Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1918 (78a0dc1151*) started at 2026-03-20T06:16:39.761 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 12.07s ################################################################################ # 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 v4.5.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.23.0 [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 v8.19.0+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 v17.8.0+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 5.2s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 7223.9 ms ✓ BGEN 7502.9 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`. 29632.6 ms ✓ MendelIHT 3 dependencies successfully precompiled in 57 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 55.01s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_dSEu2I/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 v17.8.0+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 31.1s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.9s Test Summary: | Pass Total Time _choose! | 7 7 12.5s 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 1.5s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.8s Test Summary: | Pass Total Time maf_weights | 6 6 2.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1643.8111949473532, backtracks = 0, tol = 1.7048008651613198 Iteration 2: loglikelihood = -1415.7867066254248, backtracks = 0, tol = 0.15751221756970596 Iteration 3: loglikelihood = -1387.312154596012, backtracks = 0, tol = 0.05133838047658521 Iteration 4: loglikelihood = -1386.5654364952625, backtracks = 0, tol = 0.007491293396947688 Iteration 5: loglikelihood = -1386.3380068700872, backtracks = 0, tol = 0.03929769981586442 Iteration 6: loglikelihood = -1386.1710562170172, backtracks = 0, tol = 0.003966840374423877 Iteration 7: loglikelihood = -1386.1683287091482, backtracks = 0, tol = 0.0005258527386875467 Iteration 8: loglikelihood = -1386.1682543361082, backtracks = 0, tol = 9.981265541624351e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06716012954711914 Final loglikelihood: -1386.1682543361082 SNP PVE: 0.9247196997121986 Iterations: 8 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 873 -1.27643 2 │ 1292 0.834679 3 │ 1781 1.87016 4 │ 2662 -0.250531 5 │ 5655 -0.795338 6 │ 7083 -1.94151 7 │ 7181 -0.125884 8 │ 8315 1.11479 9 │ 8556 -0.63027 10 │ 8876 0.116637 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0194741Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 34.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 5.1s **** 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 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 = -5162.319400569368, backtracks = 0, tol = 0.36144942365803706 Iteration 2: loglikelihood = -2737.155327851753, backtracks = 0, tol = 0.05886849604808333 Iteration 3: loglikelihood = -1868.395917713159, backtracks = 0, tol = 0.057331450206798217 Iteration 4: loglikelihood = -1572.3347347378653, backtracks = 0, tol = 0.05183895315758899 Iteration 5: loglikelihood = -1471.2425810689124, backtracks = 0, tol = 0.0390831118062926 Iteration 6: loglikelihood = -1407.0824156142357, backtracks = 0, tol = 0.07251675124751097 Iteration 7: loglikelihood = -1379.6915603296777, backtracks = 0, tol = 0.045700910077544205 Iteration 8: loglikelihood = -1365.7951929263388, backtracks = 0, tol = 0.025977794835020853 Iteration 9: loglikelihood = -1342.4193946894507, backtracks = 1, tol = 0.06611187925858189 Iteration 10: loglikelihood = -1337.0964176407945, backtracks = 0, tol = 0.01882942805427736 Iteration 11: loglikelihood = -1334.3691249592027, backtracks = 0, tol = 0.013095943239293814 Iteration 12: loglikelihood = -1331.94823835538, backtracks = 1, tol = 0.013807637858864833 Iteration 13: loglikelihood = -1330.7604662284443, backtracks = 0, tol = 0.009512350201327369 Iteration 14: loglikelihood = -1329.8074767184396, backtracks = 0, tol = 0.00977034951629058 Iteration 15: loglikelihood = -1329.082827857559, backtracks = 0, tol = 0.006767109081857859 Iteration 16: loglikelihood = -1328.469988773187, backtracks = 0, tol = 0.007658081565294186 Iteration 17: loglikelihood = -1327.9898005679865, backtracks = 0, tol = 0.005612887008249722 Iteration 18: loglikelihood = -1327.5741983794896, backtracks = 0, tol = 0.006425261835648115 Iteration 19: loglikelihood = -1327.254081289215, backtracks = 0, tol = 0.004646189436097506 Iteration 20: loglikelihood = -1326.9764866799956, backtracks = 0, tol = 0.006270379971921609 Iteration 21: loglikelihood = -1326.7724211247285, backtracks = 0, tol = 0.0037528329897918516 Iteration 22: loglikelihood = -1326.6416209650213, backtracks = 1, tol = 0.002907380478344736 Iteration 23: loglikelihood = -1326.5578337047652, backtracks = 0, tol = 0.0028471517217134555 Iteration 24: loglikelihood = -1326.4917551892213, backtracks = 0, tol = 0.0024162924687475113 Iteration 25: loglikelihood = -1326.440823576206, backtracks = 0, tol = 0.002091113584174915 Iteration 26: loglikelihood = -1326.4002075253513, backtracks = 0, tol = 0.0018868501071635105 Iteration 27: loglikelihood = -1326.3683538730418, backtracks = 0, tol = 0.0015799039841620057 Iteration 28: loglikelihood = -1326.3427928139804, backtracks = 0, tol = 0.001492514027271684 Iteration 29: loglikelihood = -1326.3225446084791, backtracks = 0, tol = 0.0012154553129699191 Iteration 30: loglikelihood = -1326.3062395593133, backtracks = 0, tol = 0.0011894346021130424 Iteration 31: loglikelihood = -1326.293244978754, backtracks = 0, tol = 0.0009465445384909834 Iteration 32: loglikelihood = -1326.2827613369789, backtracks = 0, tol = 0.000952146786771595 Iteration 33: loglikelihood = -1326.2743745235607, backtracks = 0, tol = 0.0007434416021999933 Iteration 34: loglikelihood = -1326.2676021105758, backtracks = 0, tol = 0.0007642712932350193 Iteration 35: loglikelihood = -1326.2621711360207, backtracks = 0, tol = 0.0005876793277797092 Iteration 36: loglikelihood = -1326.257784069242, backtracks = 0, tol = 0.000614485360248375 Iteration 37: loglikelihood = -1326.254260450863, backtracks = 0, tol = 0.00047458174990743223 Iteration 38: loglikelihood = -1326.2514140618339, backtracks = 0, tol = 0.0004945531933827981 Iteration 39: loglikelihood = -1326.2491255384214, backtracks = 0, tol = 0.0003832480845333111 Iteration 40: loglikelihood = -1326.2472771484536, backtracks = 0, tol = 0.000398269160448649 Iteration 41: loglikelihood = -1326.2457900116688, backtracks = 0, tol = 0.0003094454572482883 Iteration 42: loglikelihood = -1326.244589170235, backtracks = 0, tol = 0.0003208439735855759 Iteration 43: loglikelihood = -1326.2436225820572, backtracks = 0, tol = 0.00024980105147147554 Iteration 44: loglikelihood = -1326.2428422848373, backtracks = 0, tol = 0.0002585220756849542 Iteration 45: loglikelihood = -1326.2422140091942, backtracks = 0, tol = 0.00020160498154911253 Iteration 46: loglikelihood = -1326.2417069560424, backtracks = 0, tol = 0.0002083277229347065 Iteration 47: loglikelihood = -1326.241298603271, backtracks = 0, tol = 0.00016266986306184096 Iteration 48: loglikelihood = -1326.2409691214136, backtracks = 0, tol = 0.00016788725096367167 Iteration 49: loglikelihood = -1326.2407037360242, backtracks = 0, tol = 0.0001312259091402682 Iteration 50: loglikelihood = -1326.2404896555213, backtracks = 0, tol = 0.00013529923463757293 Iteration 51: loglikelihood = -1326.2403172040194, backtracks = 0, tol = 0.00010583981936151356 Iteration 52: loglikelihood = -1326.240178117957, backtracks = 0, tol = 0.00010903652410568594 Iteration 53: loglikelihood = -1326.2400660697772, backtracks = 0, tol = 8.53506103573202e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 4.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1560.1924623549558, backtracks = 0, tol = 0.40537570410154355 Iteration 2: loglikelihood = -1484.0346137149045, backtracks = 0, tol = 0.17361925522518046 Iteration 3: loglikelihood = -1450.5544303275658, backtracks = 0, tol = 0.08643576293236677 Iteration 4: loglikelihood = -1439.3029553909755, backtracks = 0, tol = 0.06710346311189365 Iteration 5: loglikelihood = -1437.3508163642389, backtracks = 1, tol = 0.024371087241727218 Iteration 6: loglikelihood = -1436.3781705009244, backtracks = 1, tol = 0.020468426602592824 Iteration 7: loglikelihood = -1436.098779590472, backtracks = 1, tol = 0.01116486124449095 Iteration 8: loglikelihood = -1436.0213584707924, backtracks = 1, tol = 0.005558115664478849 Iteration 9: loglikelihood = -1436.0004889940549, backtracks = 1, tol = 0.002985102436150885 Iteration 10: loglikelihood = -1435.994571974629, backtracks = 1, tol = 0.0014376065334591223 Iteration 11: loglikelihood = -1435.992832177151, backtracks = 1, tol = 0.0008285032429273542 Iteration 12: loglikelihood = -1435.992269382141, backtracks = 1, tol = 0.0004245270639037004 Iteration 13: loglikelihood = -1435.9920895455111, backtracks = 1, tol = 0.0002634396052096924 Iteration 14: loglikelihood = -1435.9920293568262, backtracks = 1, tol = 0.0001382917368574722 Iteration 15: loglikelihood = -1435.9920099937103, backtracks = 1, tol = 8.636125776191752e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1819.8771852528862, backtracks = 0, tol = 0.777641852510633 Iteration 2: loglikelihood = -1468.8833625370519, backtracks = 0, tol = 0.13047948899650683 Iteration 3: loglikelihood = -1391.3713958571302, backtracks = 0, tol = 0.04521622893024192 Iteration 4: loglikelihood = -1379.2575309159442, backtracks = 0, tol = 0.025184311541711454 Iteration 5: loglikelihood = -1378.6559747095707, backtracks = 1, tol = 0.002752476246456411 Iteration 6: loglikelihood = -1378.4996332686328, backtracks = 1, tol = 0.0013428277999280604 Iteration 7: loglikelihood = -1378.4594440963199, backtracks = 1, tol = 0.0006442281458823542 Iteration 8: loglikelihood = -1378.4492102043796, backtracks = 1, tol = 0.000306142117944797 Iteration 9: loglikelihood = -1378.446621871735, backtracks = 1, tol = 0.00014507523676204374 Iteration 10: loglikelihood = -1378.4459700743666, backtracks = 1, tol = 6.885503687201231e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 2.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1592.6586998015591, backtracks = 0, tol = 0.35277971571116545 Iteration 2: loglikelihood = -1414.2402706689688, backtracks = 0, tol = 0.09054819954631474 Iteration 3: loglikelihood = -1380.2776232724536, backtracks = 0, tol = 0.04198422411934681 Iteration 4: loglikelihood = -1379.8087205077998, backtracks = 0, tol = 0.028300871042412752 Iteration 5: loglikelihood = -1379.63504195049, backtracks = 0, tol = 0.002464247249067792 Iteration 6: loglikelihood = -1379.2861046128112, backtracks = 0, tol = 0.02831952933428556 Iteration 7: loglikelihood = -1379.180844472179, backtracks = 0, tol = 0.001789214537542146 Iteration 8: loglikelihood = -1379.1799971036965, backtracks = 1, tol = 0.00012122960356541966 Iteration 9: loglikelihood = -1379.1797747200926, backtracks = 1, tol = 6.699591538216496e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -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 17.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1569.432576848775, backtracks = 0, tol = 0.2384844855877912 Iteration 2: loglikelihood = -1523.1219666123227, backtracks = 0, tol = 0.09743998234594793 Iteration 3: loglikelihood = -1505.6766784563117, backtracks = 0, tol = 0.13683878032198118 Iteration 4: loglikelihood = -1451.288855047463, backtracks = 0, tol = 0.09667752955908548 Iteration 5: loglikelihood = -1431.1017482062514, backtracks = 0, tol = 0.06451161599711389 Iteration 6: loglikelihood = -1409.8526055099394, backtracks = 0, tol = 0.05743186800829192 Iteration 7: loglikelihood = -1409.3124093999784, backtracks = 0, tol = 0.04741404999000467 Iteration 8: loglikelihood = -1391.7728306452132, backtracks = 0, tol = 0.0536298205330856 Iteration 9: loglikelihood = -1375.8925895919283, backtracks = 0, tol = 0.04599320867496522 Iteration 10: loglikelihood = -1362.0123663352585, backtracks = 0, tol = 0.04418819859622287 Iteration 11: loglikelihood = -1347.5662511207302, backtracks = 0, tol = 0.04914439071734218 Iteration 12: loglikelihood = -1345.7585520475777, backtracks = 0, tol = 0.019206438864338274 Iteration 13: loglikelihood = -1341.4025507878432, backtracks = 0, tol = 0.05917561417724222 Iteration 14: loglikelihood = -1340.8181054571505, backtracks = 0, tol = 0.011641630192029418 Iteration 15: loglikelihood = -1340.6292012108975, backtracks = 0, tol = 0.005606365963542756 Iteration 16: loglikelihood = -1340.5467905276403, backtracks = 0, tol = 0.005743996946981365 Iteration 17: loglikelihood = -1340.5089723469555, backtracks = 0, tol = 0.0026138936797935586 Iteration 18: loglikelihood = -1340.4955815687501, backtracks = 1, tol = 0.0013805393460658434 Iteration 19: loglikelihood = -1340.4868227324778, backtracks = 2, tol = 0.0009130201401614212 Iteration 20: loglikelihood = -1340.481711682995, backtracks = 2, tol = 0.0007638348766006469 Iteration 21: loglikelihood = -1340.4788042447162, backtracks = 2, tol = 0.0005555296982104085 Iteration 22: loglikelihood = -1340.4771556953463, backtracks = 2, tol = 0.0004294187305320403 Iteration 23: loglikelihood = -1340.476224352757, backtracks = 2, tol = 0.0003187323034638978 Iteration 24: loglikelihood = -1340.4756981526966, backtracks = 2, tol = 0.00024171964334925974 Iteration 25: loglikelihood = -1340.4754011370908, backtracks = 2, tol = 0.00018082344521465606 Iteration 26: loglikelihood = -1340.4752334658394, backtracks = 2, tol = 0.00013628948103232654 Iteration 27: loglikelihood = -1340.4751388431512, backtracks = 2, tol = 0.000102234619568934 Iteration 28: loglikelihood = -1340.4750854426788, backtracks = 2, tol = 7.688964385221456e-5 1.364671 seconds (5.74 M allocations: 100.730 MiB, 2.93% gc time, 50.35% 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 = -1587.9136076035772, backtracks = 0, tol = 0.2384844855877912 Iteration 2: loglikelihood = -1552.8011905809633, backtracks = 0, tol = 0.10610712287134369 Iteration 3: loglikelihood = -1513.1547442334102, backtracks = 1, tol = 0.08749734899176198 Iteration 4: loglikelihood = -1480.9755120856607, backtracks = 0, tol = 0.10816384707625944 Iteration 5: loglikelihood = -1479.774471150836, backtracks = 0, tol = 0.08684619666358062 Iteration 6: loglikelihood = -1447.8266571260494, backtracks = 0, tol = 0.08241920860486719 Iteration 7: loglikelihood = -1426.8660895203577, backtracks = 1, tol = 0.03294801471074692 Iteration 8: loglikelihood = -1410.89455237486, backtracks = 0, tol = 0.06126107927066683 Iteration 9: loglikelihood = -1398.674636938867, backtracks = 1, tol = 0.008595391167041479 Iteration 10: loglikelihood = -1389.8573484507906, backtracks = 1, tol = 0.005144175791171903 Iteration 11: loglikelihood = -1383.274271809864, backtracks = 1, tol = 0.002683904084763259 Iteration 12: loglikelihood = -1382.0135962420225, backtracks = 0, tol = 0.09196011523687425 Iteration 13: loglikelihood = -1375.440917820378, backtracks = 0, tol = 0.08647217495158903 Iteration 14: loglikelihood = -1372.5029815531943, backtracks = 0, tol = 0.009097486967030733 Iteration 15: loglikelihood = -1370.2735007522053, backtracks = 0, tol = 0.0016178647452389562 Iteration 16: loglikelihood = -1368.2578130519198, backtracks = 0, tol = 0.0007313844030266857 Iteration 17: loglikelihood = -1366.8103268326586, backtracks = 0, tol = 0.06995160823530913 Iteration 18: loglikelihood = -1365.1638408377692, backtracks = 0, tol = 0.007257043466987778 Iteration 19: loglikelihood = -1363.6915532827904, backtracks = 0, tol = 0.0017145966455274684 Iteration 20: loglikelihood = -1362.7559026558063, backtracks = 0, tol = 0.07432430025038114 Iteration 21: loglikelihood = -1361.021820432262, backtracks = 0, tol = 0.009948578356624913 Iteration 22: loglikelihood = -1359.899796942448, backtracks = 0, tol = 0.00262037663562212 Iteration 23: loglikelihood = -1358.8505722414736, backtracks = 0, tol = 0.0009640986952538921 Iteration 24: loglikelihood = -1358.1629074167365, backtracks = 0, tol = 0.06877797386213806 Iteration 25: loglikelihood = -1357.2536014494503, backtracks = 0, tol = 0.005646547145758657 Iteration 26: loglikelihood = -1356.4405197228682, backtracks = 0, tol = 0.001717380406300215 Iteration 27: loglikelihood = -1355.839399657204, backtracks = 0, tol = 0.06385670892504627 Iteration 28: loglikelihood = -1354.9449162881062, backtracks = 0, tol = 0.004242314551551519 Iteration 29: loglikelihood = -1354.3005359748604, backtracks = 0, tol = 0.0019450782194096023 Iteration 30: loglikelihood = -1353.6808002785015, backtracks = 0, tol = 0.0007739676106690292 Iteration 31: loglikelihood = -1352.6193247536085, backtracks = 1, tol = 0.00039141571932630034 Iteration 32: loglikelihood = -1351.8334842594854, backtracks = 1, tol = 0.00023084522953389436 Iteration 33: loglikelihood = -1351.3289196022602, backtracks = 1, tol = 0.00021505339415619565 Iteration 34: loglikelihood = -1350.8971152215267, backtracks = 1, tol = 0.00015216972828156167 Iteration 35: loglikelihood = -1350.4863505463147, backtracks = 1, tol = 0.00011210254520553905 Iteration 36: loglikelihood = -1349.9993023694988, backtracks = 1, tol = 7.652229629275171e-5 0.352132 seconds (1.53 M allocations: 28.065 MiB, 3.92% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3701.9104, backtracks = 0, tol = 0.07949201119259777 Iteration 2: loglikelihood = -3658.1248, backtracks = 0, tol = 0.045067068934815976 Iteration 3: loglikelihood = -3653.1228, backtracks = 1, tol = 0.011664945076043267 Iteration 4: loglikelihood = -3651.6758, backtracks = 1, tol = 0.008116945903644753 Iteration 5: loglikelihood = -3634.4893, backtracks = 1, tol = 0.06327151621054622 Iteration 6: loglikelihood = -3627.446, backtracks = 0, tol = 0.07564029617442933 Iteration 7: loglikelihood = -3626.1465, backtracks = 1, tol = 0.005775900971104785 Iteration 8: loglikelihood = -3625.7332, backtracks = 1, tol = 0.004126351839194781 Iteration 9: loglikelihood = -3625.6187, backtracks = 1, tol = 0.0022556237109890662 Iteration 10: loglikelihood = -3625.5933, backtracks = 1, tol = 0.0012031602807744866 Iteration 11: loglikelihood = -3625.587, backtracks = 1, tol = 0.0006089155064612389 Iteration 12: loglikelihood = -3625.5828, backtracks = 1, tol = 0.00031283425470349143 Iteration 13: loglikelihood = -3625.5857, backtracks = 3, tol = 3.925026254596349e-5 32.273725 seconds (15.74 M allocations: 679.042 MiB, 4.19% gc time, 94.01% 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 = -3591.898, backtracks = 0, tol = 0.07949201119259777 Iteration 2: loglikelihood = -3474.917, backtracks = 0, tol = 0.04623412362010726 Iteration 3: loglikelihood = -3262.6086, backtracks = 1, tol = 0.011460372871539328 Iteration 4: loglikelihood = -3029.1248, backtracks = 1, tol = 0.006860346990396414 Iteration 5: loglikelihood = -2969.411, backtracks = 0, tol = 0.10119218102387628 Iteration 6: loglikelihood = -2771.5837, backtracks = 0, tol = 0.10299787233557907 Iteration 7: loglikelihood = -2634.7568, backtracks = 0, tol = 0.1027039889194282 Iteration 8: loglikelihood = -2529.8396, backtracks = 0, tol = 0.08472124099684972 Iteration 9: loglikelihood = -2428.0657, backtracks = 0, tol = 0.0847494350928837 Iteration 10: loglikelihood = -2356.5437, backtracks = 0, tol = 0.08082382355303068 Iteration 11: loglikelihood = -2292.6514, backtracks = 0, tol = 0.08497335479928064 Iteration 12: loglikelihood = -2252.265, backtracks = 0, tol = 0.07933551710925849 Iteration 13: loglikelihood = -2222.2825, backtracks = 0, tol = 0.08183290960671977 Iteration 14: loglikelihood = -2209.32, backtracks = 0, tol = 0.0915830843175466 Iteration 15: loglikelihood = -2195.5605, backtracks = 0, tol = 0.09159017105786248 Iteration 16: loglikelihood = -2191.1833, backtracks = 0, tol = 0.09256342312273319 Iteration 17: loglikelihood = -2187.0593, backtracks = 0, tol = 0.09274133292228356 Iteration 18: loglikelihood = -2186.7896, backtracks = 0, tol = 0.08778923621570993 Iteration 19: loglikelihood = -2184.8877, backtracks = 0, tol = 0.0876436223226455 Iteration 20: loglikelihood = -2184.289, backtracks = 0, tol = 0.008922889935074925 Iteration 21: loglikelihood = -2184.1099, backtracks = 0, tol = 0.00221982918001896 Iteration 22: loglikelihood = -2183.9832, backtracks = 1, tol = 0.00035399610973141675 Iteration 23: loglikelihood = -2183.955, backtracks = 1, tol = 0.00020037820495444577 Iteration 24: loglikelihood = -2183.9531, backtracks = 2, tol = 6.155752226634299e-5 0.165959 seconds (1.25 M allocations: 20.674 MiB, 11.00% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 37.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Initializing β to univariate regression values... 23%|▌ | ETA: 0:00:16Running 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 6.312379 seconds (1.22 M allocations: 141.319 MiB, 0.38% gc time, 93.45% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 6.8s 10.938713 seconds (4.00 M allocations: 82.490 MiB, 0.63% gc time, 0.50% compilation time) 5.470785 seconds (3.98 M allocations: 91.675 MiB, 0.72% gc time) 10.801510 seconds (20.41 M allocations: 439.525 MiB, 0.75% gc time, 14.96% compilation time: 78% of which was recompilation) 9.503689 seconds (20.18 M allocations: 434.188 MiB, 0.79% gc time) 63.334850 seconds (3.76 M allocations: 4.239 GiB, 7.50% gc time, 20.24% compilation time) 70.303142 seconds (71.97 k allocations: 183.459 MiB, 0.22% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 3m12.7s Test Summary: | Pass Total Time update_support! | 10 10 0.8s 14.142 ms (78 allocations: 4.56 KiB) 4.143 μs (0 allocations: 0 bytes) 144.369 μs (4 allocations: 288 bytes) 6.552 μs (0 allocations: 0 bytes) 49.659 μs (2 allocations: 64 bytes) 36.349 μs (0 allocations: 0 bytes) 23.600 μs (0 allocations: 0 bytes) 28.069 μs (0 allocations: 0 bytes) 70.189 μs (0 allocations: 0 bytes) 36.146 ms (78 allocations: 4.56 KiB) 25.499 μs (0 allocations: 0 bytes) 178.868 μs (4 allocations: 288 bytes) 31.300 μs (0 allocations: 0 bytes) 250.417 μs (2 allocations: 64 bytes) 86.789 μs (0 allocations: 0 bytes) 111.669 μs (0 allocations: 0 bytes) 138.499 μs (0 allocations: 0 bytes) 243.408 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 4m06.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 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 0.724273 seconds (49.20 k allocations: 5.484 MiB, 53.51% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 23.5s **** 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 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 3.768972 seconds (312.13 k allocations: 170.214 MiB, 61.17% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 4.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:05 Cross validating... 6%|██ | ETA: 0:02:30 Cross validating... 10%|███ | ETA: 0:01:38 Cross validating... 13%|████▏ | ETA: 0:01:12 Cross validating... 16%|█████▏ | ETA: 0:00:56 Cross validating... 19%|██████▏ | ETA: 0:00:46 Cross validating... 22%|███████▏ | ETA: 0:00:38 Cross validating... 25%|████████▏ | ETA: 0:00:33 Cross validating... 29%|█████████▏ | ETA: 0:00:28 Cross validating... 30%|█████████▋ | ETA: 0:00:27 Cross validating... 32%|██████████▏ | ETA: 0:00:25 Cross validating... 33%|██████████▋ | ETA: 0:00:24 Cross validating... 37%|███████████▋ | ETA: 0:00:21 Cross validating... 40%|████████████▊ | ETA: 0:00:18 Cross validating... 43%|█████████████▊ | ETA: 0:00:16 Cross validating... 46%|██████████████▊ | ETA: 0:00:15 Cross validating... 49%|███████████████▊ | ETA: 0:00:13 Cross validating... 52%|████████████████▊ | ETA: 0:00:12 Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:06 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 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... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 4158.128644557633 1 2986.050767618028 2 1898.97444175703 3 1332.4875077214358 4 919.675883702026 5 680.7265534651837 6 471.60085476707866 7 342.2314767114865 8 322.54552499925364 9 326.51988195403146 10 329.53264666954215 11 343.91549834828993 12 332.46514797929586 13 358.0358988975928 14 359.25203357895117 15 335.89338751148233 16 341.42039742072257 17 361.4892602768805 18 341.4335193938132 19 379.1345215899645 20 395.7491132160549 Best k = 8 15.851337 seconds (11.67 M allocations: 299.616 MiB, 0.85% gc time, 63.47% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ 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validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 4158.128644557633 1 2989.155276249607 2 1904.1810518887858 3 1334.7821185956382 4 921.53537459159 5 685.2016541841577 6 478.42704848451615 7 349.89170703165183 8 331.1347544753695 9 343.4546022340213 10 350.7734516146877 11 351.97935797587536 12 360.42780835210544 13 371.0065072916066 14 372.75230254835355 15 373.3787997894984 16 385.3914337270108 17 390.73216385776277 18 387.25248809374807 19 391.38130532481 20 395.749113216055 Best k = 8 5.930171 seconds (10.52 M allocations: 220.807 MiB, 1.53% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 23.3s **** 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: 0:08:39 Cross validating... 8%|██▌ | ETA: 0:03:19 Cross validating... 13%|████▏ | ETA: 0:01:59 Cross validating... 17%|█████▋ | ETA: 0:01:22 Cross validating... 22%|███████▏ | ETA: 0:01:01 Cross validating... 27%|████████▋ | ETA: 0:00:48 Cross validating... 30%|█████████▋ | ETA: 0:00:41 Cross 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Crossvalidation Results: k MSE 0 1526.587147216797 1 1172.3529965820312 2 920.2633023071289 3 738.2510904541016 4 591.8980643920899 5 497.6542978210449 6 420.9499700317383 7 364.9188185424805 8 328.96945599365233 9 325.3567317504883 10 320.63009088134766 11 321.49803228759765 12 325.40664639282227 13 325.44947277832034 14 328.72145028686526 15 330.1218118896485 16 341.74944403076177 17 353.0032616271973 18 339.85497381591796 19 367.317748626709 20 358.3215830993653 Best k = 10 21.833478 seconds (12.31 M allocations: 303.541 MiB, 0.48% gc time, 87.14% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 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validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 1526.587147216797 1 1172.4110212402343 2 963.0250044555664 3 742.7365011596679 4 595.2497590637207 5 500.32262609863284 6 423.42203405761717 7 370.56117697143554 8 333.82881628417965 9 335.28322842407226 10 333.386106048584 11 338.2061736755371 12 342.9980232849121 13 353.1217579650879 14 357.7164833068848 15 364.37033978271484 16 366.61675442504884 17 375.82462756347655 18 374.16421408081055 19 377.08835632324224 20 372.60355798339845 Best k = 10 3.566974 seconds (10.57 M allocations: 193.873 MiB, 1.61% gc time, 1.18% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 27.7s **** 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: 0:01:10 Cross validating... 5%|█▌ | ETA: 0:00:52 Cross validating... 6%|██ | ETA: 0:00:41 Cross validating... 8%|██▌ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:29 Cross validating... 11%|███▌ | ETA: 0:00:26 Cross validating... 13%|████▏ | ETA: 0:00:24 Cross validating... 14%|████▋ | ETA: 0:00:22 Cross validating... 16%|█████▏ | ETA: 0:00:20 Cross validating... 17%|█████▋ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 21%|██████▋ | ETA: 0:00:17 Cross validating... 22%|███████▏ | ETA: 0:00:16 Cross validating... 24%|███████▋ | ETA: 0:00:15 Cross validating... 25%|████████▏ 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81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 464.5919025779679 1 422.5802148583397 2 342.69934688332995 3 289.49398507001047 4 266.6557220263279 5 257.8597250935086 6 246.48376911711483 7 245.6457851038369 8 246.38860758779668 9 264.160364307814 10 259.6405310514474 11 258.99033960008694 12 274.8159091112967 13 268.9827038341863 14 285.08696997687196 15 259.91412929862304 16 274.0199632246668 17 275.5379484789431 18 278.86546640226834 19 309.05803966750443 20 285.87416129597386 Best k = 7 17.326946 seconds (16.92 M allocations: 393.270 MiB, 1.22% gc time, 22.58% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 5%|█▌ | ETA: 0:00:11 Cross validating... 6%|██ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 10%|███ | ETA: 0:00:13 Cross validating... 11%|███▌ | ETA: 0:00:13 Cross validating... 13%|████▏ | 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0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 464.5919025779679 1 424.7540258636128 2 346.3578934116176 3 293.27772981211547 4 271.25700128471294 5 261.77961503369283 6 251.44157787018491 7 256.06180140167174 8 258.6880414211705 9 269.2189080876131 10 271.9404434919884 11 279.639064424857 12 285.78355079168693 13 296.1161238618179 14 293.36502651759645 15 301.32854259189673 16 300.5915067167904 17 298.4979467216246 18 316.06205582921683 19 315.70439076052645 20 318.360878357625 Best k = 6 13.846335 seconds (17.53 M allocations: 362.321 MiB, 0.97% gc time, 1.15% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 32.1s **** 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: 0:01:16 Cross validating... 5%|█▌ | ETA: 0:00:53 Cross validating... 8%|██▌ | ETA: 0:00:33 Cross validating... 11%|███▌ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 0:00:22 Cross validating... 14%|████▋ | ETA: 0:00:20 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▋ | ETA: 0:00:17 Cross validating... 19%|██████▏ | ETA: 0:00:16 Cross validating... 21%|██████▋ | ETA: 0:00:15 Cross validating... 22%|███████▏ | ETA: 0:00:14 Cross validating... 24%|███████▋ | ETA: 0:00:13 Cross validating... 25%|████████▏ | ETA: 0:00:13 Cross validating... 27%|████████▋ | ETA: 0:00:12 Cross validating... 29%|█████████▏ | ETA: 0:00:12 Cross validating... 30%|█████████▋ | ETA: 0:00:12 Cross validating... 32%|██████████▏ | ETA: 0:00:11 Cross validating... 33%|██████████▋ | ETA: 0:00:11 Cross validating... 37%|███████████▋ | ETA: 0:00:10 Cross validating... 38%|████████████▎ | ETA: 0:00:09 Cross validating... 40%|████████████▊ | ETA: 0:00:09 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0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 463.21124034968784 1 445.3026016669987 2 409.1165014903827 3 392.6603486909914 4 370.98626502806144 5 353.5154126721094 6 350.8361635338333 7 343.11986258130173 8 353.2116240700519 9 357.4468586232168 10 354.77107651436455 11 352.0112902129423 12 353.5846884096962 13 354.82523348752204 14 363.66061210242594 15 373.4032041008925 16 383.50198571305083 17 362.95560587962746 18 367.4079709098525 19 410.310135179375 20 363.58321329385444 Best k = 7 12.689553 seconds (16.57 M allocations: 394.618 MiB, 11.00% gc time, 31.10% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:07 Cross validating... 14%|████▋ | ETA: 0:00:07 Cross validating... 16%|█████▏ | ETA: 0:00:07 Cross 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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: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.21124034968784 1 446.302589068511 2 411.3328843757537 3 395.30283154976155 4 374.279248816886 5 357.7615660221643 6 361.8176936249684 7 355.07086801712535 8 375.8524140716844 9 391.0748919616467 10 380.4019388897249 11 392.6979418356911 12 388.1129436514397 13 403.7060403276969 14 412.98539066610886 15 425.2173265545598 16 426.55606974077364 17 441.97180329067237 18 452.03870627136075 19 453.37318483090087 20 446.2913249712414 Best k = 7 7.795519 seconds (17.11 M allocations: 351.460 MiB, 1.08% gc time, 0.72% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 23.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:29 Cross validating... 6%|██ | ETA: 0:00:47 Cross validating... 8%|██▌ | ETA: 0:00:38 Cross validating... 10%|███ | ETA: 0:00:33 Cross validating... 11%|███▌ | ETA: 0:00:29 Cross validating... 13%|████▏ | ETA: 0:00:26 Cross validating... 14%|████▋ | ETA: 0:00:24 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▋ | ETA: 0:00:20 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 21%|██████▋ | ETA: 0:00:18 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validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 970.6151849698423 1 879.3553494929099 2 698.5573162926501 3 543.2650766526722 4 457.0916405487768 5 450.6795118565176 6 443.6782913772074 7 406.7954027110957 8 405.1442642401439 9 403.56130505472777 10 397.58680664097415 11 399.21622765872996 12 401.713200694811 13 420.35252510672296 14 419.7841724344679 15 428.87148235929794 16 411.5711760495782 17 408.759107666512 18 413.46716657763284 19 434.3962047258615 20 425.6812796894642 Best k = 10 14.610075 seconds (15.31 M allocations: 365.166 MiB, 1.47% gc time, 25.39% 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: 0:00:11 Cross validating... 5%|█▌ | ETA: 0:00:11 Cross validating... 6%|██ | ETA: 0:00:10 Cross validating... 8%|██▌ | ETA: 0:00:10 Cross validating... 11%|███▌ | ETA: 0:00:08 Cross validating... 14%|████▋ | ETA: 0:00:07 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross validating... 22%|███████▏ | ETA: 0:00:06 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 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59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:08 Crossvalidation Results: k MSE 0 970.6151849698423 1 780.9387913467115 2 660.2454033295005 3 531.2231940169722 4 453.3829825569196 5 422.73393801528806 6 401.749292948652 7 397.92064110529674 8 404.4206999649174 9 415.34719689756366 10 399.25086305587286 11 406.9143461721252 12 406.65376171938175 13 429.0141211223528 14 440.1775690510063 15 436.1524682481423 16 448.75993920893166 17 444.36217892235106 18 439.4521380730827 19 453.6672509948543 20 459.08280586958057 Best k = 7 8.492826 seconds (14.08 M allocations: 281.971 MiB, 1.31% gc time, 1.69% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 23.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:41 Cross validating... 5%|█▌ | ETA: 0:01:10 Cross validating... 8%|██▌ | ETA: 0:00:43 Cross validating... 10%|███ | ETA: 0:00:37 Cross validating... 13%|████▏ | ETA: 0:00:36 Cross validating... 14%|████▋ | ETA: 0:00:40 Cross validating... 16%|█████▏ | ETA: 0:00:36 Cross validating... 17%|█████▋ | ETA: 0:00:33 Cross validating... 19%|██████▏ | ETA: 0:00:35 Cross validating... 21%|██████▋ | ETA: 0:00:39 Cross validating... 22%|███████▏ | ETA: 0:00:40 Cross validating... 24%|███████▋ | ETA: 0:00:40 Cross validating... 25%|████████▏ | ETA: 0:00:40 Cross validating... 27%|████████▋ | ETA: 0:00:37 Cross validating... 29%|█████████▏ | ETA: 0:00:37 Cross validating... 30%|█████████▋ | ETA: 0:00:37 Cross validating... 32%|██████████▏ | ETA: 0:00:35 Cross validating... 33%|██████████▋ | ETA: 0:00:35 Cross validating... 37%|███████████▋ | ETA: 0:00:31 Cross validating... 38%|████████████▎ | ETA: 0:00:29 Cross validating... 41%|█████████████▎ | ETA: 0:00:27 Cross validating... 43%|█████████████▊ | ETA: 0:00:27 Cross validating... 44%|██████████████▎ | ETA: 0:00:27 Cross validating... 46%|██████████████▊ | ETA: 0:00:27 Cross validating... 48%|███████████████▎ | ETA: 0:00:26 Cross validating... 49%|███████████████▊ | ETA: 0:00:26 Cross validating... 51%|████████████████▎ | ETA: 0:00:25 Cross validating... 52%|████████████████▊ | ETA: 0:00:24 Cross validating... 54%|█████████████████▎ | ETA: 0:00:23 Cross validating... 56%|█████████████████▊ | ETA: 0:00:23 Cross validating... 57%|██████████████████▎ | ETA: 0:00:22 Cross validating... 59%|██████████████████▊ | ETA: 0:00:21 Cross validating... 60%|███████████████████▎ | ETA: 0:00:21 Cross validating... 62%|███████████████████▊ | ETA: 0:00:20 Cross validating... 63%|████████████████████▍ | ETA: 0:00:19 Cross validating... 65%|████████████████████▉ | ETA: 0:00:19 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:18 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:16 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:15 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:14 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:13 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:13 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:12 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:11 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:10 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:09 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:08 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:07 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:07 Cross validating... 89%|████████████████████████████▌ | 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: 0:00:54 Crossvalidation Results: k MSE 0 417.5851744200968 1 353.91734726193147 2 303.0222041943217 3 260.8246608040573 4 246.8259066444752 5 236.7089212397677 6 215.52743051552727 7 203.37477848949746 8 203.81567896592696 9 204.99815922955895 10 205.29662335115856 11 206.34035014453445 12 206.212244061373 13 206.53472419965473 14 206.1696136026221 15 207.28294005665828 16 207.16854394798122 17 209.19124256528465 18 207.7322826682938 19 206.6368900691839 20 213.14888326587896 Best k = 7 54.486702 seconds (147.49 M allocations: 3.877 GiB, 1.21% gc time, 6.23% 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: 0:00:06 Cross validating... 5%|█▌ | ETA: 0:00:12 Cross validating... 6%|██ | ETA: 0:00:11 Cross validating... 8%|██▌ | ETA: 0:00:10 Cross validating... 10%|███ | ETA: 0:00:10 Cross validating... 11%|███▌ | ETA: 0:00:09 Cross validating... 13%|████▏ | ETA: 0:00:09 Cross validating... 14%|████▋ | ETA: 0:00:09 Cross validating... 16%|█████▏ | ETA: 0:00:09 Cross validating... 17%|█████▋ | ETA: 0:00:09 Cross validating... 19%|██████▏ | ETA: 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79%|█████████████████████████▍ | ETA: 0:00:03 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: 0:00:02 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: 0:00:17 Crossvalidation Results: k MSE 0 417.5851744200968 1 354.19705639337167 2 304.16073988569644 3 261.24134874696426 4 248.141090676021 5 238.5450080656246 6 217.62103507418206 7 211.3091960309079 8 207.45706422687 9 211.88364373210044 10 212.7720319245625 11 217.45300954097473 12 223.67494725537537 13 220.51308793320112 14 222.38930907519534 15 228.77538060137564 16 224.59038615606676 17 229.7795971988852 18 226.2844842430539 19 231.8734665545615 20 242.35118334880707 Best k = 8 17.670127 seconds (42.36 M allocations: 887.002 MiB, 1.65% gc time, 0.36% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m12.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:18 Cross validating... 6%|██ | ETA: 0:00:40 Cross validating... 10%|███ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:20 Cross validating... 16%|█████▏ | ETA: 0:00:17 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: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 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 8.031177 seconds (17.00 M allocations: 337.935 MiB, 1.49% gc time, 43.12% 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: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 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86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 709.7238911132813 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 4.416895 seconds (16.18 M allocations: 286.712 MiB, 1.44% gc time, 1.43% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 14.0s **** 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... 2%|▋ | ETA: 0:01:51 Cross validating... 3%|█ | ETA: 0:01:16 Cross validating... 4%|█▎ | ETA: 0:01:00 Cross validating... 5%|█▋ | ETA: 0:00:51 Cross validating... 6%|█▉ | ETA: 0:00:45 Cross validating... 7%|██▎ | ETA: 0:00:42 Cross validating... 8%|██▌ | ETA: 0:00:40 Cross validating... 9%|██▉ | ETA: 0:00:38 Cross validating... 10%|███▎ | ETA: 0:00:37 Cross validating... 11%|███▌ | ETA: 0:00:36 Cross validating... 12%|███▉ | ETA: 0:00:37 Cross validating... 13%|████▏ | ETA: 0:00:36 Cross validating... 14%|████▌ | ETA: 0:00:36 Cross validating... 15%|████▊ | ETA: 0:00:35 Cross validating... 16%|█████▏ | ETA: 0:00:34 Cross 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ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:07 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 3522.675643242022 2 3406.7225476915546 3 3321.511171554795 4 3358.3391868079366 5 3395.173507529388 6 3417.31077853381 7 3453.269827661217 8 3504.1556754058315 9 3536.457090792158 10 3541.5005470311107 11 3594.09848285292 12 3642.054521548336 13 3644.1268581377753 14 3658.2990593497007 15 3663.475161814255 16 3736.6246735253935 17 3720.372494829515 18 3812.100072158231 19 3855.7883172315537 20 3844.6247023409715 Best k = 3 24.219903 seconds (337.49 k allocations: 243.098 MiB, 0.72% gc time, 11.11% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 32.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m24.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:18 Cross 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Cross validating... 78%|█████████████████████████ | ETA: 0:00:09 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:09 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:08 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:08 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:07 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:07 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:07 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:04 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:02 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:44 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! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:13 Cross validating... 3%|█ | ETA: 0:00:13 Cross validating... 4%|█▎ | ETA: 0:00:13 Cross validating... 5%|█▋ | ETA: 0:00:14 Cross validating... 6%|█▉ | ETA: 0:00:15 Cross validating... 7%|██▎ | ETA: 0:00:16 Cross validating... 8%|██▌ | ETA: 0:00:17 Cross validating... 9%|██▉ | ETA: 0:00:18 Cross validating... 10%|███▎ | ETA: 0:00:19 Cross validating... 11%|███▌ | ETA: 0:00:21 Cross validating... 12%|███▉ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:22 Cross validating... 14%|████▌ | ETA: 0:00:23 Cross validating... 15%|████▊ | ETA: 0:00:24 Cross validating... 16%|█████▏ | ETA: 0:00:25 Cross validating... 17%|█████▌ | ETA: 0:00:25 Cross 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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! **** **** 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: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:16 Cross validating... 7%|██▎ | ETA: 0:00:16 Cross validating... 8%|██▌ | ETA: 0:00:16 Cross validating... 9%|██▉ | ETA: 0:00:17 Cross validating... 10%|███▎ 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97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:32 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 2m15.6s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl: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 9.3s RNG of the outermost testset: Xoshiro(0xfdaddcfe4bfbb3f0, 0xd79f3d5a3cd7ba7c, 0xc0903a58bc62b98f, 0xeea505370cde6da7, 0xcddfdd4a0a8582c0) 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 1084.1s 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 1683.27s: package tests unexpectedly errored