Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1808 (1cd77b505e*) started at 2026-02-26T23:25:01.047 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.46s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 6.16s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4481.0 ms ✓ BGEN 6751.0 ms ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 24398.0 ms ✓ MendelIHT 3 dependencies successfully precompiled in 48 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 63.81s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_CE24No/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.1 [2913bbd2] StatsBase v0.34.10 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v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.6s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.5s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.6s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.4s 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 = -1654.5010903567302, backtracks = 0, tol = 1.3275748053762157 Iteration 2: loglikelihood = -1448.724645084591, backtracks = 0, tol = 0.16374023291209097 Iteration 3: loglikelihood = -1439.3473989644126, backtracks = 0, tol = 0.03272312303729804 Iteration 4: loglikelihood = -1439.26074513646, backtracks = 0, tol = 0.0037039601722373867 Iteration 5: loglikelihood = -1438.9485389771826, backtracks = 0, tol = 0.04898688278942645 Iteration 6: loglikelihood = -1438.8454754239492, backtracks = 0, tol = 0.00307161322699123 Iteration 7: loglikelihood = -1438.8447413335098, backtracks = 0, tol = 0.0002638826813054217 Iteration 8: loglikelihood = -1438.8447345692014, backtracks = 0, tol = 2.4865588247692317e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06642794609069824 Final loglikelihood: -1438.8447345692014 SNP PVE: 0.912399647721466 Iterations: 8 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 470 0.55869 2 │ 582 -1.3579 3 │ 1849 -1.50367 4 │ 2677 1.39752 5 │ 4559 0.416273 6 │ 5908 -1.4442 7 │ 8046 0.300267 8 │ 8309 0.227202 9 │ 9144 -1.41592 10 │ 9602 0.121988 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0469545Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1542.1584036231825, backtracks = 0, tol = 0.3176435984443722 Iteration 2: loglikelihood = -1428.699944409752, backtracks = 0, tol = 0.059160800391346594 Iteration 3: loglikelihood = -1385.5845628759737, backtracks = 0, tol = 0.07628068785797673 Iteration 4: loglikelihood = -1358.5900632158146, backtracks = 0, tol = 0.08516017146768602 Iteration 5: loglikelihood = -1343.0181688808643, backtracks = 0, tol = 0.04667266498752653 Iteration 6: loglikelihood = -1335.7216739912128, backtracks = 1, tol = 0.05898327130923049 Iteration 7: loglikelihood = -1333.4492780177657, backtracks = 2, tol = 0.013163676547502634 Iteration 8: loglikelihood = -1331.7572654816188, backtracks = 2, tol = 0.013971266544515259 Iteration 9: loglikelihood = -1330.7106548251234, backtracks = 2, tol = 0.06042082348951974 Iteration 10: loglikelihood = -1330.4553209212181, backtracks = 0, tol = 0.06031893202589801 Iteration 11: loglikelihood = -1329.7535455280672, backtracks = 0, tol = 0.0083807558176873 Iteration 12: loglikelihood = -1329.5012640152445, backtracks = 1, tol = 0.0055136545921390554 Iteration 13: loglikelihood = -1329.2647687543774, backtracks = 2, tol = 0.006867590192536578 Iteration 14: loglikelihood = -1329.2593840643137, backtracks = 2, tol = 0.060982974055793 Iteration 15: loglikelihood = -1328.9271726520194, backtracks = 0, tol = 0.006123766154993864 Iteration 16: loglikelihood = -1328.8320349187234, backtracks = 0, tol = 0.0046316396190420415 Iteration 17: loglikelihood = -1328.7778945880818, backtracks = 0, tol = 0.0033863140279732735 Iteration 18: loglikelihood = -1327.1070256907042, backtracks = 0, tol = 0.057968058045179426 Iteration 19: loglikelihood = -1326.8470090959381, backtracks = 1, tol = 0.007075653327822324 Iteration 20: loglikelihood = -1326.7580718247552, backtracks = 1, tol = 0.004045273020305274 Iteration 21: loglikelihood = -1326.7341235492008, backtracks = 2, tol = 0.0012268373019644501 Iteration 22: loglikelihood = -1326.7137955815776, backtracks = 2, tol = 0.001445278731668922 Iteration 23: loglikelihood = -1326.7043290427569, backtracks = 3, tol = 0.0009464810007592384 Iteration 24: loglikelihood = -1326.6962301845983, backtracks = 3, tol = 0.0009666653375687529 Iteration 25: loglikelihood = -1326.6895626304254, backtracks = 3, tol = 0.0009467595026676955 Iteration 26: loglikelihood = -1326.6841990470455, backtracks = 3, tol = 0.0008985205641610695 Iteration 27: loglikelihood = -1326.6799412057028, backtracks = 3, tol = 0.0008368030913179136 Iteration 28: loglikelihood = -1326.676590313488, backtracks = 3, tol = 0.0007683310222234333 Iteration 29: loglikelihood = -1326.6739702339, backtracks = 3, tol = 0.000697950224141255 Iteration 30: loglikelihood = -1326.6719319303054, backtracks = 3, tol = 0.0006285008477747165 Iteration 31: loglikelihood = -1326.6703524143707, backtracks = 3, tol = 0.0005621960759869179 Iteration 32: loglikelihood = -1326.66913203321, backtracks = 3, tol = 0.0005002602795666557 Iteration 33: loglikelihood = -1326.6681911946912, backtracks = 3, tol = 0.00044342288108922606 Iteration 34: loglikelihood = -1326.6674670320997, backtracks = 3, tol = 0.000391874421298732 Iteration 35: loglikelihood = -1326.666910300713, backtracks = 3, tol = 0.00034556148153737387 Iteration 36: loglikelihood = -1326.6664826597355, backtracks = 3, tol = 0.0003042091833845593 Iteration 37: loglikelihood = -1326.6661543878167, backtracks = 3, tol = 0.0002674714772345943 Iteration 38: loglikelihood = -1326.6659025169708, backtracks = 3, tol = 0.00023494073189935498 Iteration 39: loglikelihood = -1326.665709337439, backtracks = 3, tol = 0.00020621472936593579 Iteration 40: loglikelihood = -1326.6655612156956, backtracks = 3, tol = 0.00018089444617136992 Iteration 41: loglikelihood = -1326.6654476683743, backtracks = 3, tol = 0.00015861148298177614 Iteration 42: loglikelihood = -1326.6653606412658, backtracks = 3, tol = 0.00013902199958986205 Iteration 43: loglikelihood = -1326.66529395042, backtracks = 3, tol = 0.00012181682425790389 Iteration 44: loglikelihood = -1326.665242850163, backtracks = 3, tol = 0.00010671531115790386 Iteration 45: loglikelihood = -1326.6652036999776, backtracks = 3, tol = 9.346816096821041e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1520.443032087484, backtracks = 0, tol = 0.3118980089688384 Iteration 2: loglikelihood = -1477.2850803373915, backtracks = 0, tol = 0.16407376183849984 Iteration 3: loglikelihood = -1463.4979144474537, backtracks = 0, tol = 0.10590416732963435 Iteration 4: loglikelihood = -1462.5768503407264, backtracks = 0, tol = 0.10093983092716997 Iteration 5: loglikelihood = -1460.1358770346203, backtracks = 0, tol = 0.08963002903975965 Iteration 6: loglikelihood = -1459.3919683748147, backtracks = 0, tol = 0.08975498530615557 Iteration 7: loglikelihood = -1459.296291911113, backtracks = 1, tol = 0.003945669644586395 Iteration 8: loglikelihood = -1459.2659169293024, backtracks = 1, tol = 0.0025744749019928933 Iteration 9: loglikelihood = -1458.662760852992, backtracks = 1, tol = 0.06702426526031259 Iteration 10: loglikelihood = -1458.5755906648826, backtracks = 1, tol = 0.004917881134065584 Iteration 11: loglikelihood = -1458.553239449421, backtracks = 1, tol = 0.002456528101415214 Iteration 12: loglikelihood = -1458.5472774893253, backtracks = 1, tol = 0.0012436777381809446 Iteration 13: loglikelihood = -1458.5455785700708, backtracks = 1, tol = 0.0006351795272437697 Iteration 14: loglikelihood = -1458.545044101924, backtracks = 1, tol = 0.0005082511446593724 Iteration 15: loglikelihood = -1458.544864851876, backtracks = 1, tol = 0.0004060208470985933 Iteration 16: loglikelihood = -1458.5448343467494, backtracks = 2, tol = 0.0001240513997339648 Iteration 17: loglikelihood = -1458.544817385589, backtracks = 2, tol = 9.249196452060807e-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 = -1771.5219448901908, backtracks = 0, tol = 0.7793385444039893 Iteration 2: loglikelihood = -1465.6977399819689, backtracks = 0, tol = 0.11205654550837857 Iteration 3: loglikelihood = -1419.306192553913, backtracks = 0, tol = 0.05024958798638799 Iteration 4: loglikelihood = -1414.2311376202504, backtracks = 0, tol = 0.03107104229485553 Iteration 5: loglikelihood = -1414.0188132433875, backtracks = 0, tol = 0.002821096791795823 Iteration 6: loglikelihood = -1414.0157905174658, backtracks = 0, tol = 0.00028585564769490813 Iteration 7: loglikelihood = -1414.0157152922375, backtracks = 0, tol = 5.283243060153568e-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 = -1509.49679561895, backtracks = 0, tol = 0.21504621063762583 Iteration 2: loglikelihood = -1422.6563445043405, backtracks = 0, tol = 0.057530793768455706 Iteration 3: loglikelihood = -1415.5571153569772, backtracks = 0, tol = 0.0313728156357618 Iteration 4: loglikelihood = -1415.2979089631942, backtracks = 0, tol = 0.00323790915271072 Iteration 5: loglikelihood = -1414.248078973632, backtracks = 0, tol = 0.031127303142941567 Iteration 6: loglikelihood = -1414.1657181860833, backtracks = 0, tol = 0.0018485063521894672 Iteration 7: loglikelihood = -1414.1646443906939, backtracks = 0, tol = 0.00017738718171689206 Iteration 8: loglikelihood = -1414.164625880705, backtracks = 0, tol = 2.1088230268026105e-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 10.8s **** 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 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 = -1364.9213544858044, backtracks = 0, tol = 0.13441842483283536 Iteration 2: loglikelihood = -1341.9530960465147, backtracks = 0, tol = 0.06336648884514302 Iteration 3: loglikelihood = -1307.7713638479097, backtracks = 0, tol = 0.07952646554509829 Iteration 4: loglikelihood = -1295.0342680230917, backtracks = 0, tol = 0.08303535709832126 Iteration 5: loglikelihood = -1289.921778066861, backtracks = 0, tol = 0.0572164962437885 Iteration 6: loglikelihood = -1289.3840838031629, backtracks = 0, tol = 0.012258874500890722 Iteration 7: loglikelihood = -1289.1845779759292, backtracks = 0, tol = 0.01012229310270692 Iteration 8: loglikelihood = -1289.0999625467346, backtracks = 0, tol = 0.005077177221185431 Iteration 9: loglikelihood = -1289.062474979803, backtracks = 0, tol = 0.004189989009255481 Iteration 10: loglikelihood = -1289.0440573340402, backtracks = 0, tol = 0.002879742049774711 Iteration 11: loglikelihood = -1289.0337990702103, backtracks = 0, tol = 0.0019215955267755376 Iteration 12: loglikelihood = -1289.0270218492515, backtracks = 0, tol = 0.002086037036074209 Iteration 13: loglikelihood = -1289.0219238207765, backtracks = 0, tol = 0.0016018065704648974 Iteration 14: loglikelihood = -1289.017719040406, backtracks = 0, tol = 0.0017333636114812102 Iteration 15: loglikelihood = -1289.0141132959616, backtracks = 0, tol = 0.001432711002400378 Iteration 16: loglikelihood = -1289.0109565487346, backtracks = 0, tol = 0.0015023507156660299 Iteration 17: loglikelihood = -1289.0081808914522, backtracks = 0, tol = 0.0012734700902302656 Iteration 18: loglikelihood = -1289.0057336254981, backtracks = 0, tol = 0.0013208630128029523 Iteration 19: loglikelihood = -1289.003571163826, backtracks = 0, tol = 0.0011268698722949925 Iteration 20: loglikelihood = -1289.0016552520142, backtracks = 0, tol = 0.0011672161483160576 Iteration 21: loglikelihood = -1288.9999655682725, backtracks = 0, tol = 0.0009954424484133338 Iteration 22: loglikelihood = -1288.9984648491472, backtracks = 0, tol = 0.0010332753973812704 Iteration 23: loglikelihood = -1288.9971443320094, backtracks = 0, tol = 0.0008789376615772157 Iteration 24: loglikelihood = -1288.9959771461286, backtracks = 0, tol = 0.0009152235498518559 Iteration 25: loglikelihood = -1288.9949419259087, backtracks = 0, tol = 0.0007760752087431763 Iteration 26: loglikelihood = -1288.994027806585, backtracks = 0, tol = 0.0008107599469120705 Iteration 27: loglikelihood = -1288.9932186422695, backtracks = 0, tol = 0.0006853634066066289 Iteration 28: loglikelihood = -1288.9925022942612, backtracks = 0, tol = 0.0007181953647465244 Iteration 29: loglikelihood = -1288.991864979546, backtracks = 0, tol = 0.0006053766177004034 Iteration 30: loglikelihood = -1288.9913122007995, backtracks = 0, tol = 0.0006361439636088783 Iteration 31: loglikelihood = -1288.990810569112, backtracks = 0, tol = 0.0005348305068100091 Iteration 32: loglikelihood = -1288.9903749042978, backtracks = 0, tol = 0.0005634107430996504 Iteration 33: loglikelihood = -1288.9899844493573, backtracks = 0, tol = 0.0004725905076564857 Iteration 34: loglikelihood = -1288.989649379627, backtracks = 0, tol = 0.0004989446577000595 Iteration 35: loglikelihood = -1288.989341848256, backtracks = 0, tol = 0.00041766052064706505 Iteration 36: loglikelihood = -1288.989074922112, backtracks = 0, tol = 0.00044181449400883255 Iteration 37: loglikelihood = -1288.9888352673618, backtracks = 0, tol = 0.0003691672269760702 Iteration 38: loglikelihood = -1288.9886198059028, backtracks = 0, tol = 0.00039119317888613525 Iteration 39: loglikelihood = -1288.9884326438214, backtracks = 0, tol = 0.00032634474549954963 Iteration 40: loglikelihood = -1288.9882715749661, backtracks = 0, tol = 0.0003463456700960239 Iteration 41: loglikelihood = -1288.988127581295, backtracks = 0, tol = 0.000288520884656715 Iteration 42: loglikelihood = -1288.9880061710412, backtracks = 0, tol = 0.0003066187420954156 Iteration 43: loglikelihood = -1288.9878834377478, backtracks = 0, tol = 0.0002551051545287383 Iteration 44: loglikelihood = -1288.987783172074, backtracks = 0, tol = 0.0002714320382854882 Iteration 45: loglikelihood = -1288.9876942470119, backtracks = 0, tol = 0.00022557839385065273 Iteration 46: loglikelihood = -1288.987617158552, backtracks = 0, tol = 0.00024027011948615312 Iteration 47: loglikelihood = -1288.987543770253, backtracks = 0, tol = 0.00019948380214513658 Iteration 48: loglikelihood = -1288.9874818684202, backtracks = 0, tol = 0.00021267536321236647 Iteration 49: loglikelihood = -1288.9874350983887, backtracks = 0, tol = 0.00017641917525942666 Iteration 50: loglikelihood = -1288.9873891888074, backtracks = 0, tol = 0.00018824161484438958 Iteration 51: loglikelihood = -1288.9873373539492, backtracks = 0, tol = 0.0001560301684749685 Iteration 52: loglikelihood = -1288.987308383356, backtracks = 0, tol = 0.00016660851173760826 Iteration 53: loglikelihood = -1288.987270229172, backtracks = 0, tol = 0.00013800443838786892 Iteration 54: loglikelihood = -1288.987237335992, backtracks = 0, tol = 0.00014745641203129222 Iteration 55: loglikelihood = -1288.9872142886927, backtracks = 0, tol = 0.00012206653852971486 Iteration 56: loglikelihood = -1288.9871891504508, backtracks = 0, tol = 0.00013050186720619516 Iteration 57: loglikelihood = -1288.9871689991405, backtracks = 0, tol = 0.00010797346359069017 Iteration 58: loglikelihood = -1288.98715141073, backtracks = 0, tol = 0.00011549358330102985 Iteration 59: loglikelihood = -1288.9871344081828, backtracks = 0, tol = 9.551075351178064e-5 1.686830 seconds (8.26 M allocations: 138.975 MiB, 2.61% gc time, 36.87% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1431.5820239803595, backtracks = 0, tol = 0.13441842483283536 Iteration 2: loglikelihood = -1403.5060171873183, backtracks = 0, tol = 0.08066312159495805 Iteration 3: loglikelihood = -1378.1750353350149, backtracks = 0, tol = 0.08920058924883303 Iteration 4: loglikelihood = -1363.4876456184, backtracks = 0, tol = 0.049944379148267784 Iteration 5: loglikelihood = -1354.964478301426, backtracks = 0, tol = 0.018562873561163745 Iteration 6: loglikelihood = -1347.601400158775, backtracks = 0, tol = 0.011516837304826768 Iteration 7: loglikelihood = -1341.8010094410054, backtracks = 0, tol = 0.004434016330087203 Iteration 8: loglikelihood = -1336.8510188088717, backtracks = 0, tol = 0.002570062004879097 Iteration 9: loglikelihood = -1332.7459661743558, backtracks = 0, tol = 0.0017398901063161703 Iteration 10: loglikelihood = -1329.2139534211165, backtracks = 0, tol = 0.0012638582109307348 Iteration 11: loglikelihood = -1323.7906825960465, backtracks = 1, tol = 0.0006349873270937948 Iteration 12: loglikelihood = -1319.6114120015825, backtracks = 1, tol = 0.000589690993887358 Iteration 13: loglikelihood = -1316.3462211725853, backtracks = 1, tol = 0.0006384838857149589 Iteration 14: loglikelihood = -1313.7284710059196, backtracks = 1, tol = 0.0006021778247117859 Iteration 15: loglikelihood = -1311.6076349704674, backtracks = 1, tol = 0.0005518706501601135 Iteration 16: loglikelihood = -1309.847023668167, backtracks = 1, tol = 0.000495373953861564 Iteration 17: loglikelihood = -1308.4147417001511, backtracks = 1, tol = 0.0004420755607115249 Iteration 18: loglikelihood = -1307.2545771484902, backtracks = 1, tol = 0.0003918147400832583 Iteration 19: loglikelihood = -1306.5757820770966, backtracks = 1, tol = 0.00040051997818776734 Iteration 20: loglikelihood = -1306.5317418424254, backtracks = 3, tol = 0.00013972684861029687 Iteration 21: loglikelihood = -1311.7097049792726, backtracks = 3, tol = 0.0001863372740393158 Iteration 22: loglikelihood = -1311.3887574716143, backtracks = 0, tol = 0.08211080543736915 Iteration 23: loglikelihood = -1310.258029326271, backtracks = 0, tol = 0.010345949277916251 Iteration 24: loglikelihood = -1309.3716675656838, backtracks = 0, tol = 0.0012309164196773663 Iteration 25: loglikelihood = -1308.5766403814405, backtracks = 0, tol = 0.000784893478583711 Iteration 26: loglikelihood = -1307.0143627184725, backtracks = 0, tol = 0.07883679814472569 Iteration 27: loglikelihood = -1306.0444372471038, backtracks = 0, tol = 0.00731348120948829 Iteration 28: loglikelihood = -1305.4001712611523, backtracks = 0, tol = 0.002049752128841759 Iteration 29: loglikelihood = -1304.792258705885, backtracks = 0, tol = 0.0011593241919948636 Iteration 30: loglikelihood = -1304.2400338607818, backtracks = 0, tol = 0.00045985640725384243 Iteration 31: loglikelihood = -1303.3189462798223, backtracks = 1, tol = 0.00023861995030622239 Iteration 32: loglikelihood = -1302.673704676215, backtracks = 1, tol = 0.00018207101500515214 Iteration 33: loglikelihood = -1302.434893408025, backtracks = 1, tol = 0.00022249798939699594 Iteration 34: loglikelihood = -1310.182975293027, backtracks = 3, tol = 0.00011434803865947692 Iteration 35: loglikelihood = -1309.202740869234, backtracks = 0, tol = 0.0013090369001361273 Iteration 36: loglikelihood = -1308.3157807910748, backtracks = 0, tol = 0.00019409119210979283 Iteration 37: loglikelihood = -1306.7775633629958, backtracks = 1, tol = 0.00013904610583849355 Iteration 38: loglikelihood = -1306.0800228017342, backtracks = 0, tol = 0.0003372061994481733 Iteration 39: loglikelihood = -1305.6106159952706, backtracks = 1, tol = 0.000170269513364505 Iteration 40: loglikelihood = -1305.230687729482, backtracks = 1, tol = 0.00013608373146631507 Iteration 41: loglikelihood = -1305.065089720948, backtracks = 1, tol = 0.0001533337092104694 Iteration 42: loglikelihood = -1305.8617235704899, backtracks = 3, tol = 5.0227033112003786e-5 0.426198 seconds (1.94 M allocations: 36.353 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3665.0576, backtracks = 0, tol = 0.08568816594661025 Iteration 2: loglikelihood = -3630.99, backtracks = 0, tol = 0.044593083657464304 Iteration 3: loglikelihood = -3626.9429, backtracks = 1, tol = 0.009345441696386415 Iteration 4: loglikelihood = -3625.6685, backtracks = 1, tol = 0.00786927441250673 Iteration 5: loglikelihood = -3625.3335, backtracks = 1, tol = 0.0039065640282414955 Iteration 6: loglikelihood = -3625.2466, backtracks = 1, tol = 0.002093854339978734 Iteration 7: loglikelihood = -3625.2295, backtracks = 1, tol = 0.0010300077708690818 Iteration 8: loglikelihood = -3625.222, backtracks = 1, tol = 0.0005253292606869601 Iteration 9: loglikelihood = -3625.2202, backtracks = 1, tol = 0.0002589225322023216 Iteration 10: loglikelihood = -3625.2168, backtracks = 1, tol = 0.0001300897177109785 Iteration 11: loglikelihood = -3625.2236, backtracks = 3, tol = 1.6093330436533855e-5 25.510846 seconds (14.90 M allocations: 669.538 MiB, 1.20% gc time, 97.63% 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 = -3562.2625, backtracks = 0, tol = 0.08568816594661025 Iteration 2: loglikelihood = -3457.1536, backtracks = 0, tol = 0.04551590670095909 Iteration 3: loglikelihood = -3258.634, backtracks = 1, tol = 0.00935989726977094 Iteration 4: loglikelihood = -3025.5684, backtracks = 1, tol = 0.006484597622089024 Iteration 5: loglikelihood = -2973.5012, backtracks = 0, tol = 0.09153086075024791 Iteration 6: loglikelihood = -2789.875, backtracks = 0, tol = 0.10436288781248543 Iteration 7: loglikelihood = -2625.0828, backtracks = 0, tol = 0.09671415529946689 Iteration 8: loglikelihood = -2497.1318, backtracks = 0, tol = 0.08387850698599296 Iteration 9: loglikelihood = -2394.0898, backtracks = 0, tol = 0.08305051424452199 Iteration 10: loglikelihood = -2310.7383, backtracks = 0, tol = 0.09195323625462508 Iteration 11: loglikelihood = -2243.0928, backtracks = 0, tol = 0.0920323572787377 Iteration 12: loglikelihood = -2197.4297, backtracks = 0, tol = 0.08011332120488729 Iteration 13: loglikelihood = -2168.3281, backtracks = 0, tol = 0.08016154267858308 Iteration 14: loglikelihood = -2150.59, backtracks = 0, tol = 0.015506000115571685 Iteration 15: loglikelihood = -2141.0994, backtracks = 0, tol = 0.005353838807870601 Iteration 16: loglikelihood = -2136.05, backtracks = 0, tol = 0.002034656766495982 Iteration 17: loglikelihood = -2133.456, backtracks = 0, tol = 0.0008297989503965213 Iteration 18: loglikelihood = -2132.1577, backtracks = 0, tol = 0.0006348736193815718 Iteration 19: loglikelihood = -2131.5237, backtracks = 0, tol = 0.0003289307567413706 Iteration 20: loglikelihood = -2131.2185, backtracks = 0, tol = 0.00026557359107481205 Iteration 21: loglikelihood = -2131.074, backtracks = 0, tol = 0.00016752606850991043 Iteration 22: loglikelihood = -2131.0066, backtracks = 0, tol = 0.00012107130388620786 Iteration 23: loglikelihood = -2130.9722, backtracks = 0, tol = 8.081156129247646e-5 0.140132 seconds (1.08 M allocations: 17.873 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 30.5s **** 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 **** Initializing β to univariate regression values... 73%|█▌| ETA: 0:00:02Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 6.158534 seconds (1.23 M allocations: 141.789 MiB, 12.69% gc time, 93.08% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 6.6s 9.703407 seconds (4.00 M allocations: 82.517 MiB, 0.43% gc time, 0.65% compilation time) 5.624337 seconds (3.98 M allocations: 91.702 MiB, 1.02% gc time) 10.779103 seconds (20.41 M allocations: 439.424 MiB, 1.12% gc time, 18.08% compilation time: 80% of which was recompilation) 8.511023 seconds (20.18 M allocations: 434.188 MiB, 1.18% gc time) 41.428325 seconds (3.77 M allocations: 4.240 GiB, 10.76% gc time, 29.97% compilation time) 52.959542 seconds (71.97 k allocations: 183.464 MiB, 0.03% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m28.5s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.153 ms (78 allocations: 4.56 KiB) 5.041 μs (0 allocations: 0 bytes) 158.419 μs (4 allocations: 288 bytes) 6.530 μs (0 allocations: 0 bytes) 53.580 μs (2 allocations: 64 bytes) 32.699 μs (0 allocations: 0 bytes) 25.500 μs (0 allocations: 0 bytes) 24.399 μs (0 allocations: 0 bytes) 76.649 μs (0 allocations: 0 bytes) 34.634 ms (78 allocations: 4.56 KiB) 21.900 μs (0 allocations: 0 bytes) 161.918 μs (4 allocations: 288 bytes) 33.229 μs (0 allocations: 0 bytes) 242.068 μs (2 allocations: 64 bytes) 89.589 μs (0 allocations: 0 bytes) 131.299 μs (0 allocations: 0 bytes) 121.429 μs (0 allocations: 0 bytes) 189.008 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m36.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.442319 seconds (49.48 k allocations: 5.526 MiB, 62.56% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 2.186792 seconds (314.44 k allocations: 170.097 MiB, 64.60% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:49 Cross validating... 6%|██ | ETA: 0:01:53 Cross validating... 10%|███ | ETA: 0:01:14 Cross validating... 13%|████▏ | ETA: 0:00:54 Cross validating... 16%|█████▏ | ETA: 0:00:42 Cross validating... 19%|██████▏ | ETA: 0:00:35 Cross validating... 22%|███████▏ | ETA: 0:00:29 Cross validating... 25%|████████▏ | ETA: 0:00:25 Cross validating... 29%|█████████▏ | ETA: 0:00:22 Cross validating... 32%|██████████▏ | ETA: 0:00:19 Cross validating... 35%|███████████▏ | ETA: 0:00:17 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 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: 0:00:11 Crossvalidation Results: k MSE 0 3958.2067721274348 1 3319.656034185393 2 2481.404643880597 3 1863.661537944749 4 1251.8852009079064 5 563.3905257551997 6 460.94718931669547 7 398.60542216461386 8 368.4233149937834 9 351.82144370639 10 355.41312770582186 11 358.6159441987187 12 371.80781204093216 13 372.01671998391714 14 363.80917461614916 15 370.1319511449427 16 371.3199992155777 17 394.11105076280444 18 371.4981468553371 19 371.4404194967711 20 413.616308563136 Best k = 9 12.118712 seconds (11.71 M allocations: 304.800 MiB, 0.87% gc time, 62.08% 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... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross 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100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 3958.2067721274348 1 3324.1419366276787 2 2491.368804190997 3 1877.2792590516262 4 1262.6574044011602 5 571.4485317034649 6 467.58501890876045 7 403.9037237632376 8 374.92938780021626 9 360.94117829913193 10 370.66344848111925 11 378.54606560562644 12 385.67066599813734 13 389.31093683945744 14 395.18278234705787 15 412.44022182083745 16 412.0713283896515 17 429.60937082000123 18 422.68833211668465 19 419.31236013021555 20 433.58432890320637 Best k = 9 4.754033 seconds (10.84 M allocations: 228.481 MiB, 1.02% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.7s **** 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... 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92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 0 1481.258759765625 1 1249.6108459472657 2 992.3606506347656 3 814.2391735839843 4 622.5893096923828 5 511.50218597412106 6 411.9084706115723 7 362.5814059448242 8 337.97408569335937 9 322.7609576416016 10 328.1975518798828 11 326.61878845214846 12 330.515648651123 13 333.1162823486328 14 333.6913745117188 15 340.95011398315427 16 341.1774609375 17 361.6947911071777 18 356.20015838623044 19 356.28960556030273 20 358.73832427978516 Best k = 9 18.040491 seconds (12.49 M allocations: 309.262 MiB, 0.75% gc time, 85.32% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 24%|███████▋ | 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... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1481.258759765625 1 1253.0507751464845 2 994.0879583740234 3 815.0186047363281 4 625.8636935424804 5 515.575993347168 6 416.5768435668945 7 366.57330230712887 8 341.7419285583496 9 328.0911169433594 10 342.43272720336915 11 340.50700088500975 12 349.8592922973633 13 357.0057144165039 14 362.1804084777832 15 358.20938552856444 16 372.2623341369629 17 376.5735009765625 18 388.509970703125 19 390.6217837524414 20 394.9677235412598 Best k = 9 2.667157 seconds (10.95 M allocations: 201.123 MiB, 1.92% gc time, 1.64% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 22.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 5%|█▌ | ETA: 0:00:43 Cross validating... 8%|██▌ | ETA: 0:00:27 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 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: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:06 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | 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validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.7781434755103 1 428.52653156948367 2 391.57482467941406 3 345.25946614655174 4 311.0049613371891 5 260.9515897891772 6 260.3401326454357 7 257.9358329740002 8 255.42391422320534 9 257.56791653073157 10 264.29073058578916 11 264.0190470920757 12 259.7852254354691 13 267.11887922239606 14 291.1823827686872 15 287.95777818729243 16 324.6257138880578 17 327.5503251271194 18 296.38671814727354 19 305.5268718575825 20 302.9782541324077 Best k = 8 8.299599 seconds (17.62 M allocations: 411.787 MiB, 1.34% gc time, 32.86% 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... 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68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.7781434755103 1 429.93291438702647 2 394.0365903413621 3 364.07004045115804 4 316.3565439832105 5 268.7119029914256 6 268.95630923790804 7 266.9077471083231 8 270.2841950596944 9 271.84174795920484 10 282.00464796102426 11 283.8843403339061 12 291.03014723696754 13 319.059366063516 14 316.6494629558166 15 333.0916331325465 16 338.7298477698872 17 335.6884825486131 18 352.1733652870574 19 360.01478362268506 20 371.04190372537704 Best k = 7 5.795856 seconds (17.87 M allocations: 371.201 MiB, 1.29% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:51 Cross validating... 8%|██▌ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.3475333967079 1 425.18993167215706 2 397.0692373025365 3 380.69026328577854 4 351.61244862992095 5 336.8275923606568 6 338.6638543268393 7 337.24719805584016 8 333.81680314090084 9 335.79608470754806 10 329.9999117621164 11 355.26585458808177 12 352.61768994395425 13 356.2721612075034 14 339.18569378808206 15 338.9660848626059 16 383.01965223709306 17 350.09792993819434 18 374.05005777928847 19 392.0599817475803 20 349.19689422663777 Best k = 10 7.910699 seconds (16.59 M allocations: 395.465 MiB, 12.53% gc time, 35.68% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 462.3475333967079 1 426.7785635583987 2 398.8428375800487 3 383.0117618517486 4 354.63342281649693 5 340.05752488022995 6 346.2431666881636 7 343.17063567555704 8 349.551120263116 9 367.08812120293413 10 349.5391816561971 11 376.99198056105894 12 369.2941364078529 13 388.36577843748876 14 384.52694890264763 15 386.64434681398996 16 400.236945113582 17 418.511626527453 18 421.0329196060055 19 418.3130875453385 20 433.0189814372844 Best k = 5 4.397117 seconds (17.43 M allocations: 360.020 MiB, 2.01% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 757.6223921457681 1 641.2487641006708 2 585.5546914314775 3 485.49592403057875 4 426.29791842259476 5 387.2935134862375 6 386.1937471823761 7 390.05756563950655 8 399.39687081874143 9 392.60045045374284 10 394.55046871557903 11 389.8963092172374 12 412.7961899268955 13 400.11017714759294 14 406.7076048768777 15 402.7068315165856 16 405.1793670519485 17 405.84271226570775 18 420.76877006305415 19 435.40363003732136 20 418.27348189566055 Best k = 6 8.151353 seconds (16.18 M allocations: 390.607 MiB, 1.00% gc time, 32.43% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 757.6223921457681 1 631.5103570052966 2 573.2886053418122 3 498.51523265238245 4 429.2328351748831 5 392.31726325048214 6 395.3890319193405 7 404.34309478930476 8 413.34927185954564 9 416.5588062900136 10 424.7488795017561 11 415.47330634618345 12 433.12815324830876 13 439.01164782923166 14 441.5691427518015 15 442.46820331731533 16 441.15173974119534 17 438.420035160465 18 445.90720055039765 19 468.089192716217 20 466.34896346903713 Best k = 5 5.391858 seconds (15.40 M allocations: 317.803 MiB, 1.10% gc time, 1.10% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.9s **** 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: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 11%|███▌ | ETA: 0:00:26 Cross validating... 13%|████▏ | ETA: 0:00:29 Cross validating... 14%|████▋ | ETA: 0:00:26 Cross validating... 16%|█████▏ | ETA: 0:00:28 Cross validating... 17%|█████▋ | ETA: 0:00:29 Cross validating... 19%|██████▏ | ETA: 0:00:30 Cross validating... 21%|██████▋ | ETA: 0:00:32 Cross validating... 22%|███████▏ | ETA: 0:00:32 Cross validating... 24%|███████▋ | ETA: 0:00:33 Cross validating... 25%|████████▏ | ETA: 0:00:33 Cross validating... 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0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:44 Crossvalidation Results: k MSE 0 345.0968879944389 1 302.2385270211182 2 275.40667455413865 3 245.61735977823565 4 219.31642390211238 5 207.38498401399198 6 206.5848443028437 7 208.41036435781228 8 209.7196250129939 9 211.13883953598267 10 212.78219734331003 11 212.11746013179192 12 213.84833543480255 13 213.83575429570584 14 215.17990327342827 15 215.1042173846639 16 217.87560526625927 17 218.47501690516694 18 219.96575472182136 19 219.2169393646327 20 217.11022788969512 Best k = 6 44.699912 seconds (140.24 M allocations: 3.587 GiB, 1.19% gc time, 4.99% 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: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:07 Cross validating... 17%|█████▋ | ETA: 0:00:07 Cross validating... 19%|██████▏ | ETA: 0:00:07 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 25%|████████▏ | 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89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 345.0968879944389 1 302.51124432851134 2 276.7796547610789 3 247.79404993193424 4 222.01505625581137 5 209.96853812985037 6 209.75716536635912 7 214.46525383546552 8 216.95419094477052 9 220.99377808336612 10 226.39725348671323 11 227.85870593620396 12 231.0979309800028 13 238.2861836893706 14 240.2807224727726 15 244.3865219704544 16 248.0082681854836 17 246.04082400077905 18 250.6175654551161 19 258.3722687578509 20 263.10433740229274 Best k = 6 12.925369 seconds (41.46 M allocations: 871.142 MiB, 1.20% gc time, 0.51% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 58.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:07 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross 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90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 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 6.760027 seconds (17.00 M allocations: 337.200 MiB, 1.45% gc time, 41.80% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:02 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: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.909686 seconds (16.18 M allocations: 286.707 MiB, 1.48% gc time, 1.49% 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: 0:01:27 Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 4%|█▎ | ETA: 0:00:49 Cross validating... 5%|█▋ | ETA: 0:00:41 Cross validating... 6%|█▉ | ETA: 0:00:35 Cross validating... 7%|██▎ | 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Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 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: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:18 Crossvalidation Results: k MSE 1 2072.9323209655995 2 1920.6692219176812 3 1740.247727931925 4 1639.5507425578999 5 1553.9134899918558 6 1502.048928811429 7 1480.487126678334 8 1493.7541317641874 9 1489.3867370414068 10 1501.2997999912448 11 1511.5308496936727 12 1512.4830790982296 13 1527.8687281732425 14 1549.184793118591 15 1541.9594217653253 16 1556.8633910668882 17 1560.5094082469482 18 1565.7631085870255 19 1593.2877001492152 20 1585.490072112458 Best k = 7 18.772595 seconds (337.14 k allocations: 224.084 MiB, 0.56% gc time, 9.68% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 24.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m53.9s **** 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:15 Cross validating... 7%|██▎ | ETA: 0:00:15 Cross validating... 8%|██▌ | ETA: 0:00:14 Cross validating... 9%|██▉ | ETA: 0:00:15 Cross validating... 10%|███▎ | ETA: 0:00:16 Cross validating... 11%|███▌ | ETA: 0:00:17 Cross validating... 12%|███▉ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:21 Cross validating... 14%|████▌ | ETA: 0:00:21 Cross validating... 15%|████▊ | ETA: 0:00:21 Cross validating... 16%|█████▏ 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100%|████████████████████████████████| Time: 0:00:30 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:13 Cross validating... 3%|█ | ETA: 0:00:12 Cross validating... 4%|█▎ | ETA: 0:00:13 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ 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ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:05 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:05 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:04 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:03 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: 0:00:02 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: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:27 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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:14 Cross validating... 8%|██▌ | ETA: 0:00:14 Cross validating... 9%|██▉ | ETA: 0:00:16 Cross validating... 10%|███▎ | ETA: 0:00:17 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 12%|███▉ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 14%|████▌ | ETA: 0:00:19 Cross validating... 15%|████▊ | ETA: 0:00:20 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▌ | ETA: 0:00:22 Cross validating... 18%|█████▊ | ETA: 0:00:22 Cross validating... 19%|██████▏ | ETA: 0:00:22 Cross validating... 20%|██████▍ | ETA: 0:00:22 Cross validating... 21%|██████▊ | ETA: 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validating... 75%|████████████████████████ | ETA: 0:00:07 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:07 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:06 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:06 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:06 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:05 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:05 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:04 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:04 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:03 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: 0:00:02 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: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:28 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 1m41.6s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.9s RNG of the outermost testset: Xoshiro(0x6d69b11542b947a8, 0xb08a72a095cf4b76, 0x3949aa63d1a8d8f8, 0xa5f617c768b97356, 0x2734035df9858e3c) 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 1194.67s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1313.25s: package tests unexpectedly errored