Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2336 (83323976df*) started at 2026-06-12T00:43:39.656 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.91s ################################################################################ # 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 v4.6.1 [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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[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 v1.9.4+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 5.71s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.9 s ✓ BGEN 8.4 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 27.8 s ✓ MendelIHT 3 dependencies successfully precompiled in 43 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 69.57s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_JFAMQI/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 v0.25.126 [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: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:219 └ @ Distributions ~/.julia/packages/Distributions/nfRUl/src/multivariate/mvnormal.jl:219 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 18.8s 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 10.2s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.5s Test Summary: | Pass Total Time project_k! | 2 2 1.1s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 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 = -1669.4097614454195, backtracks = 0, tol = 1.7634077263392474 Iteration 2: loglikelihood = -1465.1192187344896, backtracks = 0, tol = 0.15033300880605524 Iteration 3: loglikelihood = -1456.7945225269002, backtracks = 0, tol = 0.02559275529866366 Iteration 4: loglikelihood = -1456.711941254533, backtracks = 0, tol = 0.002548887388401707 Iteration 5: loglikelihood = -1456.7106729587263, backtracks = 0, tol = 0.0003318110343994027 Iteration 6: loglikelihood = -1456.710650911559, backtracks = 0, tol = 4.613991889536108e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05415201187133789 Final loglikelihood: -1456.710650911559 SNP PVE: 0.9293095446047375 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 780 -1.60398 2 │ 1147 -0.369697 3 │ 4018 1.3305 4 │ 5937 -0.639198 5 │ 6321 1.99649 6 │ 6343 -1.58639 7 │ 6743 0.655628 8 │ 6768 0.250673 9 │ 8316 -1.28778 10 │ 8728 0.365504 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.021111Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 4.1s **** 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 = -5915.371819627611, backtracks = 0, tol = 0.5283594138280019 Iteration 2: loglikelihood = -2878.214945213806, backtracks = 0, tol = 0.07834820784864545 Iteration 3: loglikelihood = -1815.7629718144783, backtracks = 0, tol = 0.08213473490418659 Iteration 4: loglikelihood = -1518.118482348366, backtracks = 0, tol = 0.070074421474272 Iteration 5: loglikelihood = -1473.6684033137788, backtracks = 0, tol = 0.04507275397450132 Iteration 6: loglikelihood = -1437.567979096588, backtracks = 0, tol = 0.05994755205481611 Iteration 7: loglikelihood = -1412.4472905275127, backtracks = 0, tol = 0.03655480862347832 Iteration 8: loglikelihood = -1411.2398325618626, backtracks = 1, tol = 0.120011996405704 Iteration 9: loglikelihood = -1390.3050977076552, backtracks = 0, tol = 0.06034207205122885 Iteration 10: loglikelihood = -1377.7706820573346, backtracks = 0, tol = 0.026760017924316107 Iteration 11: loglikelihood = -1373.1210395510245, backtracks = 1, tol = 0.023878466342869158 Iteration 12: loglikelihood = -1370.3491977886792, backtracks = 1, tol = 0.016809735539265163 Iteration 13: loglikelihood = -1368.9846740151806, backtracks = 1, tol = 0.01296097727824007 Iteration 14: loglikelihood = -1368.2254914741202, backtracks = 1, tol = 0.006621120242727418 Iteration 15: loglikelihood = -1367.8326637413709, backtracks = 0, tol = 0.008003192877832762 Iteration 16: loglikelihood = -1367.5448557810735, backtracks = 0, tol = 0.0048487107809160965 Iteration 17: loglikelihood = -1367.3352996573274, backtracks = 0, tol = 0.005247762285641896 Iteration 18: loglikelihood = -1367.1737162046097, backtracks = 0, tol = 0.0035520528935694758 Iteration 19: loglikelihood = -1367.0514887575343, backtracks = 0, tol = 0.0038288202109162143 Iteration 20: loglikelihood = -1366.9558362000669, backtracks = 0, tol = 0.002726851620399749 Iteration 21: loglikelihood = -1366.8820284485566, backtracks = 0, tol = 0.002859605255787813 Iteration 22: loglikelihood = -1366.8237833195726, backtracks = 0, tol = 0.0021214836009901686 Iteration 23: loglikelihood = -1366.7783107611642, backtracks = 0, tol = 0.00217674359787761 Iteration 24: loglikelihood = -1366.7422416219167, backtracks = 0, tol = 0.001665596603659387 Iteration 25: loglikelihood = -1366.7138723009575, backtracks = 0, tol = 0.0016778617361074485 Iteration 26: loglikelihood = -1366.6912969925452, backtracks = 0, tol = 0.0013151903023822637 Iteration 27: loglikelihood = -1366.6734535569876, backtracks = 0, tol = 0.0013048021715914712 Iteration 28: loglikelihood = -1366.659225301138, backtracks = 0, tol = 0.0010424351794641594 Iteration 29: loglikelihood = -1366.647941578998, backtracks = 0, tol = 0.0010212211032537954 Iteration 30: loglikelihood = -1366.6389322095788, backtracks = 0, tol = 0.0008283707115234951 Iteration 31: loglikelihood = -1366.6317705210067, backtracks = 0, tol = 0.0008030935457733282 Iteration 32: loglikelihood = -1366.6260475256763, backtracks = 0, tol = 0.0006594429747988226 Iteration 33: loglikelihood = -1366.621490570629, backtracks = 0, tol = 0.0006338430165340048 Iteration 34: loglikelihood = -1366.6178470699697, backtracks = 0, tol = 0.0005256335069968173 Iteration 35: loglikelihood = -1366.6149423632708, backtracks = 0, tol = 0.0005016546240513829 Iteration 36: loglikelihood = -1366.612619096579, backtracks = 0, tol = 0.0004193637648557651 Iteration 37: loglikelihood = -1366.610765240564, backtracks = 0, tol = 0.00039789559580356924 Iteration 38: loglikelihood = -1366.6092821366442, backtracks = 0, tol = 0.00033466908478889536 Iteration 39: loglikelihood = -1366.6080978870573, backtracks = 0, tol = 0.0003160252176909701 Iteration 40: loglikelihood = -1366.6071503356595, backtracks = 0, tol = 0.0002672342883032887 Iteration 41: loglikelihood = -1366.606393332727, backtracks = 0, tol = 0.00025133763468856356 Iteration 42: loglikelihood = -1366.6057875756997, backtracks = 0, tol = 0.0002134859268580417 Iteration 43: loglikelihood = -1366.605303443808, backtracks = 0, tol = 0.00020012259110288155 Iteration 44: loglikelihood = -1366.6049160155392, backtracks = 0, tol = 0.00017060921681764582 Iteration 45: loglikelihood = -1366.604606282349, backtracks = 0, tol = 0.00015949229207306925 Iteration 46: loglikelihood = -1366.604358407451, backtracks = 0, tol = 0.00013638246844348775 Iteration 47: loglikelihood = -1366.6041601951458, backtracks = 0, tol = 0.0001272070035378979 Iteration 48: loglikelihood = -1366.6040015647427, backtracks = 0, tol = 0.00010904656410990272 Iteration 49: loglikelihood = -1366.6038746933702, backtracks = 0, tol = 0.00010151930254888796 Iteration 50: loglikelihood = -1366.6037731558727, backtracks = 0, tol = 8.720535860952984e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.5s **** 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 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 = -1625.0969134879622, backtracks = 0, tol = 0.5466255116551365 Iteration 2: loglikelihood = -1520.1022299457986, backtracks = 0, tol = 0.15534796716693888 Iteration 3: loglikelihood = -1484.3504267485926, backtracks = 0, tol = 0.10207545956276243 Iteration 4: loglikelihood = -1475.1060329924396, backtracks = 0, tol = 0.09853928838386558 Iteration 5: loglikelihood = -1471.9790516056962, backtracks = 0, tol = 0.09801042688169005 Iteration 6: loglikelihood = -1471.5758169429203, backtracks = 1, tol = 0.010381104767382996 Iteration 7: loglikelihood = -1471.4241208623814, backtracks = 1, tol = 0.00584495512851128 Iteration 8: loglikelihood = -1471.3613120691166, backtracks = 1, tol = 0.004013802709799199 Iteration 9: loglikelihood = -1471.347113586146, backtracks = 2, tol = 0.0014768010647978234 Iteration 10: loglikelihood = -1471.338953398567, backtracks = 2, tol = 0.0011433121417757618 Iteration 11: loglikelihood = -1471.3342865232337, backtracks = 2, tol = 0.0008753602318930177 Iteration 12: loglikelihood = -1471.3316221500893, backtracks = 2, tol = 0.0006665855507397419 Iteration 13: loglikelihood = -1471.330102044968, backtracks = 2, tol = 0.0005061188670094551 Iteration 14: loglikelihood = -1471.3292350412632, backtracks = 2, tol = 0.00038361270852341894 Iteration 15: loglikelihood = -1471.3287406205886, backtracks = 2, tol = 0.0002904374218762814 Iteration 16: loglikelihood = -1471.3284586995735, backtracks = 2, tol = 0.00021973142733077464 Iteration 17: loglikelihood = -1471.3282979579383, backtracks = 2, tol = 0.00016615448101576334 Iteration 18: loglikelihood = -1471.328206312861, backtracks = 2, tol = 0.00012559646565935267 Iteration 19: loglikelihood = -1471.3281540640244, backtracks = 2, tol = 9.491435954954794e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1847.9775162124545, backtracks = 0, tol = 0.7808583357648938 Iteration 2: loglikelihood = -1503.7359491045236, backtracks = 0, tol = 0.1296015444674475 Iteration 3: loglikelihood = -1445.5668466209518, backtracks = 0, tol = 0.05074790444494735 Iteration 4: loglikelihood = -1442.676379100958, backtracks = 0, tol = 0.028383188834742643 Iteration 5: loglikelihood = -1440.8468547030009, backtracks = 0, tol = 0.026266157145375457 Iteration 6: loglikelihood = -1440.6097606222322, backtracks = 1, tol = 0.001429506464941075 Iteration 7: loglikelihood = -1440.547532209027, backtracks = 1, tol = 0.0007511265713016693 Iteration 8: loglikelihood = -1440.5312870033918, backtracks = 1, tol = 0.000395200135972268 Iteration 9: loglikelihood = -1440.527077788093, backtracks = 1, tol = 0.00020512639354237645 Iteration 10: loglikelihood = -1440.5259957029664, backtracks = 1, tol = 0.00010792599225175717 Iteration 11: loglikelihood = -1440.5257194457643, backtracks = 1, tol = 5.601543205427761e-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 = -1699.0071201998962, backtracks = 0, tol = 0.4159217458492163 Iteration 2: loglikelihood = -1477.3373015227123, backtracks = 0, tol = 0.10611754192255933 Iteration 3: loglikelihood = -1444.4280485489846, backtracks = 0, tol = 0.0625760263579327 Iteration 4: loglikelihood = -1440.9035224310076, backtracks = 0, tol = 0.03187768628522618 Iteration 5: loglikelihood = -1440.2905643840213, backtracks = 0, tol = 0.031605349908014585 Iteration 6: loglikelihood = -1440.2512201188656, backtracks = 1, tol = 0.0007247725644069588 Iteration 7: loglikelihood = -1440.2411941898984, backtracks = 1, tol = 0.0003709558937976688 Iteration 8: loglikelihood = -1440.238637569531, backtracks = 1, tol = 0.0001896394805745786 Iteration 9: loglikelihood = -1440.2379855787017, backtracks = 1, tol = 9.912423524892218e-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 11.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1501.4061063569009, backtracks = 0, tol = 0.1294943127237114 Iteration 2: loglikelihood = -1440.0652179049455, backtracks = 0, tol = 0.08574666417202652 Iteration 3: loglikelihood = -1399.6681097529463, backtracks = 0, tol = 0.0925139729078874 Iteration 4: loglikelihood = -1384.3649197597867, backtracks = 0, tol = 0.04891923430433842 Iteration 5: loglikelihood = -1356.7079698241791, backtracks = 0, tol = 0.10969457818532313 Iteration 6: loglikelihood = -1336.9670581000207, backtracks = 0, tol = 0.10062609981162168 Iteration 7: loglikelihood = -1334.5956872826139, backtracks = 0, tol = 0.08321911699138873 Iteration 8: loglikelihood = -1329.3584330048507, backtracks = 0, tol = 0.031066607696069226 Iteration 9: loglikelihood = -1324.2857784157734, backtracks = 0, tol = 0.054040060109311956 Iteration 10: loglikelihood = -1321.139008458536, backtracks = 0, tol = 0.03436826088140721 Iteration 11: loglikelihood = -1320.3585946763753, backtracks = 0, tol = 0.010264287409681648 Iteration 12: loglikelihood = -1320.0170291989932, backtracks = 1, tol = 0.007885226827318037 Iteration 13: loglikelihood = -1319.7299416345606, backtracks = 1, tol = 0.00731375436138118 Iteration 14: loglikelihood = -1317.051367156418, backtracks = 0, tol = 0.07006045307916046 Iteration 15: loglikelihood = -1314.1176011511986, backtracks = 0, tol = 0.03298646758559169 Iteration 16: loglikelihood = -1313.4382895923877, backtracks = 0, tol = 0.009966722542005929 Iteration 17: loglikelihood = -1313.240912942115, backtracks = 0, tol = 0.008816186539783603 Iteration 18: loglikelihood = -1313.1747081858794, backtracks = 0, tol = 0.004165556380662174 Iteration 19: loglikelihood = -1313.1475145357658, backtracks = 0, tol = 0.0028066069949265865 Iteration 20: loglikelihood = -1313.1355896091047, backtracks = 0, tol = 0.001947071642061157 Iteration 21: loglikelihood = -1313.1300698587086, backtracks = 0, tol = 0.0010671070120878087 Iteration 22: loglikelihood = -1313.127499423514, backtracks = 0, tol = 0.0009162145941037746 Iteration 23: loglikelihood = -1313.1262920970312, backtracks = 0, tol = 0.0004625982332353026 Iteration 24: loglikelihood = -1313.1257259485556, backtracks = 0, tol = 0.00043051866028084125 Iteration 25: loglikelihood = -1313.1254599136087, backtracks = 0, tol = 0.0002115767041227627 Iteration 26: loglikelihood = -1313.125334743308, backtracks = 0, tol = 0.00020220899247863487 Iteration 27: loglikelihood = -1313.1252758178236, backtracks = 0, tol = 9.853267586579692e-5 1.278093 seconds (4.59 M allocations: 81.122 MiB, 4.27% gc time, 50.66% 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 **** 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 = -1533.1412949062976, backtracks = 0, tol = 0.1294943127237114 Iteration 2: loglikelihood = -1491.2050967968944, backtracks = 0, tol = 0.10303624219248878 Iteration 3: loglikelihood = -1462.6372312590292, backtracks = 1, tol = 0.09141579274094712 Iteration 4: loglikelihood = -1448.7337419882329, backtracks = 0, tol = 0.10040765347168867 Iteration 5: loglikelihood = -1421.9286389142615, backtracks = 1, tol = 0.10650494382429494 Iteration 6: loglikelihood = -1406.4878458673118, backtracks = 0, tol = 0.0775355126881679 Iteration 7: loglikelihood = -1395.3731260876677, backtracks = 0, tol = 0.05047740855779469 Iteration 8: loglikelihood = -1384.2220599075495, backtracks = 0, tol = 0.0939821195082061 Iteration 9: loglikelihood = -1375.1265853721543, backtracks = 0, tol = 0.07264823740991203 Iteration 10: loglikelihood = -1369.0065139607902, backtracks = 0, tol = 0.016825485043464143 Iteration 11: loglikelihood = -1365.3846936683465, backtracks = 0, tol = 0.08021986454604217 Iteration 12: loglikelihood = -1360.2607040003516, backtracks = 0, tol = 0.07976017426453501 Iteration 13: loglikelihood = -1356.3553562066686, backtracks = 0, tol = 0.00670485607731922 Iteration 14: loglikelihood = -1353.1413054678424, backtracks = 0, tol = 0.001149994940079066 Iteration 15: loglikelihood = -1350.3155226357092, backtracks = 0, tol = 0.00028797140084317846 Iteration 16: loglikelihood = -1348.7031496553407, backtracks = 0, tol = 0.07681838165819459 Iteration 17: loglikelihood = -1346.0145822329148, backtracks = 0, tol = 0.07683057974151104 Iteration 18: loglikelihood = -1343.77521880972, backtracks = 0, tol = 0.006760788913637369 Iteration 19: loglikelihood = -1342.0297209227936, backtracks = 0, tol = 0.0013729499770988025 Iteration 20: loglikelihood = -1340.4368722827087, backtracks = 0, tol = 0.0005341052395367814 Iteration 21: loglikelihood = -1337.8936917279575, backtracks = 1, tol = 0.000281059298333437 Iteration 22: loglikelihood = -1337.3925034293413, backtracks = 0, tol = 0.06836245757903464 Iteration 23: loglikelihood = -1335.8705785500104, backtracks = 0, tol = 0.06838459071113792 Iteration 24: loglikelihood = -1334.5908496332056, backtracks = 0, tol = 0.006294399955512881 Iteration 25: loglikelihood = -1333.6552895406867, backtracks = 0, tol = 0.0013809136401544432 Iteration 26: loglikelihood = -1332.775279211376, backtracks = 0, tol = 0.0005665681143305938 Iteration 27: loglikelihood = -1331.2432578078212, backtracks = 1, tol = 0.0002238663455475161 Iteration 28: loglikelihood = -1330.7591239377593, backtracks = 0, tol = 0.06738882242722592 Iteration 29: loglikelihood = -1330.6823692193118, backtracks = 0, tol = 0.06740708853687594 Iteration 30: loglikelihood = -1329.7331747246085, backtracks = 0, tol = 0.007582044511348717 Iteration 31: loglikelihood = -1329.1345374443918, backtracks = 0, tol = 0.0017920736888054638 Iteration 32: loglikelihood = -1328.567583798276, backtracks = 0, tol = 0.0006695948469152454 Iteration 33: loglikelihood = -1327.8108852222203, backtracks = 0, tol = 0.0632473731753047 Iteration 34: loglikelihood = -1327.2262278306926, backtracks = 0, tol = 0.007437133015526776 Iteration 35: loglikelihood = -1326.7474867510864, backtracks = 0, tol = 0.0011608673106014542 Iteration 36: loglikelihood = -1326.3115510225575, backtracks = 0, tol = 0.00039626706589029686 Iteration 37: loglikelihood = -1325.8911970637064, backtracks = 0, tol = 0.0002180802081512599 Iteration 38: loglikelihood = -1325.2077386508824, backtracks = 1, tol = 6.501884347677033e-5 0.380236 seconds (1.46 M allocations: 26.741 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3711.3552, backtracks = 0, tol = 0.09710519100760136 Iteration 2: loglikelihood = -3657.3037, backtracks = 0, tol = 0.04753762091999703 Iteration 3: loglikelihood = -3650.3176, backtracks = 1, tol = 0.015696222775382487 Iteration 4: loglikelihood = -3634.8596, backtracks = 1, tol = 0.06013056617510385 Iteration 5: loglikelihood = -3632.312, backtracks = 1, tol = 0.007647037019799279 Iteration 6: loglikelihood = -3631.3828, backtracks = 1, tol = 0.004490155908548425 Iteration 7: loglikelihood = -3631.0781, backtracks = 1, tol = 0.0035728480841279516 Iteration 8: loglikelihood = -3630.9912, backtracks = 1, tol = 0.002091770668626658 Iteration 9: loglikelihood = -3630.9688, backtracks = 1, tol = 0.0011072909407370344 Iteration 10: loglikelihood = -3630.9646, backtracks = 1, tol = 0.0005484076306003091 Iteration 11: loglikelihood = -3630.962, backtracks = 2, tol = 0.00013966612386003677 Iteration 12: loglikelihood = -3630.9634, backtracks = 3, tol = 5.210630546266439e-5 26.787907 seconds (14.70 M allocations: 672.208 MiB, 2.21% gc time, 96.70% 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 = -3587.933, backtracks = 0, tol = 0.09710519100760136 Iteration 2: loglikelihood = -3453.702, backtracks = 0, tol = 0.0491308557900736 Iteration 3: loglikelihood = -3231.2583, backtracks = 1, tol = 0.015073695533126532 Iteration 4: loglikelihood = -2974.5537, backtracks = 1, tol = 0.009061334734379865 Iteration 5: loglikelihood = -2965.6174, backtracks = 0, tol = 0.10111388425253243 Iteration 6: loglikelihood = -2704.2537, backtracks = 0, tol = 0.10200473405954268 Iteration 7: loglikelihood = -2597.5176, backtracks = 0, tol = 0.09061908558668862 Iteration 8: loglikelihood = -2475.3257, backtracks = 0, tol = 0.09196073796329397 Iteration 9: loglikelihood = -2385.5354, backtracks = 0, tol = 0.09215297348798886 Iteration 10: loglikelihood = -2309.4255, backtracks = 0, tol = 0.09147465077651218 Iteration 11: loglikelihood = -2258.1753, backtracks = 0, tol = 0.01149255124614703 Iteration 12: loglikelihood = -2225.3645, backtracks = 0, tol = 0.08021243530138139 Iteration 13: loglikelihood = -2201.1594, backtracks = 0, tol = 0.08643945021679607 Iteration 14: loglikelihood = -2187.7607, backtracks = 0, tol = 0.008803842212892708 Iteration 15: loglikelihood = -2179.8335, backtracks = 0, tol = 0.08131655725768251 Iteration 16: loglikelihood = -2173.1814, backtracks = 1, tol = 0.005462315828226158 Iteration 17: loglikelihood = -2171.521, backtracks = 1, tol = 0.00310650478721402 Iteration 18: loglikelihood = -2171.163, backtracks = 1, tol = 0.0017040806667171077 Iteration 19: loglikelihood = -2171.104, backtracks = 1, tol = 0.0009446730308750107 Iteration 20: loglikelihood = -2171.101, backtracks = 1, tol = 0.0005561261203328568 Iteration 21: loglikelihood = -2171.1013, backtracks = 3, tol = 8.23609512715353e-5 0.167475 seconds (1.22 M allocations: 20.301 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 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 4.963422 seconds (1.04 M allocations: 134.490 MiB, 1.71% gc time, 90.04% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.4s 9.819512 seconds (4.00 M allocations: 82.422 MiB, 0.20% gc time, 0.69% compilation time) 5.319745 seconds (3.98 M allocations: 91.678 MiB, 1.17% gc time) 10.459405 seconds (20.38 M allocations: 438.853 MiB, 0.81% gc time, 17.15% compilation time: 78% of which was recompilation) 8.329426 seconds (20.18 M allocations: 434.189 MiB, 1.13% gc time) 35.598670 seconds (3.41 M allocations: 4.232 GiB, 6.60% gc time, 29.82% compilation time) 53.693398 seconds (72.50 k allocations: 183.670 MiB, 0.19% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m22.1s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 13.919 ms (78 allocations: 4.56 KiB) 4.418 μs (0 allocations: 0 bytes) 133.440 μs (4 allocations: 288 bytes) 7.293 μs (0 allocations: 0 bytes) 48.960 μs (2 allocations: 64 bytes) 30.700 μs (0 allocations: 0 bytes) 25.500 μs (0 allocations: 0 bytes) 24.170 μs (0 allocations: 0 bytes) 102.190 μs (0 allocations: 0 bytes) 38.759 ms (78 allocations: 4.56 KiB) 18.320 μs (0 allocations: 0 bytes) 176.600 μs (4 allocations: 288 bytes) 34.730 μs (0 allocations: 0 bytes) 203.150 μs (2 allocations: 64 bytes) 72.660 μs (0 allocations: 0 bytes) 125.430 μs (0 allocations: 0 bytes) 137.690 μs (0 allocations: 0 bytes) 180.940 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m09.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, 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 0.446686 seconds (44.66 k allocations: 5.384 MiB, 65.16% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 1.988129 seconds (259.66 k allocations: 167.697 MiB, 56.28% 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:57 Cross validating... 11%|███▌ | ETA: 0:01:06 Cross validating... 14%|████▋ | ETA: 0:00:50 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:19 Cross validating... 37%|███████████▋ | ETA: 0:00:17 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ 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validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 5114.119001357793 1 3812.205407230389 2 2780.596861268535 3 1852.4991019455554 4 1295.9977522075674 5 779.7843907845245 6 640.2189250003547 7 472.3240660216398 8 432.2977992355377 9 379.53938565120745 10 358.89626673442746 11 361.1228424104471 12 364.9441798628397 13 368.3004461249163 14 370.3988845506513 15 370.9966422474582 16 398.445704593835 17 403.30387987464786 18 381.25222178519914 19 413.47437146098184 20 381.054285066564 Best k = 10 12.817429 seconds (11.44 M allocations: 304.886 MiB, 0.98% gc time, 62.41% 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... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | 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... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross 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14 405.69271645921515 15 409.00732448390306 16 421.0928173270834 17 427.1909687099517 18 438.05467404778256 19 438.6619243352678 20 434.39503754747443 Best k = 10 4.627109 seconds (10.22 M allocations: 215.182 MiB, 0.97% gc time, 1.15% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.3s **** 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: 0:06:52 Cross validating... 8%|██▌ | ETA: 0:02:38 Cross validating... 13%|████▏ | ETA: 0:01:34 Cross validating... 17%|█████▋ | ETA: 0:01:06 Cross validating... 21%|██████▋ | ETA: 0:00:54 Cross validating... 24%|███████▋ | ETA: 0:00:45 Cross validating... 27%|████████▋ | ETA: 0:00:39 Cross validating... 30%|█████████▋ | ETA: 0:00:33 Cross validating... 33%|██████████▋ 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100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 0 1601.8678837890625 1 1299.3412155761719 2 1032.9082625732422 3 805.6059440917968 4 638.304627319336 5 532.3395666503907 6 440.2518867797852 7 381.70462469482425 8 370.37956787109374 9 355.00705987548827 10 347.2098912353516 11 349.4052075805664 12 354.2978171386719 13 353.5430628662109 14 355.1051276855469 15 368.89732501220703 16 359.9573059082031 17 378.7359197998047 18 365.53075360107425 19 405.35410711669925 20 371.11994787597655 Best k = 10 17.639935 seconds (12.88 M allocations: 319.641 MiB, 0.71% gc time, 83.88% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | 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Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1601.8678837890625 1 1299.3412155761719 2 1033.200218383789 3 805.6059440917968 4 645.2727537841797 5 542.8570721435547 6 452.61973126220704 7 395.5793032226562 8 386.488552734375 9 371.4181349487305 10 367.84575744628904 11 371.8211801147461 12 381.4020340576172 13 387.8214223632813 14 395.92788177490235 15 394.0081583251953 16 407.7718129882812 17 421.6182915649414 18 425.9050197143555 19 423.13576733398435 20 443.1784666137695 Best k = 10 2.848156 seconds (11.12 M allocations: 204.490 MiB, 2.03% gc time, 1.72% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 22.3s **** 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: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | 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... 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100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.9505824435598 1 415.5115994610923 2 381.00729747612706 3 325.7201486814305 4 301.28978589897906 5 253.5846835632238 6 236.58698453856204 7 226.4014846700631 8 231.47402289655858 9 237.82884159395056 10 234.39804980508657 11 239.95614615533702 12 255.46141251991406 13 238.7272884987956 14 259.30918556516997 15 276.65696554166533 16 264.9823723892673 17 262.0057280717681 18 314.5826900820626 19 273.599215535268 20 261.64014590164254 Best k = 7 8.245366 seconds (17.39 M allocations: 404.375 MiB, 1.19% gc time, 33.94% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 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0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.9505824435598 1 415.6142504247714 2 382.65409174853994 3 327.51016308823193 4 303.7638912761583 5 257.96489305276305 6 240.7387612456613 7 239.35452163694856 8 238.15771668280945 9 248.4907824763932 10 251.91380548183363 11 254.21284482721097 12 277.82309841547317 13 284.10905043809174 14 281.121034858231 15 300.3154348464976 16 305.62084054158123 17 309.3952707085483 18 297.03393866963904 19 308.02334539863097 20 312.3772355705934 Best k = 8 5.802071 seconds (17.97 M allocations: 374.521 MiB, 1.58% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:45 Cross validating... 6%|██ | ETA: 0:00:24 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross 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ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | 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 0 461.47758306689315 1 436.37549229058703 2 398.937247422022 3 381.5419196470382 4 353.2988197377953 5 343.1951409728243 6 334.1240125760013 7 332.59174522059163 8 331.60037660334655 9 330.8936581257876 10 341.00735318623515 11 334.85013501906457 12 331.8888626866336 13 350.5081272282063 14 338.5230626296459 15 342.7312802226711 16 339.1006609549921 17 345.76736759025994 18 383.4789683712969 19 340.13797825400206 20 342.8936634146983 Best k = 9 8.277636 seconds (16.20 M allocations: 384.219 MiB, 5.73% gc time, 30.75% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 461.47758306689315 1 437.102469757374 2 399.5692245038504 3 382.84499623853156 4 355.33342715498264 5 346.6562301030983 6 337.5590546158987 7 337.8002304418795 8 342.764907826839 9 343.5951642395384 10 349.1230262603487 11 357.46457933852037 12 364.19624768078216 13 373.2812101339113 14 368.36653506923324 15 384.63169281439394 16 393.5402225066317 17 388.9690684310391 18 405.22005388893126 19 400.4179192846193 20 401.11727552902806 Best k = 6 5.831108 seconds (17.20 M allocations: 353.377 MiB, 1.05% gc time, 0.82% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 16.4s **** 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: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 8%|██▌ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 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... 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 1124.0138960565466 1 805.5401720482221 2 733.6362572381787 3 606.5607545581283 4 537.9692438295522 5 474.06835665456055 6 465.31840093103597 7 426.28878834928753 8 449.697847623616 9 437.163815101903 10 455.71583132788595 11 438.5206359209119 12 436.47808284264676 13 435.6595110145662 14 434.57015321594633 15 447.99306104397846 16 459.10705510476464 17 468.91042988350375 18 438.917908913214 19 447.04682270600017 20 442.7514912342083 Best k = 7 8.215934 seconds (15.07 M allocations: 349.199 MiB, 1.04% gc time, 31.87% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 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 1124.0138960565466 1 772.5563717687738 2 701.6755816217756 3 581.9992315971356 4 518.0336182547453 5 476.52886484038356 6 441.4801486823359 7 442.23627722164264 8 445.7942991305748 9 460.1549498602671 10 464.0571403152072 11 452.191948350634 12 464.3975984802512 13 458.29884694430825 14 442.7326787154606 15 457.6490549563771 16 459.15196142088735 17 474.0906533753782 18 469.4575261670027 19 478.33113948283574 20 474.95152658089444 Best k = 6 5.557725 seconds (13.95 M allocations: 277.896 MiB, 0.95% gc time, 1.18% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:45 Cross validating... 8%|██▌ | ETA: 0:00:37 Cross validating... 11%|███▌ | ETA: 0:00:34 Cross validating... 13%|████▏ | 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48%|███████████████▎ | ETA: 0:00:24 Cross validating... 49%|███████████████▊ | ETA: 0:00:23 Cross validating... 51%|████████████████▎ | ETA: 0:00:23 Cross validating... 52%|████████████████▊ | ETA: 0:00:22 Cross validating... 54%|█████████████████▎ | ETA: 0:00:22 Cross validating... 56%|█████████████████▊ | ETA: 0:00:21 Cross validating... 57%|██████████████████▎ | ETA: 0:00:19 Cross validating... 59%|██████████████████▊ | ETA: 0:00:19 Cross validating... 60%|███████████████████▎ | ETA: 0:00:18 Cross validating... 62%|███████████████████▊ | ETA: 0:00:18 Cross validating... 63%|████████████████████▍ | ETA: 0:00:17 Cross validating... 65%|████████████████████▉ | ETA: 0:00:17 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:16 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:14 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:14 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:13 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:12 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:12 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:11 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:10 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:09 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: 0:00:06 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: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:02 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:49 Crossvalidation Results: k MSE 0 431.944547202335 1 330.2223139071697 2 281.10386258070963 3 256.31138326336935 4 237.12743610230888 5 210.69707559634816 6 203.6381786001199 7 191.35735656747852 8 191.40682301790724 9 192.1274175626594 10 190.5037867036148 11 191.9133610334868 12 190.67098215817046 13 191.76427133477785 14 191.43607362360524 15 192.40305236912886 16 195.92113560277312 17 198.5425268371107 18 196.66291279666765 19 200.02801661358652 20 201.39511796126925 Best k = 10 49.409729 seconds (154.31 M allocations: 3.941 GiB, 1.24% gc time, 4.51% 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 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0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 431.944547202335 1 330.01365160793034 2 281.10450525660457 3 256.56789036683665 4 238.32650952201232 5 213.13297523786298 6 206.63633724671698 7 195.27374411832676 8 197.53554743784525 9 201.2527001404917 10 203.04205844730814 11 205.67822009657647 12 205.36678768152169 13 206.19572497666599 14 210.15761494650513 15 211.42330916938596 16 219.6601950348221 17 220.16684832205613 18 231.48586408320202 19 230.33793234318466 20 229.09891169533944 Best k = 7 11.881480 seconds (35.72 M allocations: 740.591 MiB, 1.37% gc time, 0.54% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m01.7s **** 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... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | 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... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | 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 6.177011 seconds (16.96 M allocations: 336.738 MiB, 1.28% gc time, 47.25% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 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... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 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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 3.209831 seconds (16.17 M allocations: 286.672 MiB, 1.70% gc time, 1.95% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:21 Cross validating... 3%|█ | ETA: 0:00:57 Cross 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validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 1 2939.9847372711733 2 2757.3906268166065 3 2714.1546947762495 4 2682.392415952566 5 2628.4369508950754 6 2549.5993114606717 7 2496.064439695922 8 2505.5955800167753 9 2553.1748587987786 10 2577.15390957051 11 2604.903010077345 12 2621.7665790960655 13 2656.2228747938752 14 2643.3106865030136 15 2687.943033290439 16 2730.994580034921 17 2720.282807438136 18 2768.266080657015 19 2708.1023311419494 20 2725.5298032733713 Best k = 7 16.909552 seconds (301.58 k allocations: 199.856 MiB, 0.32% gc time, 9.95% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 21.7s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m05.4s **** 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... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross 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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 **** 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 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94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 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74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 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: 0:00:04 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: 0:00:03 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: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m26.6s 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] 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 [5] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:327 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:327 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:521 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 4.1s RNG of the outermost testset: Xoshiro(0xb53da4173a32948f, 0x4c08288194cc8e39, 0xd02620f68951448d, 0xd616c8d288649e5a, 0x84b4402e61eeea71) 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 1112.44s 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] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:326 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1220.51s: package tests unexpectedly errored