Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2265 (73323c5146*) started at 2026-05-31T23:42:21.624 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.03s ################################################################################ # 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 v0.1.44 [79e6a3ab] + Adapt v4.6.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [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 v0.2.7 [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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v1.13.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [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 v1.13.0 [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 v1.5.2+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.3+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+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 v1.69.0+0 [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 6.02s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.6 s ✓ BGEN 7.5 s ✓ VCFTools 27.1 s ✓ SnpArrays 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`. 24.5 s ✓ MendelIHT 4 dependencies successfully precompiled in 67 seconds. 170 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 94.05s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_5F31Lb/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.125 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.11 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nghttp2_jll v1.69.0+0 [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 = cholesky!(A::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}, ::Val{true}; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at cholesky.jl:464 └ @ LinearAlgebra /opt/julia/share/julia/stdlib/v1.14/LinearAlgebra/src/cholesky.jl:464 Test Summary: | Pass Total Time loglikelihood | 4 4 15.5s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.3s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1579.757610539389, backtracks = 0, tol = 1.4644693798272752 Iteration 2: loglikelihood = -1441.3665019004575, backtracks = 0, tol = 0.14036395903247398 Iteration 3: loglikelihood = -1436.325873832681, backtracks = 0, tol = 0.018942211778677817 Iteration 4: loglikelihood = -1436.297121310497, backtracks = 0, tol = 0.0019427068558502732 Iteration 5: loglikelihood = -1436.2969101405597, backtracks = 0, tol = 0.00014264633426243041 Iteration 6: loglikelihood = -1436.2969084398628, backtracks = 0, tol = 1.5339709371748997e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05736708641052246 Final loglikelihood: -1436.2969084398628 SNP PVE: 0.8709949785908763 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 167 -1.3666 2 │ 2353 -0.618454 3 │ 2708 0.71108 4 │ 4198 0.787963 5 │ 4984 -0.183234 6 │ 5094 1.58267 7 │ 6087 -0.731616 8 │ 6663 -0.314894 9 │ 7508 0.696185 10 │ 9349 0.358844 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.013011Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1413.2798750661016, backtracks = 0, tol = 0.3793183235961419 Iteration 2: loglikelihood = -1351.8471641887857, backtracks = 0, tol = 0.06712071972584713 Iteration 3: loglikelihood = -1328.5830837975295, backtracks = 0, tol = 0.108206143395075 Iteration 4: loglikelihood = -1322.005796793867, backtracks = 0, tol = 0.044864470876261636 Iteration 5: loglikelihood = -1320.158458234044, backtracks = 0, tol = 0.05816573860653487 Iteration 6: loglikelihood = -1318.9256737852563, backtracks = 0, tol = 0.017760672063935293 Iteration 7: loglikelihood = -1318.4935934199618, backtracks = 0, tol = 0.01297750587832349 Iteration 8: loglikelihood = -1317.6307816970204, backtracks = 0, tol = 0.060216788877794 Iteration 9: loglikelihood = -1317.4308813701095, backtracks = 0, tol = 0.005536130552239324 Iteration 10: loglikelihood = -1317.4014351154594, backtracks = 1, tol = 0.0012166971826256077 Iteration 11: loglikelihood = -1317.388270955115, backtracks = 2, tol = 0.0010577511708346253 Iteration 12: loglikelihood = -1317.3798659895137, backtracks = 2, tol = 0.0009772784498509222 Iteration 13: loglikelihood = -1317.3748265599163, backtracks = 2, tol = 0.0007907699818168953 Iteration 14: loglikelihood = -1317.3719058907293, backtracks = 2, tol = 0.0006121146977325076 Iteration 15: loglikelihood = -1317.3702413164506, backtracks = 2, tol = 0.0004642982479003677 Iteration 16: loglikelihood = -1317.3692992702497, backtracks = 2, tol = 0.0003494258086972245 Iteration 17: loglikelihood = -1317.368767699683, backtracks = 2, tol = 0.00026224588981766284 Iteration 18: loglikelihood = -1317.368468152868, backtracks = 2, tol = 0.00019663334320827353 Iteration 19: loglikelihood = -1317.3682994702701, backtracks = 2, tol = 0.00014739714150935462 Iteration 20: loglikelihood = -1317.3682045174437, backtracks = 2, tol = 0.00011048590723689131 Iteration 21: loglikelihood = -1317.3681510802874, backtracks = 2, tol = 8.282198079190406e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.1s **** 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 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 = -1472.4169199914827, backtracks = 0, tol = 0.3759922209468914 Iteration 2: loglikelihood = -1437.1761847861649, backtracks = 0, tol = 0.11801587561303935 Iteration 3: loglikelihood = -1425.914951907243, backtracks = 0, tol = 0.1006117140222955 Iteration 4: loglikelihood = -1425.5849465125661, backtracks = 0, tol = 0.09302471715424736 Iteration 5: loglikelihood = -1425.029301703071, backtracks = 0, tol = 0.08596616072899523 Iteration 6: loglikelihood = -1424.8018704389985, backtracks = 0, tol = 0.012294277543912423 Iteration 7: loglikelihood = -1424.7975052115219, backtracks = 0, tol = 0.0017181987839896273 Iteration 8: loglikelihood = -1424.7973543174314, backtracks = 0, tol = 0.0002632477574391495 Iteration 9: loglikelihood = -1424.7973474229564, backtracks = 1, tol = 5.978027905159777e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1849.017871877915, backtracks = 0, tol = 0.7821223131134671 Iteration 2: loglikelihood = -1488.531458015688, backtracks = 0, tol = 0.11680443520362091 Iteration 3: loglikelihood = -1434.9279269271444, backtracks = 0, tol = 0.05516147661095942 Iteration 4: loglikelihood = -1424.2799413266475, backtracks = 0, tol = 0.030658955264195965 Iteration 5: loglikelihood = -1421.4876728027978, backtracks = 0, tol = 0.026316316690309267 Iteration 6: loglikelihood = -1421.1276478671014, backtracks = 0, tol = 0.025847179253848492 Iteration 7: loglikelihood = -1421.063680387324, backtracks = 1, tol = 0.0008769945771686177 Iteration 8: loglikelihood = -1421.047191688018, backtracks = 1, tol = 0.0004571112589434874 Iteration 9: loglikelihood = -1421.0429479877002, backtracks = 1, tol = 0.00023537180237726013 Iteration 10: loglikelihood = -1421.0418596028153, backtracks = 1, tol = 0.00011964525009150872 Iteration 11: loglikelihood = -1421.0415817835492, backtracks = 1, tol = 6.010429601173013e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1646.9282699585483, backtracks = 0, tol = 0.43622712343616865 Iteration 2: loglikelihood = -1464.2069776729925, backtracks = 0, tol = 0.08820677279535805 Iteration 3: loglikelihood = -1429.9297065282285, backtracks = 0, tol = 0.04579535761133287 Iteration 4: loglikelihood = -1423.4951241079536, backtracks = 0, tol = 0.03410070618047828 Iteration 5: loglikelihood = -1422.0555710238941, backtracks = 0, tol = 0.027482608841716025 Iteration 6: loglikelihood = -1421.3670292312652, backtracks = 0, tol = 0.027098830194451605 Iteration 7: loglikelihood = -1421.2194825561096, backtracks = 1, tol = 0.0015575124433998427 Iteration 8: loglikelihood = -1421.1813749369621, backtracks = 1, tol = 0.000802888131801145 Iteration 9: loglikelihood = -1421.1715764371966, backtracks = 1, tol = 0.0004086326545860093 Iteration 10: loglikelihood = -1421.1690712260915, backtracks = 1, tol = 0.00020556492644110714 Iteration 11: loglikelihood = -1421.1684343281897, backtracks = 1, tol = 0.00010248272365739453 Iteration 12: loglikelihood = -1421.1682731813662, backtracks = 1, tol = 5.079037930912332e-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 10.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1831.9928333019368, backtracks = 0, tol = 0.17123703037513813 Iteration 2: loglikelihood = -1705.7812798132968, backtracks = 0, tol = 0.15597187197949505 Iteration 3: loglikelihood = -1562.5451716260586, backtracks = 0, tol = 0.22687339027799908 Iteration 4: loglikelihood = -1554.7962719718062, backtracks = 0, tol = 0.1394787157015801 Iteration 5: loglikelihood = -1521.0243613028708, backtracks = 0, tol = 0.051036919710256125 Iteration 6: loglikelihood = -1498.5819774663444, backtracks = 1, tol = 0.08590094125511165 Iteration 7: loglikelihood = -1470.8730512844081, backtracks = 0, tol = 0.10263798021778572 Iteration 8: loglikelihood = -1463.4195469101473, backtracks = 0, tol = 0.06534280485398056 Iteration 9: loglikelihood = -1462.1948116444753, backtracks = 0, tol = 0.01845907249441457 Iteration 10: loglikelihood = -1461.6351812887472, backtracks = 0, tol = 0.007586821558972834 Iteration 11: loglikelihood = -1461.3320039627413, backtracks = 0, tol = 0.010162471631179042 Iteration 12: loglikelihood = -1461.16410760474, backtracks = 0, tol = 0.00367428551916282 Iteration 13: loglikelihood = -1461.0688004697704, backtracks = 0, tol = 0.005979780396746699 Iteration 14: loglikelihood = -1461.0157926763015, backtracks = 0, tol = 0.0020391088496989813 Iteration 15: loglikelihood = -1460.9852052835952, backtracks = 0, tol = 0.003591154417672799 Iteration 16: loglikelihood = -1460.9684444669779, backtracks = 0, tol = 0.001095851117744907 Iteration 17: loglikelihood = -1460.9587222551343, backtracks = 0, tol = 0.002166445509474197 Iteration 18: loglikelihood = -1460.9535988429075, backtracks = 0, tol = 0.0005732380041251081 Iteration 19: loglikelihood = -1460.9506663653792, backtracks = 0, tol = 0.0012835875424226661 Iteration 20: loglikelihood = -1460.9492373656808, backtracks = 0, tol = 0.000284596878203811 Iteration 21: loglikelihood = -1460.9486499991767, backtracks = 1, tol = 0.0003596247595816168 Iteration 22: loglikelihood = -1460.9482179930526, backtracks = 0, tol = 0.00025019225709417385 Iteration 23: loglikelihood = -1460.9480486445727, backtracks = 0, tol = 0.0001841729661071062 Iteration 24: loglikelihood = -1460.9479661818525, backtracks = 0, tol = 0.00010528022293799975 Iteration 25: loglikelihood = -1460.947930452369, backtracks = 0, tol = 8.859209278981149e-5 1.016558 seconds (2.25 M allocations: 45.475 MiB, 61.16% 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 = -1833.0585947457948, backtracks = 0, tol = 0.17123703037513813 Iteration 2: loglikelihood = -1743.7741801937766, backtracks = 0, tol = 0.16043027081517366 Iteration 3: loglikelihood = -1647.0111318668182, backtracks = 0, tol = 0.23080095932821024 Iteration 4: loglikelihood = -1629.4298874685599, backtracks = 0, tol = 0.1579195078786014 Iteration 5: loglikelihood = -1598.8357094967855, backtracks = 0, tol = 0.0658301131553195 Iteration 6: loglikelihood = -1566.0185761463313, backtracks = 0, tol = 0.16205481454295817 Iteration 7: loglikelihood = -1547.583021416164, backtracks = 0, tol = 0.06267012109559322 Iteration 8: loglikelihood = -1535.253941923062, backtracks = 0, tol = 0.024249972049343826 Iteration 9: loglikelihood = -1526.3018873286344, backtracks = 0, tol = 0.008425664471531294 Iteration 10: loglikelihood = -1518.373333199887, backtracks = 0, tol = 0.006259687079819368 Iteration 11: loglikelihood = -1511.9588568362217, backtracks = 0, tol = 0.002693975748543979 Iteration 12: loglikelihood = -1506.4045307560737, backtracks = 0, tol = 0.0016271967501159514 Iteration 13: loglikelihood = -1501.706426081652, backtracks = 0, tol = 0.001044239991468849 Iteration 14: loglikelihood = -1497.6368949983087, backtracks = 0, tol = 0.00037609096277089414 Iteration 15: loglikelihood = -1494.1207267210386, backtracks = 0, tol = 0.000525936750508504 Iteration 16: loglikelihood = -1491.0439049893266, backtracks = 0, tol = 0.0004212449451232607 Iteration 17: loglikelihood = -1488.3499317497958, backtracks = 0, tol = 0.00041096638585109974 Iteration 18: loglikelihood = -1485.9668858007135, backtracks = 0, tol = 0.0003880253980288948 Iteration 19: loglikelihood = -1483.8600835066293, backtracks = 0, tol = 0.0003613198166241464 Iteration 20: loglikelihood = -1481.9769213103932, backtracks = 0, tol = 0.0003334596505650523 Iteration 21: loglikelihood = -1480.299968739649, backtracks = 0, tol = 0.00031246675068728465 Iteration 22: loglikelihood = -1478.7861306385234, backtracks = 0, tol = 0.0002860009546524102 Iteration 23: loglikelihood = -1477.430770024262, backtracks = 0, tol = 0.00031205914753937606 Iteration 24: loglikelihood = -1476.196576192814, backtracks = 0, tol = 0.0002509343035709679 Iteration 25: loglikelihood = -1475.0865983632482, backtracks = 0, tol = 0.0003098955296087347 Iteration 26: loglikelihood = -1474.0686742605483, backtracks = 0, tol = 0.00022489273615952914 Iteration 27: loglikelihood = -1473.1495223882596, backtracks = 0, tol = 0.00030410189872365873 Iteration 28: loglikelihood = -1472.3016899108193, backtracks = 0, tol = 0.0002024870034150532 Iteration 29: loglikelihood = -1471.533378480042, backtracks = 0, tol = 0.00029439240236826244 Iteration 30: loglikelihood = -1470.8211992249978, backtracks = 0, tol = 0.0001828020512257445 Iteration 31: loglikelihood = -1470.173742396272, backtracks = 0, tol = 0.00028228010659860363 Iteration 32: loglikelihood = -1469.5710568879094, backtracks = 0, tol = 0.00016565431712688155 Iteration 33: loglikelihood = -1469.0215678726213, backtracks = 0, tol = 0.0002692157989359795 Iteration 34: loglikelihood = -1468.5081973894094, backtracks = 0, tol = 0.00015066220706950843 Iteration 35: loglikelihood = -1468.038935291946, backtracks = 0, tol = 0.00025602022338395297 Iteration 36: loglikelihood = -1467.599101818265, backtracks = 0, tol = 0.00013750572281465178 Iteration 37: loglikelihood = -1467.196130172133, backtracks = 0, tol = 0.0002431278107516963 Iteration 38: loglikelihood = -1466.8173470617276, backtracks = 0, tol = 0.00012590361685490604 Iteration 39: loglikelihood = -1466.4695878306359, backtracks = 0, tol = 0.0002307417426680883 Iteration 40: loglikelihood = -1466.1418657873878, backtracks = 0, tol = 0.00011562388435373349 Iteration 41: loglikelihood = -1465.8404202902677, backtracks = 0, tol = 0.0002189458526749699 Iteration 42: loglikelihood = -1465.555689817553, backtracks = 0, tol = 0.0001064743532122001 Iteration 43: loglikelihood = -1465.2933424554096, backtracks = 0, tol = 0.00020776252133624957 Iteration 44: loglikelihood = -1465.0450274013865, backtracks = 0, tol = 9.829636512039383e-5 0.476913 seconds (1.81 M allocations: 32.141 MiB, 4.74% 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 = -3547.733, backtracks = 0, tol = 0.0928111584824766 Iteration 2: loglikelihood = -3512.9941, backtracks = 0, tol = 0.04051787843699958 Iteration 3: loglikelihood = -3509.1953, backtracks = 1, tol = 0.010092998818690788 Iteration 4: loglikelihood = -3489.4683, backtracks = 1, tol = 0.05971164843956886 Iteration 5: loglikelihood = -3479.2502, backtracks = 0, tol = 0.0812490344981579 Iteration 6: loglikelihood = -3467.3699, backtracks = 0, tol = 0.08151423638007446 Iteration 7: loglikelihood = -3465.1453, backtracks = 0, tol = 0.008675775628882129 Iteration 8: loglikelihood = -3464.9966, backtracks = 0, tol = 0.0024896176483022473 Iteration 9: loglikelihood = -3464.9822, backtracks = 0, tol = 0.0009595064257750546 Iteration 10: loglikelihood = -3460.3013, backtracks = 0, tol = 0.07620844831838056 Iteration 11: loglikelihood = -3458.8704, backtracks = 0, tol = 0.009179414218455383 Iteration 12: loglikelihood = -3458.7468, backtracks = 0, tol = 0.002761243239162303 Iteration 13: loglikelihood = -3456.4392, backtracks = 0, tol = 0.08560367368373142 Iteration 14: loglikelihood = -3455.212, backtracks = 0, tol = 0.009739424138868582 Iteration 15: loglikelihood = -3455.1719, backtracks = 0, tol = 0.0014116189101446245 Iteration 16: loglikelihood = -3455.1687, backtracks = 0, tol = 0.0003828967674213174 Iteration 17: loglikelihood = -3455.166, backtracks = 0, tol = 0.00024981349677256155 Iteration 18: loglikelihood = -3455.169, backtracks = 3, tol = 6.239494233736423e-6 23.691258 seconds (15.58 M allocations: 687.828 MiB, 2.63% gc time, 96.06% 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 = -3450.5984, backtracks = 0, tol = 0.0928111584824766 Iteration 2: loglikelihood = -3348.3245, backtracks = 0, tol = 0.04148537387606051 Iteration 3: loglikelihood = -3151.7888, backtracks = 1, tol = 0.05413739537889768 Iteration 4: loglikelihood = -3065.5337, backtracks = 0, tol = 0.0895085311265255 Iteration 5: loglikelihood = -2936.4578, backtracks = 0, tol = 0.08832481130642329 Iteration 6: loglikelihood = -2843.976, backtracks = 0, tol = 0.08071557793297862 Iteration 7: loglikelihood = -2725.5483, backtracks = 0, tol = 0.08253816763766868 Iteration 8: loglikelihood = -2619.036, backtracks = 0, tol = 0.07306701742806333 Iteration 9: loglikelihood = -2514.3967, backtracks = 0, tol = 0.07952571914823368 Iteration 10: loglikelihood = -2419.0576, backtracks = 0, tol = 0.08369564264821468 Iteration 11: loglikelihood = -2339.426, backtracks = 0, tol = 0.08100812883416204 Iteration 12: loglikelihood = -2271.7075, backtracks = 0, tol = 0.09574879494182284 Iteration 13: loglikelihood = -2225.8977, backtracks = 0, tol = 0.09559857344599952 Iteration 14: loglikelihood = -2195.0762, backtracks = 0, tol = 0.10094646020290868 Iteration 15: loglikelihood = -2169.1106, backtracks = 0, tol = 0.10104887634492427 Iteration 16: loglikelihood = -2159.2021, backtracks = 0, tol = 0.09840336192586388 Iteration 17: loglikelihood = -2146.598, backtracks = 0, tol = 0.09801517975137386 Iteration 18: loglikelihood = -2145.609, backtracks = 0, tol = 0.09728048941604092 Iteration 19: loglikelihood = -2139.634, backtracks = 0, tol = 0.09708037221462408 Iteration 20: loglikelihood = -2136.0427, backtracks = 1, tol = 0.015979023309026518 Iteration 21: loglikelihood = -2135.2812, backtracks = 1, tol = 0.006798064306196601 Iteration 22: loglikelihood = -2135.1343, backtracks = 1, tol = 0.0029227020288144327 Iteration 23: loglikelihood = -2135.1135, backtracks = 1, tol = 0.0012969501613354732 Iteration 24: loglikelihood = -2135.1138, backtracks = 3, tol = 0.00015968704868088267 Iteration 25: loglikelihood = -2135.111, backtracks = 3, tol = 0.00013982151053544429 Iteration 26: loglikelihood = -2135.1118, backtracks = 3, tol = 0.00012249093010470693 Iteration 27: loglikelihood = -2135.1108, backtracks = 3, tol = 0.0001073359856788948 Iteration 28: loglikelihood = -2135.112, backtracks = 3, tol = 9.406923288968518e-5 0.231095 seconds (1.75 M allocations: 29.123 MiB, 8.03% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 28.2s **** 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 = -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 4.354999 seconds (1.14 M allocations: 136.629 MiB, 1.74% gc time, 89.17% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.8s 10.162960 seconds (4.00 M allocations: 82.492 MiB, 0.78% gc time, 0.60% compilation time) 5.315185 seconds (3.98 M allocations: 91.675 MiB, 0.17% gc time) 9.080578 seconds (20.41 M allocations: 439.363 MiB, 0.80% gc time, 21.18% compilation time: 79% of which was recompilation) 6.229746 seconds (20.18 M allocations: 434.187 MiB, 1.07% gc time) 37.791294 seconds (3.77 M allocations: 4.239 GiB, 5.83% gc time, 30.99% compilation time) 55.319308 seconds (70.38 k allocations: 183.438 MiB, 0.15% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m19.2s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.330 ms (78 allocations: 4.56 KiB) 4.486 μs (0 allocations: 0 bytes) 119.129 μs (4 allocations: 288 bytes) 6.826 μs (0 allocations: 0 bytes) 40.269 μs (2 allocations: 64 bytes) 26.720 μs (0 allocations: 0 bytes) 27.600 μs (0 allocations: 0 bytes) 29.459 μs (0 allocations: 0 bytes) 93.749 μs (0 allocations: 0 bytes) 35.080 ms (78 allocations: 4.56 KiB) 18.910 μs (0 allocations: 0 bytes) 170.829 μs (4 allocations: 288 bytes) 29.679 μs (0 allocations: 0 bytes) 201.458 μs (2 allocations: 64 bytes) 84.639 μs (0 allocations: 0 bytes) 144.889 μs (0 allocations: 0 bytes) 157.159 μs (0 allocations: 0 bytes) 232.748 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m10.6s **** 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 **** **** 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 0.446356 seconds (49.36 k allocations: 5.489 MiB, 63.41% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.5s **** 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 1.938869 seconds (282.00 k allocations: 168.112 MiB, 54.61% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** 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: 0:03:43 Cross validating... 11%|███▌ | ETA: 0:01:03 Cross validating... 14%|████▋ | ETA: 0:00:48 Cross validating... 17%|█████▋ | ETA: 0:00:38 Cross validating... 21%|██████▋ | ETA: 0:00:32 Cross validating... 24%|███████▋ | ETA: 0:00:27 Cross validating... 27%|████████▋ | ETA: 0:00:23 Cross validating... 30%|█████████▋ | ETA: 0:00:20 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | 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validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 2698.9553513627616 1 1868.5858442689039 2 1236.9640214017447 3 1070.8663429738847 4 858.3978214452786 5 719.526733456041 6 558.572703417586 7 435.62203999572455 8 387.78083430220306 9 357.41148570702177 10 353.9310435823433 11 357.68451019091265 12 353.2081226416713 13 355.76944755255136 14 363.5916745952586 15 368.54855463992635 16 372.2834919072021 17 367.8024594490211 18 389.3871517350982 19 382.9505769094786 20 400.5968071003696 Best k = 12 12.105928 seconds (11.19 M allocations: 296.729 MiB, 1.17% gc time, 62.01% 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 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 2698.9553513627616 1 1872.5802706674813 2 1245.1407126432944 3 1079.0421968091518 4 864.1361523257383 5 724.7655930513653 6 568.7516533049892 7 444.56396950196546 8 407.56949855591563 9 365.1644304890805 10 363.39995600518154 11 373.4674532236917 12 372.12855774286754 13 379.53477494412834 14 392.3542990569981 15 398.97075871403797 16 414.4954437691245 17 408.73012727286834 18 416.76184149017706 19 416.3476316020432 20 420.1489479619802 Best k = 10 4.528874 seconds (10.25 M allocations: 215.499 MiB, 1.11% gc time, 1.08% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.5s **** 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: 0:05:55 Cross validating... 8%|██▌ | ETA: 0:02:16 Cross validating... 14%|████▋ | ETA: 0:01:12 Cross validating... 19%|██████▏ | ETA: 0:00:51 Cross validating... 24%|███████▋ | ETA: 0:00:39 Cross validating... 29%|█████████▏ | ETA: 0:00:31 Cross validating... 33%|██████████▋ | ETA: 0:00:25 Cross validating... 40%|████████████▊ | ETA: 0:00:19 Cross validating... 44%|██████████████▎ | ETA: 0:00:16 Cross validating... 51%|████████████████▎ | ETA: 0:00:12 Cross validating... 56%|█████████████████▊ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 63%|████████████████████▍ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1693.4619478759764 1 1399.7482474365236 2 1024.96146875 3 791.539776184082 4 631.8313858642578 5 528.6220491027832 6 450.966287109375 7 393.3900693359375 8 363.48558126831057 9 348.184387298584 10 353.340052734375 11 355.2998885192871 12 358.2321233215332 13 358.1649797668457 14 359.85037551879884 15 374.743947265625 16 364.6690641784668 17 363.97078869628905 18 384.7787978820801 19 406.2227967834473 20 398.7238057556152 Best k = 9 15.340332 seconds (12.63 M allocations: 313.348 MiB, 0.73% gc time, 83.45% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:01 Cross validating... 49%|███████████████▊ | ETA: 0:00:01 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1693.4619478759764 1 1402.3092275390625 2 1025.7350112304687 3 794.0293334350586 4 632.4169924926758 5 532.9570816345215 6 454.3054750671387 7 403.7908529052735 8 372.87998138427736 9 360.65015524291994 10 373.3667459716797 11 381.25679943847655 12 396.815744720459 13 389.1606020202637 14 395.316774597168 15 402.00215185546875 16 406.0286167907715 17 411.4966612548828 18 420.70216610717773 19 423.22809719848635 20 412.6186153259277 Best k = 9 2.593587 seconds (10.85 M allocations: 199.576 MiB, 1.96% gc time, 1.57% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:07 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:16 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:12 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 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validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.4489645279442 1 401.6570107388118 2 351.9803072715303 3 337.6997708359023 4 314.5991618337209 5 290.2845346391307 6 264.85982765785167 7 251.8197188036519 8 256.5080264555219 9 261.0841500850269 10 265.1373639840185 11 269.87527633428397 12 269.4631324701995 13 302.02438546765745 14 307.74444985349265 15 272.1959204746215 16 297.3045788513366 17 300.0812981435986 18 278.1334737912997 19 319.30579557830794 20 321.13988066991607 Best k = 7 8.526272 seconds (17.25 M allocations: 408.222 MiB, 1.41% gc time, 33.26% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 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94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.4489645279442 1 402.6238131422449 2 354.3546775865304 3 341.28656365864106 4 319.5956875410509 5 296.83228234774464 6 272.8793175383015 7 277.9296412509463 8 275.4312560714735 9 290.1377934098763 10 313.2627470472461 11 333.9834581807975 12 333.8139092882691 13 342.4100064278916 14 348.2605889831731 15 361.64965332412123 16 366.1982114239709 17 377.2734847731809 18 366.4059742178405 19 373.4545224788808 20 389.65498011145894 Best k = 6 6.022239 seconds (17.61 M allocations: 365.022 MiB, 1.10% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.08949891591726 1 445.9621098858156 2 413.56544441434704 3 385.2032961683458 4 361.49660980914666 5 334.4753328434024 6 321.2255269583436 7 325.0019630482143 8 325.868882142664 9 326.22211687397885 10 326.3167133816245 11 328.48906639982147 12 351.46575443276487 13 338.1314292476813 14 336.5239303603463 15 343.1119505507321 16 339.43118195590716 17 387.3256225365478 18 344.3798972030329 19 396.99434672386053 20 355.34239935031974 Best k = 6 7.160712 seconds (16.53 M allocations: 390.491 MiB, 7.04% gc time, 38.76% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 463.08949891591726 1 448.58907441999224 2 418.1843185331694 3 390.0241970499389 4 366.5999408338781 5 341.35939035265375 6 327.18536334515943 7 339.04902874734705 8 342.8459577601551 9 348.84357234218135 10 355.02552862352405 11 364.0509052091798 12 376.97539612827137 13 385.9973699166965 14 378.7501163179737 15 393.6440826578932 16 394.1161237736359 17 406.94376780670314 18 416.3520848805769 19 422.4214310496054 20 419.6452473114999 Best k = 6 4.273014 seconds (17.30 M allocations: 354.713 MiB, 1.16% gc time, 1.13% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | 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... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 599.897907016423 1 491.01968548782366 2 441.50380840827205 3 417.7308889778066 4 410.494442831798 5 398.0769884606826 6 397.40670543100424 7 380.9314063988017 8 388.60109036058253 9 380.33353838813355 10 391.2633985162862 11 389.50279901309057 12 388.7131040480894 13 386.6973246220185 14 399.7483259675457 15 403.3883024124581 16 392.15979128770266 17 417.31392709907055 18 416.8884152390134 19 391.79493436262896 20 393.88602307404324 Best k = 9 8.263054 seconds (15.34 M allocations: 375.694 MiB, 1.00% gc time, 33.66% 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: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross 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100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 599.897907016423 1 488.60521587455236 2 442.475707661398 3 419.26414088916897 4 414.1611662657831 5 403.30581887216505 6 406.0522733062778 7 412.4514045659914 8 401.3674135081003 9 407.48412767335196 10 414.0416029228419 11 418.55347393307335 12 419.54778760282306 13 417.8705620277611 14 430.07159243091724 15 431.8173235268539 16 444.396710694265 17 445.83280915183605 18 450.4588675496989 19 450.9849207898137 20 458.4267241935977 Best k = 8 5.728792 seconds (14.45 M allocations: 292.085 MiB, 0.87% gc time, 0.99% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 6%|██ | ETA: 0:00:44 Cross validating... 8%|██▌ | ETA: 0:00:36 Cross validating... 11%|███▌ | ETA: 0:00:26 Cross validating... 13%|████▏ | ETA: 0:00:29 Cross validating... 14%|████▋ | ETA: 0:00:32 Cross validating... 16%|█████▏ | ETA: 0:00:34 Cross validating... 17%|█████▋ | ETA: 0:00:31 Cross validating... 21%|██████▋ | ETA: 0:00:30 Cross validating... 22%|███████▏ | ETA: 0:00:31 Cross validating... 24%|███████▋ | ETA: 0:00:29 Cross validating... 25%|████████▏ | ETA: 0:00:30 Cross validating... 27%|████████▋ | ETA: 0:00:30 Cross validating... 29%|█████████▏ | ETA: 0:00:31 Cross validating... 30%|█████████▋ | ETA: 0:00:31 Cross validating... 32%|██████████▏ | ETA: 0:00:31 Cross validating... 33%|██████████▋ | ETA: 0:00:31 Cross validating... 37%|███████████▋ | ETA: 0:00:27 Cross validating... 40%|████████████▊ | ETA: 0:00:26 Cross validating... 43%|█████████████▊ | ETA: 0:00:23 Cross validating... 46%|██████████████▊ | ETA: 0:00:21 Cross validating... 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79%|█████████████████████████▍ | ETA: 0:00:07 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:07 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:06 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:05 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:40 Crossvalidation Results: k MSE 0 333.6591150469943 1 286.66700998441365 2 262.51506510594083 3 255.29534165199715 4 250.12469019063417 5 236.82930478428477 6 231.02919482277957 7 229.59219258970273 8 226.98189636831432 9 230.15371609894254 10 230.2587476940451 11 232.790322749359 12 232.47507773430937 13 233.85431485239803 14 234.4378992253408 15 235.18397493490139 16 235.67193877831286 17 235.13224133882034 18 238.09351940128613 19 239.10379913037983 20 239.62657308655344 Best k = 8 41.158773 seconds (127.33 M allocations: 3.318 GiB, 1.21% gc time, 5.27% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross 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validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:09 Crossvalidation Results: k MSE 0 333.6591150469943 1 287.3583740741824 2 264.20697910328204 3 257.8833497262617 4 248.35025420084537 5 242.3209356578103 6 233.56489301445458 7 234.35894698258323 8 231.4894139457247 9 241.33725425614858 10 244.19191869581505 11 246.11755912300916 12 249.0744404015444 13 254.18706823202507 14 260.2195866458126 15 262.95849609853315 16 265.621806045265 17 261.9066686556801 18 269.42085364105884 19 276.5777225269129 20 282.3411849241837 Best k = 8 10.050361 seconds (29.36 M allocations: 600.190 MiB, 1.32% gc time, 0.61% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 51.7s **** 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: 0:01:13 Cross validating... 6%|██ | ETA: 0:00:37 Cross validating... 10%|███ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 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0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 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 6.418085 seconds (17.00 M allocations: 337.669 MiB, 1.75% gc time, 47.41% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 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 2.856315 seconds (16.17 M allocations: 286.692 MiB, 1.70% gc time, 1.96% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:25 Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 4%|█▎ | ETA: 0:00:47 Cross validating... 5%|█▋ | ETA: 0:00:39 Cross validating... 6%|█▉ | ETA: 0:00:34 Cross validating... 7%|██▎ | ETA: 0:00:31 Cross validating... 8%|██▌ | ETA: 0:00:29 Cross validating... 9%|██▉ | ETA: 0:00:27 Cross validating... 10%|███▎ | ETA: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:23 Cross validating... 12%|███▉ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:22 Cross 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:17 Crossvalidation Results: k MSE 1 3602.8640684324705 2 3359.521769456568 3 3206.3241703921653 4 3099.334373902313 5 3017.9030439577427 6 2974.6917755872455 7 2950.551637176802 8 2933.0980381618324 9 2968.2344443336838 10 2983.806030050941 11 2996.4935614396945 12 3040.9842701834427 13 3024.561905552723 14 3053.6206379476616 15 3048.9501568342303 16 3061.777095639618 17 3081.3025964046233 18 3133.943949573665 19 3092.588462664131 20 3116.1012083163964 Best k = 8 17.517541 seconds (318.25 k allocations: 219.680 MiB, 0.33% gc time, 10.21% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 22.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m06.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | 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2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:13 Cross validating... 3%|█ | ETA: 0:00:12 Cross validating... 4%|█▎ | ETA: 0:00:13 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross 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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: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:14 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ 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| ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 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 1m26.4s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/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] collect(itr::Base.Generator{UnitRange{Int64}, MendelIHT.var"#convert_bgen_gt##0#convert_bgen_gt##1"}) @ Base ~/.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:741 [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:2246 [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:327 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [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:321 [18] _start() @ Base ./client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.2s RNG of the outermost testset: Xoshiro(0x4cd2493a3f2618cf, 0xf27d14ec419136d3, 0x1413eb073fb2b68a, 0xecf9d92479dd0782, 0x03820f2297628288) 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 1084.3s 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:3247 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [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:587 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:355 [12] _start() @ Base ./client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1221.11s: package tests unexpectedly errored