590819 Iteration 5: loglikelihood = -1406.867667496718, backtracks = 0, tol = 0.0320386094806884 Iteration 6: loglikelihood = -1406.429672153941, backtracks = 0, tol = 0.031687072055475635 Iteration 7: loglikelihood = -1406.2484563566536, backtracks = 0, tol = 0.00419289863178571 Iteration 8: loglikelihood = -1406.2462385333342, backtracks = 1, tol = 0.0002194885042923091 Iteration 9: loglikelihood = -1406.2456426207136, backtracks = 1, tol = 0.00011173590794203098 Iteration 10: loglikelihood = -1406.2454850477309, backtracks = 1, tol = 5.65134123812055e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.17548894882202148 Final loglikelihood: -1406.2454850477309 SNP PVE: 0.9526769684915112 Iterations: 10 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 16 -0.398515 2 │ 905 0.122477 3 │ 1410 -2.40989 4 │ 3002 -0.129265 5 │ 3501 -1.43681 6 │ 4249 -0.115854 7 │ 6745 -0.108718 8 │ 7403 -0.391023 9 │ 8369 2.48836 10 │ 9150 1.85939 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0301443Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 26.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 3.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -9119.683098663812, backtracks = 0, tol = 0.4584130252780955 Iteration 2: loglikelihood = -5193.340952475234, backtracks = 0, tol = 0.04300916021118127 Iteration 3: loglikelihood = -2807.373276373555, backtracks = 0, tol = 0.051384294910218585 Iteration 4: loglikelihood = -1732.1942023779231, backtracks = 0, tol = 0.07155981788448122 Iteration 5: loglikelihood = -1530.2056367085995, backtracks = 0, tol = 0.045451191091742026 Iteration 6: loglikelihood = -1469.8052199928125, backtracks = 0, tol = 0.06994358740960102 Iteration 7: loglikelihood = -1429.6089639075294, backtracks = 0, tol = 0.050921025560558865 Iteration 8: loglikelihood = -1407.8659321070259, backtracks = 0, tol = 0.03761135052240885 Iteration 9: loglikelihood = -1381.7187534550942, backtracks = 0, tol = 0.032692238463594196 Iteration 10: loglikelihood = -1367.7484450180139, backtracks = 0, tol = 0.024913363450616812 Iteration 11: loglikelihood = -1358.4223746005925, backtracks = 0, tol = 0.03663187397453361 Iteration 12: loglikelihood = -1349.443548830818, backtracks = 0, tol = 0.016315304594002225 Iteration 13: loglikelihood = -1342.288255470184, backtracks = 1, tol = 0.037016788026299006 Iteration 14: loglikelihood = -1339.040034520661, backtracks = 0, tol = 0.014968127697218734 Iteration 15: loglikelihood = -1336.6828100469984, backtracks = 0, tol = 0.011103690165224207 Iteration 16: loglikelihood = -1334.7722015768418, backtracks = 0, tol = 0.010677806965604017 Iteration 17: loglikelihood = -1333.125561632886, backtracks = 0, tol = 0.010861996399438276 Iteration 18: loglikelihood = -1331.7485489825117, backtracks = 0, tol = 0.008172823837329354 Iteration 19: loglikelihood = -1330.535438778848, backtracks = 0, tol = 0.010632493622715546 Iteration 20: loglikelihood = -1329.505613435454, backtracks = 0, tol = 0.006464583170691087 Iteration 21: loglikelihood = -1328.5842992603532, backtracks = 0, tol = 0.010400378668012128 Iteration 22: loglikelihood = -1327.7957877380402, backtracks = 0, tol = 0.0052330509416927485 Iteration 23: loglikelihood = -1325.5152294629868, backtracks = 0, tol = 0.03064907492259876 Iteration 24: loglikelihood = -1324.288854107685, backtracks = 0, tol = 0.006541779805695563 Iteration 25: loglikelihood = -1323.5671184660418, backtracks = 0, tol = 0.0049293821963794626 Iteration 26: loglikelihood = -1323.031342502375, backtracks = 0, tol = 0.005751176179178382 Iteration 27: loglikelihood = -1322.5958881598926, backtracks = 0, tol = 0.004204766216308625 Iteration 28: loglikelihood = -1322.2322946522356, backtracks = 0, tol = 0.004815369583134148 Iteration 29: loglikelihood = -1321.9161401512124, backtracks = 0, tol = 0.003884425765418035 Iteration 30: loglikelihood = -1321.6422606942356, backtracks = 0, tol = 0.004020503592024197 Iteration 31: loglikelihood = -1321.398956386964, backtracks = 0, tol = 0.0035899901761550185 Iteration 32: loglikelihood = -1321.1846764217362, backtracks = 0, tol = 0.0033876561033316316 Iteration 33: loglikelihood = -1320.9923765248357, backtracks = 0, tol = 0.003326240193056716 Iteration 34: loglikelihood = -1320.82132920665, backtracks = 0, tol = 0.0028922983548080637 Iteration 35: loglikelihood = -1320.666842197913, backtracks = 0, tol = 0.0030863847778380446 Iteration 36: loglikelihood = -1320.5284745511015, backtracks = 0, tol = 0.002498839672947394 Iteration 37: loglikelihood = -1320.4029253206081, backtracks = 0, tol = 0.0028663132297052072 Iteration 38: loglikelihood = -1320.2898917400573, backtracks = 0, tol = 0.0021809233795662152 Iteration 39: loglikelihood = -1320.1869673306685, backtracks = 0, tol = 0.0026632993502345996 Iteration 40: loglikelihood = -1320.0939292792198, backtracks = 0, tol = 0.0019197121632085474 Iteration 41: loglikelihood = -1320.0089770550858, backtracks = 0, tol = 0.0024753807070940844 Iteration 42: loglikelihood = -1319.9319386665952, backtracks = 0, tol = 0.0017017748470315821 Iteration 43: loglikelihood = -1319.8614399008798, backtracks = 0, tol = 0.002301044449406677 Iteration 44: loglikelihood = -1319.7973429395431, backtracks = 0, tol = 0.0015174480310511916 Iteration 45: loglikelihood = -1319.73858245737, backtracks = 0, tol = 0.0021390620774242746 Iteration 46: loglikelihood = -1319.6850446080684, backtracks = 0, tol = 0.001359684001607901 Iteration 47: loglikelihood = -1319.6358932140806, backtracks = 0, tol = 0.0019883983766231144 Iteration 48: loglikelihood = -1319.5910318954468, backtracks = 0, tol = 0.0012232627018157935 Iteration 49: loglikelihood = -1319.5497977598725, backtracks = 0, tol = 0.0018481583190691187 Iteration 50: loglikelihood = -1319.5121076321848, backtracks = 0, tol = 0.0011042551770346688 Iteration 51: loglikelihood = -1319.4774317325835, backtracks = 0, tol = 0.0017175540796577973 Iteration 52: loglikelihood = -1319.4456972383005, backtracks = 0, tol = 0.0009996564542807528 Iteration 53: loglikelihood = -1319.416477946151, backtracks = 0, tol = 0.0015958831705977369 Iteration 54: loglikelihood = -1319.3897094356203, backtracks = 0, tol = 0.0009071320333144464 Iteration 55: loglikelihood = -1319.365046955034, backtracks = 0, tol = 0.001482513045687827 Iteration 56: loglikelihood = -1319.3424331199415, backtracks = 0, tol = 0.000824840857731666 Iteration 57: loglikelihood = -1319.3215877930043, backtracks = 0, tol = 0.0013768696999283694 Iteration 58: loglikelihood = -1319.3024596397065, backtracks = 0, tol = 0.000751310185945153 Iteration 59: loglikelihood = -1319.284820152741, backtracks = 0, tol = 0.0012784288976738153 Iteration 60: loglikelihood = -1319.2686233093393, backtracks = 0, tol = 0.0006853460373006647 Iteration 61: loglikelihood = -1319.2536821067831, backtracks = 0, tol = 0.0011867092384117502 Iteration 62: loglikelihood = -1319.2399552579363, backtracks = 0, tol = 0.0006259682923350152 Iteration 63: loglikelihood = -1319.2272892942992, backtracks = 0, tol = 0.0011012665757519611 Iteration 64: loglikelihood = -1319.215647194691, backtracks = 0, tol = 0.0005723630733111312 Iteration 65: loglikelihood = -1319.2049027012276, backtracks = 0, tol = 0.0010216894731771362 Iteration 66: loglikelihood = -1319.1950226597805, backtracks = 0, tol = 0.0005238473751547296 Iteration 67: loglikelihood = -1319.1859029726556, backtracks = 0, tol = 0.0009475954758616346 Iteration 68: loglikelihood = -1319.1775140021248, backtracks = 0, tol = 0.00047984247933968493 Iteration 69: loglikelihood = -1319.1697697544248, backtracks = 0, tol = 0.0008786280353497921 Iteration 70: loglikelihood = -1319.1626437919358, backtracks = 0, tol = 0.0004398537348294073 Iteration 71: loglikelihood = -1319.1560649515002, backtracks = 0, tol = 0.0008144539607514128 Iteration 72: loglikelihood = -1319.1500097053702, backtracks = 0, tol = 0.0004034550050662529 Iteration 73: loglikelihood = -1319.144419068765, backtracks = 0, tol = 0.000754761295510481 Iteration 74: loglikelihood = -1319.1392721547463, backtracks = 0, tol = 0.0003702765709538287 Iteration 75: loglikelihood = -1319.134520000436, backtracks = 0, tol = 0.0006992575376258398 Iteration 76: loglikelihood = -1319.1301441092119, backtracks = 0, tol = 0.0003399956203269863 Iteration 77: loglikelihood = -1319.126103781369, backtracks = 0, tol = 0.0006476681359395963 Iteration 78: loglikelihood = -1319.122382677242, backtracks = 0, tol = 0.00031238237232347526 Iteration 79: loglikelihood = -1317.1344269008864, backtracks = 0, tol = 0.026145189753701545 Iteration 80: loglikelihood = -1315.8738781149925, backtracks = 0, tol = 0.009791387851030795 Iteration 81: loglikelihood = -1315.3210174590813, backtracks = 0, tol = 0.0035436115990973346 Iteration 82: loglikelihood = -1315.0602502726508, backtracks = 0, tol = 0.004436995596538005 Iteration 83: loglikelihood = -1314.9414261907957, backtracks = 0, tol = 0.0016326434131710827 Iteration 84: loglikelihood = -1314.8830549751658, backtracks = 0, tol = 0.0018791330428818346 Iteration 85: loglikelihood = -1314.8541535660986, backtracks = 0, tol = 0.0007961910327400486 Iteration 86: loglikelihood = -1314.8380300052097, backtracks = 0, tol = 0.0008228415456756722 Iteration 87: loglikelihood = -1314.8286640427893, backtracks = 0, tol = 0.0005317383078168322 Iteration 88: loglikelihood = -1314.8223764388906, backtracks = 0, tol = 0.0005079976623971855 Iteration 89: loglikelihood = -1314.8179759986747, backtracks = 0, tol = 0.0003996929693553023 Iteration 90: loglikelihood = -1314.814544894362, backtracks = 0, tol = 0.00045503559160356275 Iteration 91: loglikelihood = -1314.8118073353244, backtracks = 0, tol = 0.0003158501443098158 Iteration 92: loglikelihood = -1314.8094929884362, backtracks = 0, tol = 0.000450226040919732 Iteration 93: loglikelihood = -1314.8075171126868, backtracks = 0, tol = 0.0002578695219639544 Iteration 94: loglikelihood = -1314.8057797323445, backtracks = 0, tol = 0.00043599492464823145 Iteration 95: loglikelihood = -1314.8042467637222, backtracks = 0, tol = 0.00021623026105661907 Iteration 96: loglikelihood = -1314.8028727874694, backtracks = 0, tol = 0.00041465718248788 Iteration 97: loglikelihood = -1314.8016407859682, backtracks = 0, tol = 0.0001853732222300516 Iteration 98: loglikelihood = -1314.8005263869657, backtracks = 0, tol = 0.00038915395030043106 Iteration 99: loglikelihood = -1314.7995193537593, backtracks = 0, tol = 0.00016440148012754775 Iteration 100: loglikelihood = -1314.798604570692, backtracks = 0, tol = 0.0003618472865290499 Iteration 101: loglikelihood = -1314.7977748939745, backtracks = 0, tol = 0.00015012155569726787 Iteration 102: loglikelihood = -1314.797019807437, backtracks = 0, tol = 0.000334330007335568 Iteration 103: loglikelihood = -1314.7963338173886, backtracks = 0, tol = 0.00013705001024688456 Iteration 104: loglikelihood = -1314.79570902677, backtracks = 0, tol = 0.0003075723782443322 Iteration 105: loglikelihood = -1314.7951409822833, backtracks = 0, tol = 0.00012503957359550862 Iteration 106: loglikelihood = -1314.7946234882097, backtracks = 0, tol = 0.0002821176247257839 Iteration 107: loglikelihood = -1314.7941528436932, backtracks = 0, tol = 0.0001140086982166592 Iteration 108: loglikelihood = -1314.793724075156, backtracks = 0, tol = 0.00025823703738574546 Iteration 109: loglikelihood = -1314.7933340750064, backtracks = 0, tol = 0.00010389415003363477 Iteration 110: loglikelihood = -1314.7929788046054, backtracks = 0, tol = 0.0002360355409575619 Iteration 111: loglikelihood = -1314.7926556453692, backtracks = 0, tol = 9.463597940546789e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.9s **** 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 = -1715.7883049991692, backtracks = 0, tol = 0.4617536548697438 Iteration 2: loglikelihood = -1588.4734543132372, backtracks = 0, tol = 0.16869430922726555 Iteration 3: loglikelihood = -1534.079302334462, backtracks = 0, tol = 0.11368315848599458 Iteration 4: loglikelihood = -1508.2566048209726, backtracks = 0, tol = 0.08859550208458318 Iteration 5: loglikelihood = -1503.5892466165296, backtracks = 0, tol = 0.06729194782601113 Iteration 6: loglikelihood = -1500.078191109732, backtracks = 0, tol = 0.06134879118715219 Iteration 7: loglikelihood = -1499.3733903643038, backtracks = 1, tol = 0.015887820120024775 Iteration 8: loglikelihood = -1499.031941129264, backtracks = 2, tol = 0.011404753509831072 Iteration 9: loglikelihood = -1498.8098007350893, backtracks = 2, tol = 0.009992629879835362 Iteration 10: loglikelihood = -1498.6766248411066, backtracks = 2, tol = 0.007949406078162032 Iteration 11: loglikelihood = -1498.5991264969955, backtracks = 2, tol = 0.006184501244136962 Iteration 12: loglikelihood = -1498.554728355779, backtracks = 2, tol = 0.004747064546318416 Iteration 13: loglikelihood = -1498.529626974534, backtracks = 2, tol = 0.003607157214645541 Iteration 14: loglikelihood = -1498.5155660124556, backtracks = 2, tol = 0.0027205240680724845 Iteration 15: loglikelihood = -1498.507747946415, backtracks = 2, tol = 0.002040081314497977 Iteration 16: loglikelihood = -1498.5034243251314, backtracks = 2, tol = 0.0015233862700914204 Iteration 17: loglikelihood = -1498.5010431808548, backtracks = 2, tol = 0.0011339483996317494 Iteration 18: loglikelihood = -1498.500340444781, backtracks = 3, tol = 0.00042105196864835665 Iteration 19: loglikelihood = -1498.4998083994844, backtracks = 3, tol = 0.00036664767446560837 Iteration 20: loglikelihood = -1498.4994057347867, backtracks = 3, tol = 0.0003191823092664585 Iteration 21: loglikelihood = -1498.4991010874394, backtracks = 3, tol = 0.0002777926484675091 Iteration 22: loglikelihood = -1498.4988706632303, backtracks = 3, tol = 0.00024171765249261706 Iteration 23: loglikelihood = -1498.498696421798, backtracks = 3, tol = 0.00021028759883936612 Iteration 24: loglikelihood = -1498.4985646928706, backtracks = 3, tol = 0.00018291408689962823 Iteration 25: loglikelihood = -1498.498465122676, backtracks = 3, tol = 0.0001590809065300228 Iteration 26: loglikelihood = -1498.498389872664, backtracks = 3, tol = 0.00013833575105531528 Iteration 27: loglikelihood = -1498.4983330106795, backtracks = 3, tol = 0.00012028274173419362 Iteration 28: loglikelihood = -1498.4982900487616, backtracks = 3, tol = 0.00010457571956197157 Iteration 29: loglikelihood = -1498.4982575925044, backtracks = 3, tol = 9.091225281465921e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1918.764850524114, backtracks = 0, tol = 0.7190916940946745 Iteration 2: loglikelihood = -1520.0718495602498, backtracks = 0, tol = 0.12509992467148262 Iteration 3: loglikelihood = -1409.8049453171047, backtracks = 0, tol = 0.05626507299556426 Iteration 4: loglikelihood = -1394.583835741781, backtracks = 0, tol = 0.029596157366431154 Iteration 5: loglikelihood = -1392.6410696607215, backtracks = 0, tol = 0.029043080684212737 Iteration 6: loglikelihood = -1392.5149526331506, backtracks = 0, tol = 0.0019062782334546568 Iteration 7: loglikelihood = -1392.5126066694272, backtracks = 0, tol = 0.0003382975139184533 Iteration 8: loglikelihood = -1392.5125318979537, backtracks = 0, tol = 4.528103743026697e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 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 = -1650.1259596248426, backtracks = 0, tol = 0.4865207135045329 Iteration 2: loglikelihood = -1427.5090161393146, backtracks = 0, tol = 0.09456142096671881 Iteration 3: loglikelihood = -1396.4534371777513, backtracks = 0, tol = 0.04268995900318452 Iteration 4: loglikelihood = -1394.2152804789232, backtracks = 0, tol = 0.03132075673428916 Iteration 5: loglikelihood = -1393.9923221173083, backtracks = 0, tol = 0.003144021542869633 Iteration 6: loglikelihood = -1393.9889200042187, backtracks = 0, tol = 0.0004274216253577073 Iteration 7: loglikelihood = -1393.988851743118, backtracks = 0, tol = 5.5566883659528806e-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 = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 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 = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 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 = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, 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 = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 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 = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, 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 = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 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 13.0s **** 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 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 = -1531.2205574569014, backtracks = 0, tol = 0.20005042177759746 Iteration 2: loglikelihood = -1456.1681646674592, backtracks = 0, tol = 0.09980492524111531 Iteration 3: loglikelihood = -1427.6057872785152, backtracks = 0, tol = 0.0632446224934991 Iteration 4: loglikelihood = -1407.0245942797794, backtracks = 0, tol = 0.05156986911709888 Iteration 5: loglikelihood = -1375.06965406924, backtracks = 0, tol = 0.07518937851394347 Iteration 6: loglikelihood = -1365.2957658722585, backtracks = 1, tol = 0.03452349001921743 Iteration 7: loglikelihood = -1360.7439349343015, backtracks = 1, tol = 0.03154036152041619 Iteration 8: loglikelihood = -1359.7143863538995, backtracks = 2, tol = 0.00993367143080781 Iteration 9: loglikelihood = -1359.0114795278766, backtracks = 2, tol = 0.010188771951511123 Iteration 10: loglikelihood = -1358.5949349552366, backtracks = 2, tol = 0.007639136875319076 Iteration 11: loglikelihood = -1358.3520838132445, backtracks = 2, tol = 0.006016998205321284 Iteration 12: loglikelihood = -1358.2117021096412, backtracks = 2, tol = 0.004523631016437438 Iteration 13: loglikelihood = -1358.1306633859995, backtracks = 2, tol = 0.003472992324486173 Iteration 14: loglikelihood = -1358.0839177799958, backtracks = 2, tol = 0.0026176616630725095 Iteration 15: loglikelihood = -1358.0568774612518, backtracks = 2, tol = 0.0019938974974436914 Iteration 16: loglikelihood = -1358.0411822455894, backtracks = 2, tol = 0.0015044988716211758 Iteration 17: loglikelihood = -1358.0320142003006, backtracks = 2, tol = 0.0011420941548279686 Iteration 18: loglikelihood = -1358.0266190372845, backtracks = 2, tol = 0.0008609349063224844 Iteration 19: loglikelihood = -1358.023411939656, backtracks = 2, tol = 0.0006507675469892711 Iteration 20: loglikelihood = -1358.0214849557508, backtracks = 2, tol = 0.00048696900770089485 Iteration 21: loglikelihood = -1358.0203133243845, backtracks = 2, tol = 0.00036324431386995176 Iteration 22: loglikelihood = -1358.0195945555004, backtracks = 2, tol = 0.0002822132876530923 Iteration 23: loglikelihood = -1358.019151291975, backtracks = 2, tol = 0.00024594804074906207 Iteration 24: loglikelihood = -1358.0190057495647, backtracks = 3, tol = 0.00010613796687263297 Iteration 25: loglikelihood = -1358.0188906827946, backtracks = 3, tol = 9.687388634208896e-5 2.154173 seconds (13.67 M allocations: 223.024 MiB, 3.00% gc time, 31.31% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1572.9575314428894, backtracks = 0, tol = 0.20005042177759746 Iteration 2: loglikelihood = -1524.7978158538706, backtracks = 0, tol = 0.1209788796476684 Iteration 3: loglikelihood = -1501.2185386023177, backtracks = 0, tol = 0.06884351960824636 Iteration 4: loglikelihood = -1480.1534000262957, backtracks = 0, tol = 0.08709936745953052 Iteration 5: loglikelihood = -1460.4714473166966, backtracks = 1, tol = 0.06165632384746538 Iteration 6: loglikelihood = -1446.2793477658104, backtracks = 0, tol = 0.059647211996027225 Iteration 7: loglikelihood = -1429.7978438379175, backtracks = 1, tol = 0.03323751513059482 Iteration 8: loglikelihood = -1426.1502050439738, backtracks = 0, tol = 0.10869835864592099 Iteration 9: loglikelihood = -1409.020561158213, backtracks = 0, tol = 0.10472891738598558 Iteration 10: loglikelihood = -1401.4168104543776, backtracks = 0, tol = 0.06612529894200637 Iteration 11: loglikelihood = -1397.8278128183376, backtracks = 0, tol = 0.06794444533072985 Iteration 12: loglikelihood = -1393.0291723015291, backtracks = 0, tol = 0.06777225376442086 Iteration 13: loglikelihood = -1389.6149729391032, backtracks = 0, tol = 0.008813515652181109 Iteration 14: loglikelihood = -1386.6535652235307, backtracks = 0, tol = 0.0016251452227803288 Iteration 15: loglikelihood = -1384.1085451704005, backtracks = 0, tol = 0.0006181031941397562 Iteration 16: loglikelihood = -1381.8448672347952, backtracks = 0, tol = 0.00044640479851919794 Iteration 17: loglikelihood = -1379.8543799038503, backtracks = 0, tol = 0.00032940586151353223 Iteration 18: loglikelihood = -1378.075284602791, backtracks = 0, tol = 0.00025779945543655676 Iteration 19: loglikelihood = -1376.4910500476938, backtracks = 0, tol = 0.0002385935590910733 Iteration 20: loglikelihood = -1375.0648462746835, backtracks = 0, tol = 0.00022664654904727786 Iteration 21: loglikelihood = -1373.782600131987, backtracks = 0, tol = 0.00021093653279503222 Iteration 22: loglikelihood = -1372.6200370423383, backtracks = 0, tol = 0.0002004925577742646 Iteration 23: loglikelihood = -1372.5184906332593, backtracks = 0, tol = 0.06334672700063192 Iteration 24: loglikelihood = -1370.6073949704883, backtracks = 0, tol = 0.0633380739199597 Iteration 25: loglikelihood = -1369.728510564341, backtracks = 0, tol = 0.005047449643362617 Iteration 26: loglikelihood = -1368.9122719455233, backtracks = 0, tol = 0.0011882835940768112 Iteration 27: loglikelihood = -1368.1842466386522, backtracks = 0, tol = 0.0004722560145020542 Iteration 28: loglikelihood = -1367.503399613595, backtracks = 0, tol = 0.00021003743068304735 Iteration 29: loglikelihood = -1366.8783427347907, backtracks = 0, tol = 0.00017066032888696207 Iteration 30: loglikelihood = -1366.2965399333507, backtracks = 0, tol = 0.00012873384423252838 Iteration 31: loglikelihood = -1365.288483667704, backtracks = 1, tol = 6.761118584980888e-5 0.297217 seconds (1.20 M allocations: 21.967 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 = -3721.4731, backtracks = 0, tol = 0.08194172459667906 Iteration 2: loglikelihood = -3686.4321, backtracks = 0, tol = 0.0648708945215475 Iteration 3: loglikelihood = -3667.598, backtracks = 0, tol = 0.07858561605817761 Iteration 4: loglikelihood = -3661.9893, backtracks = 1, tol = 0.010247263093006326 Iteration 5: loglikelihood = -3660.0532, backtracks = 1, tol = 0.006765910531504672 Iteration 6: loglikelihood = -3659.4531, backtracks = 1, tol = 0.004405289696177433 Iteration 7: loglikelihood = -3659.2922, backtracks = 1, tol = 0.002412882187554634 Iteration 8: loglikelihood = -3659.2463, backtracks = 1, tol = 0.001258672702078077 Iteration 9: loglikelihood = -3659.2368, backtracks = 1, tol = 0.0006446791474518322 Iteration 10: loglikelihood = -3659.239, backtracks = 3, tol = 8.181586024578867e-5 27.413627 seconds (14.25 M allocations: 656.134 MiB, 4.03% gc time, 95.30% 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 = -3629.3635, backtracks = 0, tol = 0.08194172459667906 Iteration 2: loglikelihood = -3529.511, backtracks = 0, tol = 0.0648708945215475 Iteration 3: loglikelihood = -3431.9578, backtracks = 0, tol = 0.08046937826216123 Iteration 4: loglikelihood = -3348.3645, backtracks = 0, tol = 0.08058709132897234 Iteration 5: loglikelihood = -3244.2534, backtracks = 0, tol = 0.07941311638397633 Iteration 6: loglikelihood = -3139.8376, backtracks = 0, tol = 0.07634109178866649 Iteration 7: loglikelihood = -3021.1257, backtracks = 0, tol = 0.07577315645979829 Iteration 8: loglikelihood = -2902.4795, backtracks = 0, tol = 0.009786539242549479 Iteration 9: loglikelihood = -2782.7449, backtracks = 0, tol = 0.0027948800881373655 Iteration 10: loglikelihood = -2667.6401, backtracks = 0, tol = 0.08154922178476746 Iteration 11: loglikelihood = -2553.5095, backtracks = 0, tol = 0.0923915185787646 Iteration 12: loglikelihood = -2454.5176, backtracks = 0, tol = 0.09223516017134796 Iteration 13: loglikelihood = -2374.742, backtracks = 0, tol = 0.09251534748751437 Iteration 14: loglikelihood = -2309.9531, backtracks = 0, tol = 0.09217164312045024 Iteration 15: loglikelihood = -2268.628, backtracks = 0, tol = 0.08853944921066607 Iteration 16: loglikelihood = -2236.811, backtracks = 0, tol = 0.08852816089432602 Iteration 17: loglikelihood = -2221.2673, backtracks = 0, tol = 0.08735519490559927 Iteration 18: loglikelihood = -2208.3254, backtracks = 0, tol = 0.08845324975923409 Iteration 19: loglikelihood = -2204.6472, backtracks = 0, tol = 0.08828250688885274 Iteration 20: loglikelihood = -2204.0623, backtracks = 0, tol = 0.10138828091463745 Iteration 21: loglikelihood = -2200.1472, backtracks = 1, tol = 0.011509970222662149 Iteration 22: loglikelihood = -2199.287, backtracks = 1, tol = 0.004707253254420524 Iteration 23: loglikelihood = -2199.0913, backtracks = 1, tol = 0.0024414669505258336 Iteration 24: loglikelihood = -2199.0496, backtracks = 1, tol = 0.0013506352456101609 Iteration 25: loglikelihood = -2199.0405, backtracks = 1, tol = 0.0007474407240727654 Iteration 26: loglikelihood = -2199.0403, backtracks = 2, tol = 0.00020577352387983618 Iteration 27: loglikelihood = -2199.0403, backtracks = 1, tol = 0.0003185716519928053 Iteration 28: loglikelihood = -2199.0396, backtracks = 1, tol = 0.00017545912043526112 Iteration 29: loglikelihood = -2199.0396, backtracks = 1, tol = 9.694495855724916e-5 0.253189 seconds (1.58 M allocations: 26.190 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 33.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, 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 = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.252359 seconds (1.18 M allocations: 138.738 MiB, 1.55% gc time, 91.59% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.7s 9.155851 seconds (4.00 M allocations: 82.516 MiB, 0.26% gc time, 0.76% compilation time) 5.231302 seconds (3.98 M allocations: 91.703 MiB, 1.23% gc time) 10.674657 seconds (20.41 M allocations: 439.515 MiB, 0.97% gc time, 21.41% compilation time: 80% of which was recompilation) 8.038450 seconds (20.18 M allocations: 434.188 MiB, 0.85% gc time) 59.392411 seconds (3.77 M allocations: 4.240 GiB, 8.04% gc time, 22.09% compilation time) 50.961750 seconds (71.97 k allocations: 183.460 MiB, 0.17% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m44.5s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 14.775 ms (78 allocations: 4.56 KiB) 4.992 μs (0 allocations: 0 bytes) 152.599 μs (4 allocations: 288 bytes) 6.607 μs (0 allocations: 0 bytes) 53.100 μs (2 allocations: 64 bytes) 39.510 μs (0 allocations: 0 bytes) 24.790 μs (0 allocations: 0 bytes) 33.620 μs (0 allocations: 0 bytes) 86.939 μs (0 allocations: 0 bytes) 38.316 ms (78 allocations: 4.56 KiB) 26.310 μs (0 allocations: 0 bytes) 171.828 μs (4 allocations: 288 bytes) 32.580 μs (0 allocations: 0 bytes) 255.848 μs (2 allocations: 64 bytes) 93.439 μs (0 allocations: 0 bytes) 123.889 μs (0 allocations: 0 bytes) 166.338 μs (0 allocations: 0 bytes) 213.538 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m39.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.440063 seconds (49.10 k allocations: 5.482 MiB, 63.84% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.183098 seconds (312.50 k allocations: 169.939 MiB, 62.75% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:59 Cross validating... 19%|██████▏ | ETA: 0:00:37 Cross validating... 22%|███████▏ | ETA: 0:00:31 Cross validating... 25%|████████▏ | ETA: 0:00:27 Cross validating... 29%|█████████▏ | ETA: 0:00:23 Cross validating... 32%|██████████▏ | ETA: 0:00:20 Cross validating... 35%|███████████▏ | ETA: 0:00:18 Cross validating... 38%|████████████▎ | ETA: 0:00:16 Cross validating... 41%|█████████████▎ | ETA: 0:00:14 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 6888.601687613576 1 4747.664399301084 2 2199.9814508839927 3 1144.1076174168638 4 447.09108848656194 5 399.23357107584116 6 345.64603424380175 7 348.57063298286823 8 352.17368628974185 9 352.5828131851494 10 356.42798885797936 11 359.2782736758017 12 372.7504174401581 13 364.0057133772917 14 367.81541729893917 15 380.0074343034442 16 377.3860407059672 17 418.4264555862517 18 367.77565575864014 19 387.3605362627218 20 403.7723166684092 Best k = 6 12.732483 seconds (12.03 M allocations: 311.580 MiB, 1.08% gc time, 63.15% 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... 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... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 6888.601687613576 1 4751.4995436560375 2 2205.7561440670556 3 1163.3647406946768 4 451.41340654195324 5 403.2409244741324 6 350.1800752702766 7 358.1649181678766 8 366.8524907204535 9 374.018098356295 10 377.09519972218 11 386.71515869430567 12 388.79698921358204 13 392.9558407705689 14 405.7844558550604 15 401.5637573601264 16 412.54231033291626 17 425.5854240582123 18 412.92883382483257 19 425.17216565147214 20 437.86314972681953 Best k = 6 4.859642 seconds (11.24 M allocations: 236.930 MiB, 1.35% gc time, 1.07% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:07:23 Cross validating... 6%|██ | ETA: 0:03:36 Cross validating... 10%|███ | ETA: 0:02:20 Cross validating... 14%|████▋ | ETA: 0:01:30 Cross validating... 19%|██████▏ | ETA: 0:01:04 Cross validating... 22%|███████▏ | ETA: 0:00:53 Cross validating... 25%|████████▏ | ETA: 0:00:45 Cross validating... 29%|█████████▏ | ETA: 0:00:39 Cross validating... 32%|██████████▏ | ETA: 0:00:34 Cross validating... 35%|███████████▏ | ETA: 0:00:29 Cross validating... 40%|████████████▊ | ETA: 0:00:24 Cross validating... 44%|██████████████▎ | ETA: 0:00:20 Cross validating... 49%|███████████████▊ | ETA: 0:00:17 Cross validating... 54%|█████████████████▎ | ETA: 0:00:14 Cross validating... 57%|██████████████████▎ | ETA: 0:00:12 Cross validating... 60%|███████████████████▎ | ETA: 0:00:11 Cross validating... 63%|████████████████████▍ | ETA: 0:00:10 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:06 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 0 1594.8066723632812 1 1270.3010512695312 2 1020.994346069336 3 804.7944259033203 4 638.3147141723632 5 520.9517094421386 6 424.5737991027832 7 364.033272491455 8 347.7649632568359 9 324.5097322998047 10 321.5444577331543 11 325.4113318786621 12 328.98538552856445 13 322.59369326782223 14 334.68567019653324 15 322.87875512695314 16 324.09429049682615 17 328.267522064209 18 352.4676266479492 19 348.4190896911621 20 342.77852770996094 Best k = 10 19.352187 seconds (12.82 M allocations: 316.456 MiB, 0.70% gc time, 80.75% 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... 10%|███ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1594.8066723632812 1 1281.947327758789 2 1025.5915498657228 3 804.7944259033203 4 643.4803618774414 5 520.9591850280761 6 430.1927010803223 7 367.56010620117183 8 354.1279506530762 9 330.8062821960449 10 329.48814062499997 11 338.3821114196777 12 343.9044285888672 13 343.8556536254883 14 343.3863701171875 15 349.38391525268554 16 358.8721128234863 17 364.7135299377441 18 390.685278503418 19 382.4555886230469 20 399.21643847656253 Best k = 10 3.572879 seconds (10.90 M allocations: 200.381 MiB, 1.30% gc time, 1.21% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 25.2s **** 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: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ 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validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.72611464367117 1 386.8283510960438 2 331.4887395914949 3 291.38027194053325 4 234.45657459952167 5 222.35458909006633 6 227.39112440135816 7 233.91534786372188 8 237.01157889892716 9 238.79093157934935 10 242.53829490465463 11 253.64293450667847 12 240.04190167614286 13 250.6946038688326 14 246.88121780089736 15 247.6078338263829 16 264.97174494010073 17 286.9776362459155 18 262.15613531141247 19 309.1997902580668 20 311.58716615318343 Best k = 5 8.024935 seconds (17.37 M allocations: 397.980 MiB, 1.54% gc time, 33.02% 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 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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... 90%|█████████████████████████████ | 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 0 462.72611464367117 1 386.96260320582707 2 332.6852263683368 3 293.0387002898471 4 237.66594357186221 5 225.8037108408003 6 230.01046078760987 7 237.79087042896356 8 246.09619346062956 9 253.85925832035832 10 255.42184133788405 11 262.1498586713243 12 266.0007516159442 13 262.7067769470717 14 287.63466377541346 15 293.91577238226233 16 298.71177382701376 17 309.6884538301614 18 307.2978266236972 19 325.82840462853454 20 320.9654997673982 Best k = 5 5.652569 seconds (18.07 M allocations: 376.148 MiB, 1.30% gc time, 1.17% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:54 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▋ | ETA: 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ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:04 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:08 Crossvalidation Results: k MSE 0 462.0840431794285 1 451.213268681607 2 435.49666073347 3 401.4562223214547 4 361.92062292291973 5 340.386769621435 6 327.0616697494966 7 328.8715567037451 8 326.5692928802239 9 328.67591855551444 10 333.4325920650739 11 335.9256330771322 12 335.58517187577297 13 339.1556998631928 14 341.3156147395514 15 343.8010904141844 16 361.30723152207474 17 360.5574427706393 18 363.8310083784199 19 381.04436089223765 20 379.7557089419682 Best k = 8 9.846470 seconds (16.52 M allocations: 390.727 MiB, 11.27% gc time, 28.44% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | 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... 52%|████████████████▊ | 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... 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 0 462.0840431794285 1 452.43541195780745 2 437.21189448448604 3 403.09981345979077 4 363.2626748560026 5 342.24378730376327 6 329.45501898360345 7 336.0616310490133 8 335.0286526728271 9 339.2354199764811 10 349.8732404316714 11 358.24707328650027 12 358.6558045686504 13 372.0628107849574 14 381.1324920626978 15 392.09926167155015 16 390.01504333062564 17 418.1907162063712 18 412.5994522896393 19 434.8244655184674 20 426.94832441673094 Best k = 6 5.926047 seconds (17.68 M allocations: 364.836 MiB, 0.98% gc time, 0.82% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 17.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 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0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1488.1265773580267 1 1021.2084921009605 2 650.612532801995 3 531.6987314798063 4 393.62081180066366 5 399.20438053743993 6 420.78000665548296 7 399.08789028282627 8 423.75512905944606 9 410.1172142737326 10 418.3714679599608 11 511.63065625193946 12 417.7166501731458 13 418.5283481754275 14 421.9962153301875 15 444.044763002133 16 431.55192444764396 17 493.9315604009233 18 495.6300807341726 19 477.229038611068 20 473.5498522176166 Best k = 4 8.038170 seconds (15.18 M allocations: 348.157 MiB, 1.04% gc time, 33.84% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 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 1488.1265773580267 1 942.6855266130838 2 599.2617647489756 3 483.409555327389 4 382.40860464795037 5 382.76530714129984 6 406.2291323240331 7 410.6510363037173 8 421.4954730361852 9 424.3271197435494 10 445.87935244924404 11 453.9928173881567 12 449.08426595708437 13 452.64155564983486 14 461.4786015630042 15 468.00008216242543 16 478.4929043973955 17 483.01070762700255 18 495.7228420639286 19 506.2239676190841 20 513.6644209344564 Best k = 4 5.312072 seconds (13.91 M allocations: 277.177 MiB, 1.09% gc time, 1.09% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:36 Cross validating... 5%|█▌ | ETA: 0:01:22 Cross validating... 8%|██▌ | ETA: 0:01:00 Cross validating... 10%|███ | ETA: 0:00:59 Cross validating... 11%|███▌ | ETA: 0:00:57 Cross validating... 13%|████▏ | ETA: 0:00:57 Cross validating... 14%|████▋ | ETA: 0:00:55 Cross validating... 16%|█████▏ | ETA: 0:00:54 Cross validating... 17%|█████▋ | ETA: 0:00:53 Cross validating... 19%|██████▏ | ETA: 0:00:52 Cross validating... 21%|██████▋ | ETA: 0:00:51 Cross validating... 22%|███████▏ | ETA: 0:00:49 Cross validating... 24%|███████▋ | ETA: 0:00:48 Cross validating... 25%|████████▏ | ETA: 0:00:47 Cross validating... 27%|████████▋ | ETA: 0:00:46 Cross validating... 29%|█████████▏ | ETA: 0:00:45 Cross validating... 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| ETA: 0:00:06 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:05 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:03 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:02 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:53 Crossvalidation Results: k MSE 0 500.21752107411254 1 348.14109062276555 2 252.00863768553546 3 218.48221903100898 4 196.95506853063858 5 198.60299810114975 6 199.32077383451917 7 201.66063051063742 8 201.30703538579908 9 202.15266039611998 10 203.61693184069446 11 204.7848195740918 12 206.36851643764624 13 205.79971117268508 14 208.74702283833446 15 208.35071929342092 16 205.0817435934186 17 209.0444218995217 18 208.39812422175223 19 209.31046869136787 20 212.33411928100202 Best k = 4 54.194299 seconds (173.19 M allocations: 4.299 GiB, 1.30% gc time, 4.62% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:08 Cross validating... 8%|██▌ | ETA: 0:00:08 Cross validating... 10%|███ | ETA: 0:00:10 Cross validating... 11%|███▌ | ETA: 0:00:12 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:15 Cross validating... 21%|██████▋ | ETA: 0:00:16 Cross validating... 22%|███████▏ | ETA: 0:00:16 Cross validating... 24%|███████▋ | ETA: 0:00:16 Cross validating... 25%|████████▏ | ETA: 0:00:16 Cross validating... 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ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 62%|███████████████████▊ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:07 Cross validating... 65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 0 500.21752107411254 1 346.1683092963286 2 252.01860547075268 3 215.35584884742102 4 198.17810848960335 5 202.29919476754822 6 204.8454888067889 7 210.85127312206706 8 213.4709605414157 9 217.11923606144 10 224.19788284560101 11 229.50623183349734 12 229.69223181549026 13 228.19122090016842 14 229.88999708957493 15 238.55367443625684 16 232.72087704555537 17 240.12821898568606 18 237.74626385706495 19 245.18239885679856 20 261.9349970100101 Best k = 4 19.664160 seconds (70.71 M allocations: 1.497 GiB, 1.51% gc time, 0.37% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m14.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:16 Cross validating... 6%|██ | ETA: 0:00:39 Cross validating... 10%|███ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:20 Cross validating... 16%|█████▏ | ETA: 0:00:16 Cross validating... 19%|██████▏ | ETA: 0:00:14 Cross validating... 22%|███████▏ | ETA: 0:00:12 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 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86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 7.741405 seconds (17.00 M allocations: 337.891 MiB, 1.21% gc time, 39.50% 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... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 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Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 4.467664 seconds (16.18 M allocations: 286.717 MiB, 1.93% gc time, 1.45% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 13.6s **** 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! **** **** 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14 650.2169297400208 15 655.1112804332713 16 661.024621371185 17 658.6107113277316 18 669.3562502377758 19 675.791321966855 20 671.2607153771169 Best k = 11 19.336274 seconds (343.37 k allocations: 253.077 MiB, 0.63% gc time, 9.74% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.6s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m52.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross 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| ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** 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2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 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: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m30.1s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.3s RNG of the outermost testset: Xoshiro(0x5df223d23830de1a, 0xf98a3f75d1c8fc39, 0xeee957fead922431, 0x794f35f973741b9a, 0x464a13ff399348f0) 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 1239.63s 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:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] 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:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1346.55s: package tests unexpectedly errored