Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2108 (df12394092*) started at 2026-04-30T23:32:20.522 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.11s ################################################################################ # 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 v4.5.2 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.24.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.1+0 [deac9b47] + LibCURL_jll v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 6.37s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.2 s ✓ BGEN 8.0 s ✓ VCFTools 27.8 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 25.9 s ✓ MendelIHT 4 dependencies successfully precompiled in 70 seconds. 170 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 96.72s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_8nSDcy/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.125 [38e38edf] GLM v1.9.4 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.2 [2913bbd2] StatsBase v0.34.10 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v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = cholesky!(A::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}, ::Val{true}; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:215 └ @ LinearAlgebra ./deprecated.jl:215 Test Summary: | Pass Total Time loglikelihood | 4 4 18.3s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.3s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.5s 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 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1537.7357188365838, backtracks = 0, tol = 1.108217453503396 Iteration 2: loglikelihood = -1436.8432967425392, backtracks = 0, tol = 0.12059937179333612 Iteration 3: loglikelihood = -1425.66626488133, backtracks = 0, tol = 0.05519167869686915 Iteration 4: loglikelihood = -1425.5500194763397, backtracks = 0, tol = 0.005156887562122563 Iteration 5: loglikelihood = -1425.549084341747, backtracks = 0, tol = 0.0004569664738333282 Iteration 6: loglikelihood = -1425.549071834833, backtracks = 0, tol = 4.126712396269585e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06598210334777832 Final loglikelihood: -1425.549071834833 SNP PVE: 0.8215180946993823 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 93 0.431555 2 │ 230 -0.129455 3 │ 2436 0.449161 4 │ 3937 -0.405656 5 │ 4201 -0.898942 6 │ 5128 0.345451 7 │ 5358 -1.11218 8 │ 7342 -0.208219 9 │ 7363 0.195401 10 │ 7373 -1.36761 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0815761Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1328.9511710484892, backtracks = 0, tol = 0.20102730548729297 Iteration 2: loglikelihood = -1310.9688654624824, backtracks = 0, tol = 0.05070349838320154 Iteration 3: loglikelihood = -1296.5074042814933, backtracks = 1, tol = 0.07883638541677086 Iteration 4: loglikelihood = -1291.656628296364, backtracks = 1, tol = 0.0293871585256584 Iteration 5: loglikelihood = -1289.991324394714, backtracks = 2, tol = 0.01410601759839097 Iteration 6: loglikelihood = -1288.8543121417697, backtracks = 2, tol = 0.013378551067030996 Iteration 7: loglikelihood = -1288.159859108692, backtracks = 2, tol = 0.010848292750833259 Iteration 8: loglikelihood = -1287.7449139144098, backtracks = 2, tol = 0.008572056282942374 Iteration 9: loglikelihood = -1287.5004906414304, backtracks = 2, tol = 0.006671954854442449 Iteration 10: loglikelihood = -1285.895279470779, backtracks = 2, tol = 0.058311364230711565 Iteration 11: loglikelihood = -1285.6918464515566, backtracks = 1, tol = 0.004756393382853832 Iteration 12: loglikelihood = -1285.6081120098474, backtracks = 2, tol = 0.0033802675017384804 Iteration 13: loglikelihood = -1285.5477199627423, backtracks = 2, tol = 0.003354967966004286 Iteration 14: loglikelihood = -1285.527441626269, backtracks = 3, tol = 0.0014160938066958755 Iteration 15: loglikelihood = -1285.5116859405318, backtracks = 3, tol = 0.0012574919701858487 Iteration 16: loglikelihood = -1285.4994959050816, backtracks = 3, tol = 0.0011102348373302597 Iteration 17: loglikelihood = -1285.490088599536, backtracks = 3, tol = 0.000976764587790018 Iteration 18: loglikelihood = -1285.482840385368, backtracks = 3, tol = 0.0008574022245546616 Iteration 19: loglikelihood = -1285.4772616646037, backtracks = 3, tol = 0.0007514818871155513 Iteration 20: loglikelihood = -1285.4729711448522, backtracks = 3, tol = 0.0006579334724709838 Iteration 21: loglikelihood = -1285.4696732448758, backtracks = 3, tol = 0.0005755643706439971 Iteration 22: loglikelihood = -1285.4671394650602, backtracks = 3, tol = 0.0005031907741500224 Iteration 23: loglikelihood = -1285.4651934812766, backtracks = 3, tol = 0.0004396962467140616 Iteration 24: loglikelihood = -1285.4636994007603, backtracks = 3, tol = 0.00038405533520260055 Iteration 25: loglikelihood = -1285.4625525874935, backtracks = 3, tol = 0.000335340296776812 Iteration 26: loglikelihood = -1285.4616725304122, backtracks = 3, tol = 0.000292719650829478 Iteration 27: loglikelihood = -1285.4609973169122, backtracks = 3, tol = 0.00025545284637034326 Iteration 28: loglikelihood = -1285.4604793593348, backtracks = 3, tol = 0.0002228832197551153 Iteration 29: loglikelihood = -1285.460082095435, backtracks = 3, tol = 0.00019443037522290892 Iteration 30: loglikelihood = -1285.4597774437293, backtracks = 3, tol = 0.00016958258742010696 Iteration 31: loglikelihood = -1285.4595438428657, backtracks = 3, tol = 0.00014788954091249083 Iteration 32: loglikelihood = -1285.4593647421152, backtracks = 3, tol = 0.00012895556445266474 Iteration 33: loglikelihood = -1285.4592274398858, backtracks = 3, tol = 0.00011243342824424948 Iteration 34: loglikelihood = -1285.4591221905418, backtracks = 3, tol = 9.801872070604752e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.4s **** 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 = -1438.8108106517182, backtracks = 0, tol = 0.19377920040504262 Iteration 2: loglikelihood = -1429.5787082013123, backtracks = 0, tol = 0.0967102851686223 Iteration 3: loglikelihood = -1428.135331503969, backtracks = 0, tol = 0.10250612958300336 Iteration 4: loglikelihood = -1422.0495961540564, backtracks = 0, tol = 0.04149799084441225 Iteration 5: loglikelihood = -1419.3332460617187, backtracks = 0, tol = 0.07160182156445358 Iteration 6: loglikelihood = -1418.7247081447838, backtracks = 1, tol = 0.0117781118331725 Iteration 7: loglikelihood = -1416.8496065557154, backtracks = 1, tol = 0.061063233321118425 Iteration 8: loglikelihood = -1414.7020186290133, backtracks = 0, tol = 0.08274616222397052 Iteration 9: loglikelihood = -1414.5243664901723, backtracks = 1, tol = 0.007323266314886472 Iteration 10: loglikelihood = -1413.749124096108, backtracks = 1, tol = 0.08077244959205247 Iteration 11: loglikelihood = -1413.738547171702, backtracks = 0, tol = 0.08034049834251827 Iteration 12: loglikelihood = -1413.7005709213224, backtracks = 1, tol = 0.0029007268503776634 Iteration 13: loglikelihood = -1413.688991752519, backtracks = 1, tol = 0.0015517377085152038 Iteration 14: loglikelihood = -1413.6459067262285, backtracks = 1, tol = 0.07611715967091146 Iteration 15: loglikelihood = -1413.5810973016753, backtracks = 1, tol = 0.004755793887636674 Iteration 16: loglikelihood = -1413.5641795258357, backtracks = 1, tol = 0.002347214916165093 Iteration 17: loglikelihood = -1413.5598042801853, backtracks = 1, tol = 0.0011309732204749109 Iteration 18: loglikelihood = -1413.558659290555, backtracks = 1, tol = 0.0005355099497811342 Iteration 19: loglikelihood = -1413.5583489038538, backtracks = 1, tol = 0.00024942106410955685 Iteration 20: loglikelihood = -1413.5582587297824, backtracks = 1, tol = 0.0001234204306754491 Iteration 21: loglikelihood = -1413.5582293872471, backtracks = 1, tol = 9.835840844325567e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1799.0603114943335, backtracks = 0, tol = 0.7889142990689512 Iteration 2: loglikelihood = -1448.721000877449, backtracks = 0, tol = 0.12469597594653879 Iteration 3: loglikelihood = -1404.408579573871, backtracks = 0, tol = 0.04980032479252396 Iteration 4: loglikelihood = -1402.4147612696038, backtracks = 0, tol = 0.032019625113617806 Iteration 5: loglikelihood = -1401.625618260915, backtracks = 0, tol = 0.0034968769336636207 Iteration 6: loglikelihood = -1400.9631646280225, backtracks = 0, tol = 0.029189872861815864 Iteration 7: loglikelihood = -1400.742550695374, backtracks = 0, tol = 0.0023879912407831364 Iteration 8: loglikelihood = -1400.7405292657813, backtracks = 0, tol = 0.00037898518629404077 Iteration 9: loglikelihood = -1400.7405040362023, backtracks = 0, tol = 2.4160799800205857e-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 = -1499.0889387348116, backtracks = 0, tol = 0.2949563233586517 Iteration 2: loglikelihood = -1409.322253063308, backtracks = 0, tol = 0.07407165030513313 Iteration 3: loglikelihood = -1400.9570281382314, backtracks = 0, tol = 0.036172761011802015 Iteration 4: loglikelihood = -1400.7510114366755, backtracks = 0, tol = 0.0034319898168808957 Iteration 5: loglikelihood = -1400.7480054700004, backtracks = 0, tol = 0.00045396103233146103 Iteration 6: loglikelihood = -1400.747955234412, backtracks = 0, tol = 6.019978231752161e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 11.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1469.3439479826093, backtracks = 0, tol = 0.1671621445208782 Iteration 2: loglikelihood = -1429.4645385917452, backtracks = 0, tol = 0.0644939029550493 Iteration 3: loglikelihood = -1394.900279103525, backtracks = 0, tol = 0.0734709779450252 Iteration 4: loglikelihood = -1384.9839590846696, backtracks = 0, tol = 0.07370629475692676 Iteration 5: loglikelihood = -1376.82708723746, backtracks = 0, tol = 0.06480032959499657 Iteration 6: loglikelihood = -1367.950843555247, backtracks = 0, tol = 0.06931744555843875 Iteration 7: loglikelihood = -1363.2849863736383, backtracks = 0, tol = 0.04550609133928941 Iteration 8: loglikelihood = -1362.4459396899624, backtracks = 0, tol = 0.018400592596345945 Iteration 9: loglikelihood = -1362.1927176032343, backtracks = 0, tol = 0.009070841039960748 Iteration 10: loglikelihood = -1362.1095665200855, backtracks = 0, tol = 0.006216643140610075 Iteration 11: loglikelihood = -1362.08037369204, backtracks = 0, tol = 0.0028417636561790093 Iteration 12: loglikelihood = -1362.0700932866785, backtracks = 0, tol = 0.0021962328994447333 Iteration 13: loglikelihood = -1362.0664149838167, backtracks = 0, tol = 0.000977674471626614 Iteration 14: loglikelihood = -1362.0651012078702, backtracks = 0, tol = 0.0007839593453983093 Iteration 15: loglikelihood = -1362.0646298837344, backtracks = 0, tol = 0.000345665947368315 Iteration 16: loglikelihood = -1362.0644609770889, backtracks = 0, tol = 0.00028076622750714794 Iteration 17: loglikelihood = -1362.0644003622294, backtracks = 0, tol = 0.000123375638886947 Iteration 18: loglikelihood = -1362.0643786204598, backtracks = 0, tol = 0.0001006680256536836 Iteration 19: loglikelihood = -1362.06437081811, backtracks = 0, tol = 4.418513736808078e-5 0.985739 seconds (2.13 M allocations: 43.020 MiB, 63.66% 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 = -1525.243559746016, backtracks = 0, tol = 0.1671621445208782 Iteration 2: loglikelihood = -1494.292345908353, backtracks = 0, tol = 0.09039327904031912 Iteration 3: loglikelihood = -1464.4644793235632, backtracks = 0, tol = 0.1000182565814758 Iteration 4: loglikelihood = -1456.6998514032155, backtracks = 0, tol = 0.11482635618507049 Iteration 5: loglikelihood = -1436.456712953734, backtracks = 0, tol = 0.11204441228002844 Iteration 6: loglikelihood = -1424.9594395232082, backtracks = 0, tol = 0.07366676830790167 Iteration 7: loglikelihood = -1417.7661722729254, backtracks = 0, tol = 0.07560915227785599 Iteration 8: loglikelihood = -1412.4392068542174, backtracks = 0, tol = 0.07501452540574173 Iteration 9: loglikelihood = -1406.3785316169617, backtracks = 0, tol = 0.07568804849349063 Iteration 10: loglikelihood = -1402.2109457076476, backtracks = 0, tol = 0.006423742049380814 Iteration 11: loglikelihood = -1398.8235684973624, backtracks = 0, tol = 0.0009430246175380468 Iteration 12: loglikelihood = -1395.867212094823, backtracks = 0, tol = 0.0004460014603495792 Iteration 13: loglikelihood = -1393.2959136922632, backtracks = 0, tol = 0.0005938568111785525 Iteration 14: loglikelihood = -1391.0318808363359, backtracks = 0, tol = 0.0004519519519177161 Iteration 15: loglikelihood = -1390.6532305811936, backtracks = 0, tol = 0.08076291058025088 Iteration 16: loglikelihood = -1388.563326068933, backtracks = 0, tol = 0.00861478943712499 Iteration 17: loglikelihood = -1385.6765615546913, backtracks = 0, tol = 0.0743795991382391 Iteration 18: loglikelihood = -1384.2453679385512, backtracks = 0, tol = 0.00764911472524115 Iteration 19: loglikelihood = -1382.9494707794295, backtracks = 0, tol = 0.0016242595047530788 Iteration 20: loglikelihood = -1381.783498737377, backtracks = 0, tol = 0.0006322099289175276 Iteration 21: loglikelihood = -1380.7110501019224, backtracks = 0, tol = 0.00020480694851797126 Iteration 22: loglikelihood = -1379.7296746319391, backtracks = 0, tol = 0.00031204169153813165 Iteration 23: loglikelihood = -1378.8271197627803, backtracks = 0, tol = 0.00026152353844477346 Iteration 24: loglikelihood = -1377.9967714392217, backtracks = 0, tol = 0.0002612336370054137 Iteration 25: loglikelihood = -1377.2295956558075, backtracks = 0, tol = 0.00023470531485387736 Iteration 26: loglikelihood = -1376.5197796919342, backtracks = 0, tol = 0.00022975391447767983 Iteration 27: loglikelihood = -1375.8607567951442, backtracks = 0, tol = 0.00021319230694368926 Iteration 28: loglikelihood = -1375.2479010064844, backtracks = 0, tol = 0.00020770294979641384 Iteration 29: loglikelihood = -1374.6763823965132, backtracks = 0, tol = 0.000195541449755041 Iteration 30: loglikelihood = -1374.142543271352, backtracks = 0, tol = 0.0001895778102582377 Iteration 31: loglikelihood = -1373.6427431446696, backtracks = 0, tol = 0.0001800276264858896 Iteration 32: loglikelihood = -1373.1740745084971, backtracks = 0, tol = 0.0001741087199845758 Iteration 33: loglikelihood = -1372.7337334630536, backtracks = 0, tol = 0.00016632082204171141 Iteration 34: loglikelihood = -1372.3193924671307, backtracks = 0, tol = 0.00016071571953613233 Iteration 35: loglikelihood = -1371.9288522625372, backtracks = 0, tol = 0.00015418009367035112 Iteration 36: loglikelihood = -1371.560235097949, backtracks = 0, tol = 0.00014899578176273562 Iteration 37: loglikelihood = -1371.2117890860375, backtracks = 0, tol = 0.00014339033032533888 Iteration 38: loglikelihood = -1370.8819872019337, backtracks = 0, tol = 0.00013865166271091045 Iteration 39: loglikelihood = -1370.5694152971002, backtracks = 0, tol = 0.00013376462733733817 Iteration 40: loglikelihood = -1370.2728216661258, backtracks = 0, tol = 0.00012945689821168758 Iteration 41: loglikelihood = -1369.9910515886938, backtracks = 0, tol = 0.0001251431912235968 Iteration 42: loglikelihood = -1369.7230710847991, backtracks = 0, tol = 0.00012123441378913445 Iteration 43: loglikelihood = -1369.467927715875, backtracks = 0, tol = 0.00011739050464910808 Iteration 44: loglikelihood = -1369.2247610060936, backtracks = 0, tol = 0.0001138428502487595 Iteration 45: loglikelihood = -1368.9927783098346, backtracks = 0, tol = 0.00011039200369212523 Iteration 46: loglikelihood = -1368.7712584841504, backtracks = 0, tol = 0.00010716745747959721 Iteration 47: loglikelihood = -1368.5595365654624, backtracks = 0, tol = 0.00010405084770768781 Iteration 48: loglikelihood = -1368.357004152109, backtracks = 0, tol = 0.00010111380802879987 Iteration 49: loglikelihood = -1368.1630993447811, backtracks = 0, tol = 9.828502680142905e-5 0.538373 seconds (1.75 M allocations: 31.740 MiB, 11.67% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3722.473, backtracks = 0, tol = 0.08931055209822077 Iteration 2: loglikelihood = -3681.4387, backtracks = 0, tol = 0.045378405803060504 Iteration 3: loglikelihood = -3676.9763, backtracks = 1, tol = 0.010834993265397868 Iteration 4: loglikelihood = -3675.665, backtracks = 1, tol = 0.007872568480033136 Iteration 5: loglikelihood = -3675.3123, backtracks = 1, tol = 0.0038988727939267744 Iteration 6: loglikelihood = -3675.2285, backtracks = 1, tol = 0.0020903018364189776 Iteration 7: loglikelihood = -3675.2068, backtracks = 1, tol = 0.0010263451136614948 Iteration 8: loglikelihood = -3660.4814, backtracks = 1, tol = 0.0694732532402538 Iteration 9: loglikelihood = -3658.2063, backtracks = 1, tol = 0.008865198237053357 Iteration 10: loglikelihood = -3657.55, backtracks = 1, tol = 0.004974716328831937 Iteration 11: loglikelihood = -3657.368, backtracks = 1, tol = 0.002441146415937895 Iteration 12: loglikelihood = -3657.3198, backtracks = 1, tol = 0.0011773246678882846 Iteration 13: loglikelihood = -3657.311, backtracks = 1, tol = 0.0005753316444829311 Iteration 14: loglikelihood = -3657.3093, backtracks = 1, tol = 0.00035584504333722105 Iteration 15: loglikelihood = -3657.3054, backtracks = 1, tol = 0.00020322120103506738 Iteration 16: loglikelihood = -3657.3052, backtracks = 1, tol = 0.00010782283987845304 Iteration 17: loglikelihood = -3657.3088, backtracks = 3, tol = 1.3723372403848948e-5 27.050885 seconds (18.03 M allocations: 730.044 MiB, 3.65% gc time, 94.47% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3608.6763, backtracks = 0, tol = 0.08931055209822077 Iteration 2: loglikelihood = -3490.4924, backtracks = 0, tol = 0.04645174760645656 Iteration 3: loglikelihood = -3268.0347, backtracks = 1, tol = 0.01071966977930592 Iteration 4: loglikelihood = -3034.2102, backtracks = 1, tol = 0.005792899172725373 Iteration 5: loglikelihood = -2941.9597, backtracks = 0, tol = 0.08086336982091484 Iteration 6: loglikelihood = -2789.2405, backtracks = 0, tol = 0.09835793762565649 Iteration 7: loglikelihood = -2653.7593, backtracks = 0, tol = 0.0867430829118967 Iteration 8: loglikelihood = -2537.4302, backtracks = 0, tol = 0.09619710662576043 Iteration 9: loglikelihood = -2427.515, backtracks = 0, tol = 0.09525775119318124 Iteration 10: loglikelihood = -2346.2234, backtracks = 0, tol = 0.08594509890558973 Iteration 11: loglikelihood = -2287.5125, backtracks = 0, tol = 0.08562523366263478 Iteration 12: loglikelihood = -2250.7832, backtracks = 0, tol = 0.08693063097696378 Iteration 13: loglikelihood = -2223.1987, backtracks = 0, tol = 0.09131561661617121 Iteration 14: loglikelihood = -2209.8823, backtracks = 0, tol = 0.09127484055121936 Iteration 15: loglikelihood = -2199.0479, backtracks = 0, tol = 0.09440384617844169 Iteration 16: loglikelihood = -2196.037, backtracks = 0, tol = 0.09424415795423534 Iteration 17: loglikelihood = -2191.3708, backtracks = 1, tol = 0.009956047848231755 Iteration 18: loglikelihood = -2190.264, backtracks = 1, tol = 0.004282744639091162 Iteration 19: loglikelihood = -2190.0227, backtracks = 1, tol = 0.0019386039636007028 Iteration 20: loglikelihood = -2189.9744, backtracks = 1, tol = 0.0009022893150771919 Iteration 21: loglikelihood = -2189.9648, backtracks = 1, tol = 0.00043532761082107 Iteration 22: loglikelihood = -2189.9626, backtracks = 1, tol = 0.00022839172109974943 Iteration 23: loglikelihood = -2189.9622, backtracks = 1, tol = 0.00012389128294746594 Iteration 24: loglikelihood = -2189.9624, backtracks = 3, tol = 1.7338478617023024e-5 0.232027 seconds (1.41 M allocations: 23.387 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 32.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 4.781766 seconds (1.15 M allocations: 137.126 MiB, 1.35% gc time, 89.11% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.2s 11.014313 seconds (4.00 M allocations: 82.499 MiB, 0.58% gc time, 0.57% compilation time) 5.808286 seconds (3.98 M allocations: 91.678 MiB, 0.23% gc time) 11.452140 seconds (20.41 M allocations: 439.461 MiB, 0.83% gc time, 15.22% compilation time: 78% of which was recompilation) 9.054202 seconds (20.18 M allocations: 434.186 MiB, 0.99% gc time) 40.158197 seconds (3.85 M allocations: 4.244 GiB, 10.31% gc time, 27.76% compilation time) 57.267016 seconds (70.38 k allocations: 183.439 MiB, 0.23% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m33.0s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.801 ms (78 allocations: 4.56 KiB) 4.234 μs (0 allocations: 0 bytes) 141.679 μs (4 allocations: 288 bytes) 6.768 μs (0 allocations: 0 bytes) 46.399 μs (2 allocations: 64 bytes) 29.390 μs (0 allocations: 0 bytes) 24.560 μs (0 allocations: 0 bytes) 28.560 μs (0 allocations: 0 bytes) 105.949 μs (0 allocations: 0 bytes) 38.055 ms (78 allocations: 4.56 KiB) 18.180 μs (0 allocations: 0 bytes) 164.389 μs (4 allocations: 288 bytes) 33.420 μs (0 allocations: 0 bytes) 233.879 μs (2 allocations: 64 bytes) 79.829 μs (0 allocations: 0 bytes) 123.150 μs (0 allocations: 0 bytes) 137.779 μs (0 allocations: 0 bytes) 198.989 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m18.7s **** 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 **** **** 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 0.430492 seconds (49.47 k allocations: 5.503 MiB, 60.81% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.003169 seconds (282.53 k allocations: 168.675 MiB, 53.34% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:45 Cross validating... 19%|██████▏ | ETA: 0:00:35 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:22 Cross validating... 32%|██████████▏ | ETA: 0:00:19 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 1909.238853861057 1 1332.783129505827 2 900.3924871531864 3 602.7506138388985 4 534.1645364744683 5 456.9422959426688 6 405.5043652826842 7 368.45034512053303 8 357.58067565329475 9 343.5891856082796 10 346.77677119407747 11 349.08168879381276 12 352.32771354640886 13 354.25753887589616 14 355.22494982727267 15 358.11695875594273 16 379.20621941205894 17 369.1137519558597 18 376.3747591624422 19 378.3165825664482 20 366.54153527543116 Best k = 9 12.677324 seconds (11.55 M allocations: 306.739 MiB, 1.80% gc time, 59.70% 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 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 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... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 1909.238853861057 1 1334.3108862469962 2 903.4697734530316 3 606.6819680298973 4 539.9804829335969 5 463.80246321695466 6 410.94922980853653 7 375.7093313417978 8 365.15775164137386 9 350.97761769222166 10 359.23799042621954 11 365.92540479859974 12 373.78142039430554 13 377.5644600570878 14 380.7455704622734 15 386.9242187805698 16 391.3811757127398 17 398.8798367443803 18 397.8033293215254 19 410.53855692952277 20 414.1063324850464 Best k = 9 4.698712 seconds (10.68 M allocations: 225.163 MiB, 0.95% gc time, 1.08% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.2s **** 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: 0:05:27 Cross validating... 10%|███ | ETA: 0:01:43 Cross validating... 13%|████▏ | ETA: 0:01:16 Cross validating... 17%|█████▋ | ETA: 0:00:53 Cross validating... 22%|███████▏ | ETA: 0:00:39 Cross validating... 27%|████████▋ | ETA: 0:00:31 Cross validating... 32%|██████████▏ | ETA: 0:00:25 Cross validating... 37%|███████████▋ | ETA: 0:00:20 Cross validating... 43%|█████████████▊ | ETA: 0:00:16 Cross validating... 48%|███████████████▎ | ETA: 0:00:13 Cross validating... 52%|████████████████▊ | ETA: 0:00:11 Cross validating... 57%|██████████████████▎ | ETA: 0:00:09 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 1494.5526452636718 1 1199.0427104492187 2 951.258173828125 3 797.1435096435548 4 625.5640584716797 5 505.94259332275385 6 418.9382634277344 7 373.7309626159668 8 342.78760220336915 9 345.9631118774414 10 346.55337008666993 11 349.8164137573242 12 350.37249197387695 13 353.4651879272461 14 351.8751675415039 15 357.86235525512694 16 379.3536486816406 17 369.9273492431641 18 380.6394177856445 19 383.4355258483887 20 385.7470408935547 Best k = 8 14.333898 seconds (12.88 M allocations: 317.886 MiB, 0.68% gc time, 81.77% 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... 10%|███ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1494.5526452636718 1 1199.0427104492187 2 952.2044452514649 3 800.0365028076172 4 626.6522004394532 5 507.04384954833984 6 420.749393157959 7 377.6464563903809 8 345.49550238037114 9 355.70632464599606 10 358.7113270263672 11 366.82569302368165 12 366.7519169311524 13 378.7285088806152 14 381.9181354675293 15 388.4360783081055 16 381.74212872314456 17 388.4481951904297 18 396.2723020324707 19 395.6266749572754 20 408.81143576049806 Best k = 8 2.609948 seconds (10.96 M allocations: 201.830 MiB, 2.92% gc time, 1.74% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 18.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross 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validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 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... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 460.8023448091852 1 407.4411729234042 2 364.11084745815043 3 343.03812472175116 4 335.8237589382585 5 330.6217769465451 6 317.4864492699389 7 322.69459274442454 8 327.56371806771347 9 326.3799859846312 10 331.3362065614984 11 323.52960887893107 12 326.3819997394719 13 337.735593182659 14 333.89950892189245 15 330.95265304053726 16 354.4279703851399 17 383.33364349744147 18 348.83299488225276 19 362.7040923610707 20 380.13250419442375 Best k = 6 8.278576 seconds (18.05 M allocations: 431.272 MiB, 0.91% gc time, 33.33% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 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: 0:00:04 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... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 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... 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... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 460.8023448091852 1 408.01595946979165 2 365.362213777621 3 344.1662045505891 4 338.1809528195937 5 336.7627691980572 6 323.86794665771407 7 336.57035973442606 8 347.0770357357673 9 349.50897540329015 10 354.42688643483814 11 348.9820039161214 12 361.3129138961032 13 388.9749673944822 14 393.200234711212 15 393.63669007206266 16 428.811840872948 17 437.274425910331 18 418.4942402575696 19 436.0769104923345 20 449.032454745133 Best k = 6 5.716661 seconds (17.79 M allocations: 369.160 MiB, 1.11% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:51 Cross validating... 6%|██ | ETA: 0:00:27 Cross validating... 10%|███ | ETA: 0:00:19 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:12 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 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92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.2908694288702 1 426.217019233627 2 403.3709437373369 3 371.8222100466471 4 361.5075501768695 5 351.0367942555756 6 338.19095798146986 7 334.12158004628714 8 335.6671990522971 9 337.8570099165947 10 341.545747908117 11 336.99678211935304 12 337.41009320327635 13 340.6125657382577 14 344.28441301777724 15 343.9392673000222 16 349.81171798491164 17 340.86040072992324 18 344.58926631574457 19 361.52235914496157 20 373.15239736161254 Best k = 7 9.142335 seconds (16.50 M allocations: 392.713 MiB, 9.99% gc time, 30.29% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 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Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.2908694288702 1 426.48005988173037 2 404.6482477259691 3 374.1998091218984 4 365.1685804881109 5 356.01261810479025 6 340.9478346961455 7 339.83971976819697 8 351.67414002059127 9 354.63419150107404 10 358.80296801678986 11 364.5742161411566 12 370.41171761732255 13 379.24551878228283 14 388.67642087675677 15 397.31681186517676 16 408.5337548647447 17 405.1823973452116 18 413.34370583096126 19 419.5604520862513 20 433.53791363387154 Best k = 7 6.086328 seconds (17.29 M allocations: 355.628 MiB, 0.94% gc time, 0.76% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 17.4s **** 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: 0:01:05 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:09 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 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100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 470.3718435529875 1 433.1706526498258 2 411.4254252403453 3 394.0049755077904 4 390.86931526959444 5 387.4252317693391 6 381.5454072992909 7 384.9573375300879 8 382.8396522663679 9 384.0988510587948 10 376.67814076040776 11 382.06907008444 12 389.1602806806106 13 392.67353435787686 14 398.9291392330758 15 383.67174130920705 16 391.5207183862213 17 384.5048328508858 18 388.9487713875685 19 384.6348037571278 20 382.422738820214 Best k = 10 8.557599 seconds (17.22 M allocations: 430.503 MiB, 1.01% gc time, 32.65% 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... 5%|█▌ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 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Results: k MSE 0 470.3718435529875 1 432.5339131665706 2 410.7971198691098 3 394.24903896449996 4 392.4334648173346 5 390.8117446070228 6 385.94283941263757 7 391.1710133404963 8 389.9673588827397 9 399.0902531794129 10 398.42456408903007 11 406.7630662308949 12 406.3494468696055 13 421.7762116900029 14 424.35091046889886 15 428.31853506184933 16 424.411226663285 17 423.4674620177659 18 439.36099426989017 19 433.5420369640208 20 440.0858483806825 Best k = 6 5.909147 seconds (16.91 M allocations: 359.144 MiB, 1.07% gc time, 1.09% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:06 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 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Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:41 Crossvalidation Results: k MSE 0 263.3276815517668 1 243.43361652078136 2 228.65831150818775 3 226.20579252970842 4 223.47048778225872 5 225.099432863284 6 222.52115622808765 7 222.7114192961215 8 225.04969076107602 9 225.81332601207276 10 226.1535380060094 11 226.6748069050243 12 225.35979724076594 13 225.84851656261998 14 230.91542214335053 15 229.9853960307922 16 230.82331964388325 17 234.21705932974476 18 235.20881514670265 19 229.60289332392364 20 237.48133722582887 Best k = 6 41.718247 seconds (132.24 M allocations: 3.450 GiB, 1.30% gc time, 5.79% 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... 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95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 0 263.3276815517668 1 243.3409237828766 2 228.8727484312383 3 228.0501116799418 4 225.96254944340276 5 233.96694009486316 6 232.8606482094184 7 229.44339013439696 8 235.51529303034766 9 236.78227204248537 10 240.6449903419982 11 241.7859569690089 12 241.93676770919643 13 244.69459899137905 14 247.76491426522523 15 255.48948150376498 16 251.5815271895878 17 250.6315527801732 18 267.81366093954944 19 260.67768678371954 20 276.20023103469794 Best k = 4 16.613218 seconds (56.80 M allocations: 1.199 GiB, 1.40% gc time, 0.39% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 58.7s **** 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: 0:01:09 Cross validating... 6%|██ | ETA: 0:00:36 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 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100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 7.144110 seconds (17.01 M allocations: 337.915 MiB, 1.54% gc time, 40.18% 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: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 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: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 4.145628 seconds (16.18 M allocations: 286.716 MiB, 1.23% gc time, 1.42% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 11.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:17 Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 4%|█▎ | ETA: 0:00:46 Cross validating... 5%|█▋ | ETA: 0:00:40 Cross validating... 6%|█▉ | ETA: 0:00:35 Cross validating... 7%|██▎ | ETA: 0:00:32 Cross validating... 8%|██▌ | ETA: 0:00:30 Cross validating... 9%|██▉ | ETA: 0:00:28 Cross validating... 10%|███▎ | ETA: 0:00:27 Cross validating... 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97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:19 Crossvalidation Results: k MSE 1 2829.3269072630396 2 2259.7736879739327 3 1679.9377721132332 4 1337.6867792271476 5 1230.0838826793238 6 1126.37385981975 7 1086.0271888233474 8 1055.8817573217398 9 1027.9455362976064 10 1039.1882193751665 11 1040.4582628781197 12 1042.0859253048136 13 1045.1443011923166 14 1046.0687513749695 15 1054.71623389776 16 1049.1833808762576 17 1052.1290624985072 18 1068.3664626571106 19 1068.3710293180081 20 1076.886470108006 Best k = 9 19.586957 seconds (347.84 k allocations: 251.088 MiB, 0.73% gc time, 7.82% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.6s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m48.9s **** 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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 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 validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | 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57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 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: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 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: 0:00:10 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 validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:18 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:16 Cross validating... 24%|███████▋ | ETA: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:15 Cross validating... 27%|████████▋ | ETA: 0:00:15 Cross validating... 28%|█████████ | ETA: 0:00:15 Cross validating... 29%|█████████▎ | ETA: 0:00:15 Cross validating... 30%|█████████▋ | ETA: 0:00:15 Cross validating... 31%|█████████▉ | ETA: 0:00:15 Cross 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67%|█████████████████████▌ | ETA: 0:00:07 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:05 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: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 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: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 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... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | 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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: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 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 1m25.7s 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] getproperty(x::Nothing, f::Symbol) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] collect(itr::Base.Generator{UnitRange{Int64}, MendelIHT.var"#convert_bgen_gt##0#convert_bgen_gt##1"}) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [18] _start() @ Base ./client.jl:593 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.0s RNG of the outermost testset: Xoshiro(0x324893369479dcc8, 0xd9fdfebbf9556239, 0x6ae8307cf3d34397, 0x8c05cd186e20447d, 0xaaf41d86467c34d1) 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 1099.74s 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:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1245.09s: package tests unexpectedly errored