Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2058 (afc71c255e*) started at 2026-04-19T23:34:31.405 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.02s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.5.2 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.24.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.1+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 6.08s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.3 s ✓ BGEN 8.4 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 27.2 s ✓ MendelIHT 3 dependencies successfully precompiled in 47 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 69.23s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_rXq6my/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.124 [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 v2.7.2 [2913bbd2] StatsBase v0.34.10 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v1.68.1+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = cholesky!(A::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}, ::Val{true}; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:215 └ @ LinearAlgebra ./deprecated.jl:215 Test Summary: | Pass Total Time loglikelihood | 4 4 17.6s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.5s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.5s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.3s **** 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 = -1724.6558526349593, backtracks = 0, tol = 2.4300259663949273 Iteration 2: loglikelihood = -1423.4206546402038, backtracks = 0, tol = 0.13926992325826051 Iteration 3: loglikelihood = -1374.727484511694, backtracks = 0, tol = 0.0535027894268261 Iteration 4: loglikelihood = -1372.7544678330594, backtracks = 0, tol = 0.008746986562578633 Iteration 5: loglikelihood = -1372.3394825249216, backtracks = 0, tol = 0.028846891428661346 Iteration 6: loglikelihood = -1371.9396834941292, backtracks = 0, tol = 0.028386186792162437 Iteration 7: loglikelihood = -1371.8654002636188, backtracks = 1, tol = 0.0009785793227574866 Iteration 8: loglikelihood = -1371.8461572237018, backtracks = 1, tol = 0.0004977771903871217 Iteration 9: loglikelihood = -1371.8411879705986, backtracks = 1, tol = 0.00025170015228791556 Iteration 10: loglikelihood = -1371.8399108841138, backtracks = 1, tol = 0.00012672380798126693 Iteration 11: loglikelihood = -1371.8395844328452, backtracks = 1, tol = 6.368532965405068e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.10360312461853027 Final loglikelihood: -1371.8395844328452 SNP PVE: 0.9505486604245371 Iterations: 11 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 642 1.19593 2 │ 2250 -0.105081 3 │ 3183 0.111183 4 │ 3518 1.12444 5 │ 3566 -0.32279 6 │ 3982 -0.11332 7 │ 8180 0.238337 8 │ 9531 2.77699 9 │ 9602 -2.59219 10 │ 9956 -0.588611 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0281209Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2753.358682246026, backtracks = 0, tol = 0.4738347645620102 Iteration 2: loglikelihood = -1753.479307810878, backtracks = 0, tol = 0.06300019585971564 Iteration 3: loglikelihood = -1509.4949848153608, backtracks = 0, tol = 0.05306348519468546 Iteration 4: loglikelihood = -1432.5249195317872, backtracks = 0, tol = 0.07575320455069431 Iteration 5: loglikelihood = -1390.601441368779, backtracks = 0, tol = 0.07212863882134517 Iteration 6: loglikelihood = -1361.876709540612, backtracks = 0, tol = 0.040749485884773735 Iteration 7: loglikelihood = -1344.2132294970102, backtracks = 0, tol = 0.04364420809895762 Iteration 8: loglikelihood = -1329.591432789586, backtracks = 0, tol = 0.026468594469086837 Iteration 9: loglikelihood = -1323.1757033250874, backtracks = 2, tol = 0.0364243297556947 Iteration 10: loglikelihood = -1322.845299191069, backtracks = 0, tol = 0.0360922331219521 Iteration 11: loglikelihood = -1316.901863755534, backtracks = 0, tol = 0.03731348500521125 Iteration 12: loglikelihood = -1313.2369253684856, backtracks = 0, tol = 0.014376263023574695 Iteration 13: loglikelihood = -1311.229754631825, backtracks = 0, tol = 0.017020310811392433 Iteration 14: loglikelihood = -1309.8329593316323, backtracks = 0, tol = 0.009204823536076143 Iteration 15: loglikelihood = -1308.8885264942787, backtracks = 0, tol = 0.0105063187790203 Iteration 16: loglikelihood = -1308.201285411938, backtracks = 0, tol = 0.006559163557056896 Iteration 17: loglikelihood = -1307.7157829583057, backtracks = 0, tol = 0.007010584390779471 Iteration 18: loglikelihood = -1307.3583627505311, backtracks = 0, tol = 0.004793491847341253 Iteration 19: loglikelihood = -1307.1027290199597, backtracks = 0, tol = 0.004835038145553686 Iteration 20: loglikelihood = -1306.9146907553936, backtracks = 0, tol = 0.00351203163584863 Iteration 21: loglikelihood = -1306.7800258564198, backtracks = 0, tol = 0.003383652097302845 Iteration 22: loglikelihood = -1306.68157088777, backtracks = 0, tol = 0.002560810140328085 Iteration 23: loglikelihood = -1306.6112491585764, backtracks = 0, tol = 0.002381709660894604 Iteration 24: loglikelihood = -1304.7352189709297, backtracks = 0, tol = 0.037399414754316594 Iteration 25: loglikelihood = -1304.1098334980686, backtracks = 0, tol = 0.005817568204333616 Iteration 26: loglikelihood = -1303.8629509557384, backtracks = 0, tol = 0.0035491155754917188 Iteration 27: loglikelihood = -1303.7336675236224, backtracks = 0, tol = 0.002529066691049545 Iteration 28: loglikelihood = -1303.656903310413, backtracks = 0, tol = 0.0024806991032891622 Iteration 29: loglikelihood = -1303.6036170459006, backtracks = 0, tol = 0.001907237464962514 Iteration 30: loglikelihood = -1303.5661729005483, backtracks = 0, tol = 0.0017640240539683295 Iteration 31: loglikelihood = -1303.5389606301178, backtracks = 0, tol = 0.001385616922499772 Iteration 32: loglikelihood = -1303.5193983559898, backtracks = 0, tol = 0.0012558155624867132 Iteration 33: loglikelihood = -1303.505167958377, backtracks = 0, tol = 0.0009951711428280389 Iteration 34: loglikelihood = -1303.4949266080437, backtracks = 0, tol = 0.0008962135404208129 Iteration 35: loglikelihood = -1303.4875033896428, backtracks = 0, tol = 0.0007146623878686428 Iteration 36: loglikelihood = -1303.4821684030399, backtracks = 0, tol = 0.000640551445862763 Iteration 37: loglikelihood = -1303.4783151225308, backtracks = 0, tol = 0.0005134534236045642 Iteration 38: loglikelihood = -1303.4755499127407, backtracks = 0, tol = 0.0004580838135114136 Iteration 39: loglikelihood = -1303.4735584360221, backtracks = 0, tol = 0.00036874604105928107 Iteration 40: loglikelihood = -1303.4721310481368, backtracks = 0, tol = 0.0003276126809191423 Iteration 41: loglikelihood = -1303.4711053283543, backtracks = 0, tol = 0.00026459160873742223 Iteration 42: loglikelihood = -1303.470370834818, backtracks = 0, tol = 0.00023426529821003462 Iteration 43: loglikelihood = -1303.469843901135, backtracks = 0, tol = 0.0001896746301145553 Iteration 44: loglikelihood = -1303.4694668403745, backtracks = 0, tol = 0.0001674791913913752 Iteration 45: loglikelihood = -1303.4691966627074, backtracks = 0, tol = 0.0001361233267153689 Iteration 46: loglikelihood = -1303.469003429538, backtracks = 0, tol = 0.00011970797269627624 Iteration 47: loglikelihood = -1303.468865094284, backtracks = 0, tol = 9.756946295620393e-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 = -1607.7451862820226, backtracks = 0, tol = 0.4980126832973871 Iteration 2: loglikelihood = -1495.3235570332215, backtracks = 0, tol = 0.2067672153267252 Iteration 3: loglikelihood = -1460.8677777839225, backtracks = 0, tol = 0.13588294259522618 Iteration 4: loglikelihood = -1451.5619355392994, backtracks = 0, tol = 0.08032407042206335 Iteration 5: loglikelihood = -1444.8994741984213, backtracks = 0, tol = 0.0697499821636934 Iteration 6: loglikelihood = -1444.0230770631028, backtracks = 1, tol = 0.01311861110716342 Iteration 7: loglikelihood = -1443.663797945508, backtracks = 1, tol = 0.011714925752920166 Iteration 8: loglikelihood = -1443.603646439345, backtracks = 2, tol = 0.00284875787910263 Iteration 9: loglikelihood = -1443.5685955427216, backtracks = 2, tol = 0.002327099335594135 Iteration 10: loglikelihood = -1443.5485402624008, backtracks = 2, tol = 0.0017925148714324423 Iteration 11: loglikelihood = -1443.5371106707762, backtracks = 2, tol = 0.001359889411603897 Iteration 12: loglikelihood = -1443.5306089241913, backtracks = 2, tol = 0.001026975900192195 Iteration 13: loglikelihood = -1443.5269148077193, backtracks = 2, tol = 0.0007742910035925355 Iteration 14: loglikelihood = -1443.5248176710468, backtracks = 2, tol = 0.0005833573389961208 Iteration 15: loglikelihood = -1443.5236278567609, backtracks = 2, tol = 0.00043933748535858344 Iteration 16: loglikelihood = -1443.522953114449, backtracks = 2, tol = 0.0003307961846730743 Iteration 17: loglikelihood = -1443.5225705952216, backtracks = 2, tol = 0.0002490327437656138 Iteration 18: loglikelihood = -1443.5223537939657, backtracks = 2, tol = 0.00018745948933263234 Iteration 19: loglikelihood = -1443.522230939613, backtracks = 2, tol = 0.00014110007819031375 Iteration 20: loglikelihood = -1443.5221613315503, backtracks = 2, tol = 0.00010620018007702293 Iteration 21: loglikelihood = -1443.5221218963745, backtracks = 2, tol = 7.992963704328385e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1911.3735472871542, backtracks = 0, tol = 0.7364916861025813 Iteration 2: loglikelihood = -1504.8446847881596, backtracks = 0, tol = 0.1468597309978562 Iteration 3: loglikelihood = -1392.5029830249018, backtracks = 0, tol = 0.05737585044916152 Iteration 4: loglikelihood = -1382.8196975023639, backtracks = 0, tol = 0.028439199938085868 Iteration 5: loglikelihood = -1382.5028474237768, backtracks = 0, tol = 0.0031060977242835268 Iteration 6: loglikelihood = -1382.495049569439, backtracks = 0, tol = 0.000523500570479601 Iteration 7: loglikelihood = -1382.4948404801858, backtracks = 0, tol = 8.815666030398407e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** 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 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 = -1685.7850102298703, backtracks = 0, tol = 0.4870749477329684 Iteration 2: loglikelihood = -1413.043922908802, backtracks = 0, tol = 0.09245422144776133 Iteration 3: loglikelihood = -1384.7208536304129, backtracks = 0, tol = 0.0430222226644503 Iteration 4: loglikelihood = -1383.0751040823254, backtracks = 0, tol = 0.03248348086721289 Iteration 5: loglikelihood = -1382.9087515009703, backtracks = 0, tol = 0.0028077555961546746 Iteration 6: loglikelihood = -1382.9064629199083, backtracks = 0, tol = 0.0002954257576512318 Iteration 7: loglikelihood = -1382.9064223826197, backtracks = 0, tol = 4.732095214986169e-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 9.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1417.5097379133113, backtracks = 0, tol = 0.14861514255623934 Iteration 2: loglikelihood = -1391.2853485313567, backtracks = 0, tol = 0.09728009539226701 Iteration 3: loglikelihood = -1364.9047479243513, backtracks = 0, tol = 0.10197572578138865 Iteration 4: loglikelihood = -1349.3797745186853, backtracks = 0, tol = 0.09833468338545229 Iteration 5: loglikelihood = -1342.1145994620872, backtracks = 0, tol = 0.10087245001386028 Iteration 6: loglikelihood = -1341.2848525779018, backtracks = 0, tol = 0.0235672963036827 Iteration 7: loglikelihood = -1341.0827509573214, backtracks = 0, tol = 0.007175524000092707 Iteration 8: loglikelihood = -1341.0293093467715, backtracks = 0, tol = 0.006150118602460594 Iteration 9: loglikelihood = -1341.0148713304498, backtracks = 0, tol = 0.001984345640767953 Iteration 10: loglikelihood = -1341.010990902835, backtracks = 0, tol = 0.0016434173551520806 Iteration 11: loglikelihood = -1341.0102097021368, backtracks = 1, tol = 0.00026713219169832437 Iteration 12: loglikelihood = -1341.0097429220507, backtracks = 1, tol = 0.0003532670437043416 Iteration 13: loglikelihood = -1341.009620038896, backtracks = 1, tol = 0.00022242577367020337 Iteration 14: loglikelihood = -1341.0095869399233, backtracks = 1, tol = 9.076332160808242e-5 0.851805 seconds (1.87 M allocations: 38.999 MiB, 70.89% 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 = -1460.6743832994887, backtracks = 0, tol = 0.14861514255623934 Iteration 2: loglikelihood = -1438.0560992418143, backtracks = 0, tol = 0.09728009539226701 Iteration 3: loglikelihood = -1418.7559909149406, backtracks = 0, tol = 0.09875300852227883 Iteration 4: loglikelihood = -1400.9965966357079, backtracks = 0, tol = 0.09884256914272542 Iteration 5: loglikelihood = -1398.0442697176852, backtracks = 0, tol = 0.09730525483746158 Iteration 6: loglikelihood = -1386.3456430126514, backtracks = 0, tol = 0.09164991738876384 Iteration 7: loglikelihood = -1386.087301628944, backtracks = 0, tol = 0.0876479356075184 Iteration 8: loglikelihood = -1377.9371056725283, backtracks = 0, tol = 0.08746779169972621 Iteration 9: loglikelihood = -1371.6531988668248, backtracks = 1, tol = 0.011642339184764657 Iteration 10: loglikelihood = -1367.2522591210736, backtracks = 1, tol = 0.005782048278267416 Iteration 11: loglikelihood = -1364.1054457745086, backtracks = 1, tol = 0.002891365120208536 Iteration 12: loglikelihood = -1361.6669013380729, backtracks = 1, tol = 0.0014608901742629939 Iteration 13: loglikelihood = -1359.729609106371, backtracks = 1, tol = 0.0007447750618415955 Iteration 14: loglikelihood = -1358.140703464492, backtracks = 1, tol = 0.00038028569069468803 Iteration 15: loglikelihood = -1356.7757327202228, backtracks = 1, tol = 0.00019804145844730742 Iteration 16: loglikelihood = -1355.4836202467839, backtracks = 1, tol = 0.00016902912010562524 Iteration 17: loglikelihood = -1354.375522855568, backtracks = 1, tol = 0.000182663102316194 Iteration 18: loglikelihood = -1353.4312969321372, backtracks = 1, tol = 0.00018694962315636362 Iteration 19: loglikelihood = -1352.6247481880448, backtracks = 1, tol = 0.00018265892967835907 Iteration 20: loglikelihood = -1351.9319244654823, backtracks = 1, tol = 0.00017288220069994846 Iteration 21: loglikelihood = -1351.3328515154299, backtracks = 1, tol = 0.00016048139172035895 Iteration 22: loglikelihood = -1350.8112333317588, backtracks = 1, tol = 0.00014736230836948574 Iteration 23: loglikelihood = -1350.3538242254037, backtracks = 1, tol = 0.00013462328555964332 Iteration 24: loglikelihood = -1349.9498585628191, backtracks = 1, tol = 0.00012282593323947123 Iteration 25: loglikelihood = -1349.6611211823185, backtracks = 1, tol = 0.00011220487920214144 Iteration 26: loglikelihood = -1349.4099343260805, backtracks = 1, tol = 9.373764618949343e-5 0.276965 seconds (1.23 M allocations: 23.206 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 = -3614.4827, backtracks = 0, tol = 0.09006222784002962 Iteration 2: loglikelihood = -3561.9417, backtracks = 0, tol = 0.053143488874400104 Iteration 3: loglikelihood = -3553.7, backtracks = 1, tol = 0.015716047673930908 Iteration 4: loglikelihood = -3551.1223, backtracks = 1, tol = 0.012039089452126115 Iteration 5: loglikelihood = -3550.3909, backtracks = 1, tol = 0.005753082287409303 Iteration 6: loglikelihood = -3534.245, backtracks = 1, tol = 0.07355334442083267 Iteration 7: loglikelihood = -3532.203, backtracks = 0, tol = 0.013681761192666961 Iteration 8: loglikelihood = -3531.9348, backtracks = 0, tol = 0.005326777815961538 Iteration 9: loglikelihood = -3531.8677, backtracks = 0, tol = 0.0014388515820509045 Iteration 10: loglikelihood = -3531.852, backtracks = 0, tol = 0.0014019322707280967 Iteration 11: loglikelihood = -3531.85, backtracks = 0, tol = 0.00036261610047798163 Iteration 12: loglikelihood = -3531.848, backtracks = 0, tol = 0.0003721827958286209 Iteration 13: loglikelihood = -3531.849, backtracks = 3, tol = 1.1885821293364413e-5 27.196530 seconds (14.73 M allocations: 677.641 MiB, 3.71% gc time, 95.66% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3497.1455, backtracks = 0, tol = 0.09006222784002962 Iteration 2: loglikelihood = -3371.0662, backtracks = 0, tol = 0.05474712541035126 Iteration 3: loglikelihood = -3173.4534, backtracks = 1, tol = 0.015370228941959104 Iteration 4: loglikelihood = -2956.719, backtracks = 1, tol = 0.010950020824749706 Iteration 5: loglikelihood = -2730.784, backtracks = 1, tol = 0.005285969051192312 Iteration 6: loglikelihood = -2690.8535, backtracks = 0, tol = 0.10090411192401945 Iteration 7: loglikelihood = -2549.306, backtracks = 0, tol = 0.11919187854091484 Iteration 8: loglikelihood = -2444.629, backtracks = 0, tol = 0.11779182532033379 Iteration 9: loglikelihood = -2428.3186, backtracks = 0, tol = 0.1259707402072092 Iteration 10: loglikelihood = -2324.8186, backtracks = 0, tol = 0.12430170854359661 Iteration 11: loglikelihood = -2294.7803, backtracks = 0, tol = 0.11870247863394624 Iteration 12: loglikelihood = -2247.9927, backtracks = 0, tol = 0.1178650203752544 Iteration 13: loglikelihood = -2239.513, backtracks = 0, tol = 0.11117205272296754 Iteration 14: loglikelihood = -2224.3474, backtracks = 0, tol = 0.11086330867360912 Iteration 15: loglikelihood = -2209.1833, backtracks = 1, tol = 0.02385745768278115 Iteration 16: loglikelihood = -2201.0002, backtracks = 1, tol = 0.05802770222409603 Iteration 17: loglikelihood = -2198.952, backtracks = 1, tol = 0.02474308368950276 Iteration 18: loglikelihood = -2198.444, backtracks = 1, tol = 0.012808611937897327 Iteration 19: loglikelihood = -2198.2947, backtracks = 1, tol = 0.006744364963242676 Iteration 20: loglikelihood = -2198.2463, backtracks = 1, tol = 0.003610291491064877 Iteration 21: loglikelihood = -2198.232, backtracks = 1, tol = 0.001973191676403 Iteration 22: loglikelihood = -2198.2268, backtracks = 1, tol = 0.0010962733734857844 Iteration 23: loglikelihood = -2198.2114, backtracks = 1, tol = 0.0006153335171795515 Iteration 24: loglikelihood = -2198.2031, backtracks = 1, tol = 0.00034807881929728885 Iteration 25: loglikelihood = -2198.2014, backtracks = 1, tol = 0.00019747220940740076 Iteration 26: loglikelihood = -2198.1719, backtracks = 2, tol = 5.611563165814748e-5 0.200706 seconds (1.59 M allocations: 26.475 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 4.691705 seconds (1.15 M allocations: 137.112 MiB, 1.04% gc time, 91.39% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.1s 10.525767 seconds (4.00 M allocations: 82.500 MiB, 0.82% gc time, 0.61% compilation time) 5.396371 seconds (3.98 M allocations: 91.675 MiB, 0.19% gc time) 10.481917 seconds (20.41 M allocations: 439.475 MiB, 1.06% gc time, 16.67% compilation time: 79% of which was recompilation) 8.320541 seconds (20.18 M allocations: 434.188 MiB, 0.94% gc time) 38.226160 seconds (3.85 M allocations: 4.245 GiB, 10.26% gc time, 27.16% compilation time) 55.987176 seconds (70.38 k allocations: 183.439 MiB, 1.43% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m26.7s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.102 ms (78 allocations: 4.56 KiB) 4.204 μs (0 allocations: 0 bytes) 119.939 μs (4 allocations: 288 bytes) 5.766 μs (0 allocations: 0 bytes) 47.969 μs (2 allocations: 64 bytes) 30.840 μs (0 allocations: 0 bytes) 26.300 μs (0 allocations: 0 bytes) 29.409 μs (0 allocations: 0 bytes) 103.319 μs (0 allocations: 0 bytes) 38.833 ms (78 allocations: 4.56 KiB) 27.940 μs (0 allocations: 0 bytes) 153.188 μs (4 allocations: 288 bytes) 29.030 μs (0 allocations: 0 bytes) 201.788 μs (2 allocations: 64 bytes) 89.299 μs (0 allocations: 0 bytes) 126.238 μs (0 allocations: 0 bytes) 151.749 μs (0 allocations: 0 bytes) 196.128 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m20.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.439617 seconds (49.46 k allocations: 5.502 MiB, 63.59% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.6s **** 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 Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.943274 seconds (282.39 k allocations: 168.152 MiB, 56.13% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:41 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... 30%|█████████▋ | ETA: 0:00:20 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 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90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 6142.867068516929 1 3534.4266654665394 2 1348.853220819424 3 887.3291426059034 4 480.05604585741867 5 364.93403539435934 6 332.8873782254266 7 315.1831037756344 8 317.64919891735667 9 321.4705126108566 10 324.11964803050137 11 327.7033529199341 12 327.25464001711373 13 333.2924544645301 14 352.9837142104433 15 360.1530729755988 16 334.6137049640386 17 350.78291824317984 18 336.04267446997665 19 335.556286493345 20 371.224448801975 Best k = 7 12.486970 seconds (11.79 M allocations: 308.576 MiB, 1.43% gc time, 59.33% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 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: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 6142.867068516929 1 3544.741045849803 2 1358.7415379918723 3 895.3161863587594 4 486.0988834649718 5 371.01063377177843 6 338.27035257353754 7 320.7262967088156 8 326.0025835537185 9 337.2876372348968 10 342.1290759054042 11 354.68495405338143 12 352.29873273998146 13 368.17029204561805 14 365.3569556991612 15 373.7899087541242 16 370.0899052979116 17 375.25999670829697 18 381.38455980465665 19 381.447917898828 20 385.22262052971934 Best k = 7 5.054284 seconds (10.74 M allocations: 227.094 MiB, 0.89% gc time, 0.91% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:05:57 Cross validating... 8%|██▌ | ETA: 0:02:17 Cross validating... 14%|████▋ | ETA: 0:01:12 Cross validating... 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1687.6033742675781 1 1331.006035888672 2 1025.015342529297 3 834.1183255615234 4 678.5915557861329 5 584.6221239013672 6 447.0865593261718 7 389.5536657104492 8 353.67288568115237 9 352.56867602539063 10 343.20128601074214 11 343.9840926513672 12 346.21193518066406 13 352.2329663696289 14 360.25592388916016 15 353.1547747192383 16 356.3956490478516 17 384.9898409423828 18 387.4320050048828 19 377.5458517456055 20 359.2474739379883 Best k = 10 15.439701 seconds (12.92 M allocations: 321.325 MiB, 0.88% gc time, 82.73% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1687.6033742675781 1 1332.8293952636718 2 1025.944502685547 3 853.7298089599609 4 684.2426647949219 5 585.7186000976562 6 451.0610962524414 7 393.2904761352539 8 357.8271596069336 9 357.13869555664064 10 356.30953234863284 11 359.7060040893555 12 366.3278251953125 13 374.6603873291016 14 377.7141424560547 15 392.92931109619144 16 392.5845758666992 17 405.6343919067383 18 416.0642141723633 19 415.1116756591797 20 413.5738993530273 Best k = 10 2.568300 seconds (10.83 M allocations: 199.445 MiB, 1.78% gc time, 1.82% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:53 Cross validating... 6%|██ | ETA: 0:00:28 Cross validating... 8%|██▌ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 14%|████▋ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 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402.61166163904056 2 286.2749186929459 3 253.8991965854822 4 220.89228730191206 5 223.1971020458471 6 226.14522958387914 7 237.78858497930975 8 254.90548584603675 9 247.16835558799227 10 250.7340512110075 11 257.6442586419869 12 232.27950003463644 13 237.53521673962302 14 260.72689184206433 15 235.20708441061106 16 236.96607494375053 17 256.6446982345381 18 267.49460319686256 19 245.36406325687167 20 276.7108420944437 Best k = 4 8.029446 seconds (17.64 M allocations: 410.051 MiB, 1.23% gc time, 30.24% 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: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross 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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 0 462.20097964891323 1 405.29938634514144 2 291.4133657623366 3 259.164654032363 4 225.22138023085068 5 233.6800549059251 6 240.0311590480395 7 243.11520650311024 8 246.01055161369277 9 253.15489190572697 10 259.3046065492226 11 261.3791281914032 12 261.1584361205233 13 273.9363265197259 14 286.388543375637 15 294.95935240633605 16 298.18367505964056 17 285.89837242719614 18 313.82542158317705 19 319.25600616574354 20 319.4034809801261 Best k = 4 5.851290 seconds (17.60 M allocations: 364.357 MiB, 1.05% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.3s **** 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: 0:00:49 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:18 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: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 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: 0:00:04 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... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | 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... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.0206967554516 1 441.1071689122215 2 411.0012403150507 3 386.8219358577503 4 353.78177807178304 5 336.4922434441238 6 326.6394141259635 7 308.85010184861255 8 311.78608729859775 9 312.18438235127525 10 318.3248283448971 11 315.204666572757 12 317.8569696841779 13 321.7993133803179 14 322.09988239063966 15 338.20341150827073 16 323.62812686314595 17 351.61411168910575 18 335.21797270874197 19 327.49495237046216 20 374.8695841608827 Best k = 7 7.760230 seconds (16.35 M allocations: 386.577 MiB, 13.04% gc time, 35.47% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 462.0206967554516 1 442.2437706218095 2 413.1425278703766 3 389.966912108456 4 358.21249392119336 5 342.2416524401136 6 333.1051964102928 7 317.4733083737731 8 325.83727200891826 9 331.47715489025455 10 328.8028850986745 11 342.47028084151 12 353.0698183132032 13 360.27727326720935 14 364.5193064452063 15 367.5658366058931 16 378.5504850575224 17 400.5951228302432 18 383.06292831559676 19 395.9494333066817 20 402.8472250723041 Best k = 7 4.326682 seconds (17.22 M allocations: 354.362 MiB, 1.27% gc time, 1.04% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:04 Cross validating... 5%|█▌ | ETA: 0:00:45 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:21 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 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%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1313.2966893021835 1 836.786836437884 2 504.9617672515685 3 434.3067880552095 4 354.97771987229544 5 347.9798721120831 6 358.25656951435644 7 358.4240306829343 8 358.5196872459779 9 360.7377715779235 10 383.3881274257758 11 387.2695649032115 12 378.75990835944015 13 371.97743915559715 14 375.7974985437671 15 382.88947268528426 16 376.43475070434056 17 404.5262541223047 18 425.3017382281464 19 406.61523904207513 20 378.1811244894776 Best k = 5 8.496430 seconds (15.48 M allocations: 354.259 MiB, 1.07% gc time, 32.60% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:04 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 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81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1313.2966893021835 1 778.2004473813461 2 491.4965935275784 3 434.4294246404256 4 366.67210988857687 5 358.04483074019777 6 361.15686785130595 7 371.12185676617344 8 367.0058733016725 9 372.04852453918375 10 379.6529881999052 11 387.3760341247878 12 389.01527548922127 13 396.0227090481603 14 412.2523499868785 15 398.35313914494435 16 402.3407031090951 17 428.0135648568788 18 422.5923617053917 19 454.71648148019676 20 455.5315716647201 Best k = 5 6.019133 seconds (14.37 M allocations: 289.797 MiB, 1.25% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 5%|█▌ | ETA: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:59 Cross validating... 8%|██▌ | ETA: 0:00:57 Cross validating... 10%|███ | ETA: 0:00:54 Cross validating... 11%|███▌ | ETA: 0:00:52 Cross validating... 13%|████▏ | ETA: 0:00:51 Cross validating... 14%|████▋ | ETA: 0:00:50 Cross validating... 16%|█████▏ | ETA: 0:00:49 Cross validating... 17%|█████▋ | ETA: 0:00:49 Cross validating... 19%|██████▏ | ETA: 0:00:48 Cross validating... 21%|██████▋ | ETA: 0:00:48 Cross 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ETA: 0:00:06 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:05 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:02 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:49 Crossvalidation Results: k MSE 0 481.87870475421175 1 316.20447459629366 2 235.7578758405981 3 211.3772865471831 4 195.57644560968959 5 195.30436328192388 6 197.39040092798822 7 198.82197716891636 8 198.5265693494622 9 200.39660486308367 10 202.9173323918264 11 203.48338442232824 12 205.08369105995442 13 206.3333686825261 14 206.34271352629835 15 207.33324104357828 16 209.38330011682518 17 206.98011583161463 18 207.03071942457342 19 207.11552931285618 20 211.35516093333 Best k = 5 49.485161 seconds (157.75 M allocations: 3.920 GiB, 1.19% gc time, 4.67% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:06 Cross validating... 6%|██ | ETA: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:07 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:07 Cross validating... 14%|████▋ | ETA: 0:00:07 Cross validating... 16%|█████▏ | ETA: 0:00:08 Cross validating... 17%|█████▋ | ETA: 0:00:08 Cross validating... 19%|██████▏ | ETA: 0:00:08 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross 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0:00:06 Cross validating... 57%|██████████████████▎ | ETA: 0:00:06 Cross validating... 59%|██████████████████▊ | ETA: 0:00:05 Cross validating... 60%|███████████████████▎ | ETA: 0:00:05 Cross validating... 62%|███████████████████▊ | ETA: 0:00:05 Cross validating... 63%|████████████████████▍ | ETA: 0:00:05 Cross validating... 65%|████████████████████▉ | ETA: 0:00:05 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 481.87870475421175 1 315.19154914717797 2 236.90175942451808 3 213.2060228414502 4 196.99990668010204 5 197.11112357679366 6 201.8832631659725 7 204.3791823056003 8 208.6235278235548 9 210.71787473951719 10 216.43098051490387 11 219.09533332991373 12 224.1282559653555 13 223.51165215669414 14 228.02273740568978 15 235.83782972233195 16 235.78646133247076 17 248.12503104926307 18 235.39928617977054 19 251.2481240363348 20 239.77618205042688 Best k = 4 13.527668 seconds (40.42 M allocations: 842.419 MiB, 1.40% gc time, 0.50% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m03.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:08 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 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Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.329049 seconds (17.01 M allocations: 337.905 MiB, 1.69% gc time, 45.37% 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: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | 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: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | 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: 0:00:00 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: 0:00:03 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 3.394606 seconds (16.18 M allocations: 286.714 MiB, 1.70% gc time, 1.77% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.2s **** 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... 2%|▋ | ETA: 0:01:20 Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 4%|█▎ | ETA: 0:00:48 Cross validating... 5%|█▋ | ETA: 0:00:41 Cross validating... 6%|█▉ | ETA: 0:00:37 Cross 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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: 0:00:20 Crossvalidation Results: k MSE 1 7736.925403148768 2 6031.873146422489 3 3876.5566901666016 4 2918.522136822169 5 2664.8055784081057 6 2421.5816992008095 7 2414.2115078492516 8 2424.3005944933393 9 2433.574344408989 10 2449.3565038084926 11 2456.7061377627524 12 2453.737944431742 13 2506.672492636854 14 2528.3565406223856 15 2579.0610618219193 16 2607.741572789282 17 2630.602564823087 18 2637.5260021200593 19 2653.698384056481 20 2691.448129020177 Best k = 7 20.936175 seconds (357.16 k allocations: 326.797 MiB, 0.53% gc time, 7.98% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 26.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m41.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 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100%|████████████████████████████████| Time: 0:00:26 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: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ 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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: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 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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 1m29.9s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] getproperty(x::Nothing, f::Symbol) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] collect(itr::Base.Generator{UnitRange{Int64}, MendelIHT.var"#convert_bgen_gt##0#convert_bgen_gt##1"}) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [18] _start() @ Base ./client.jl:593 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.1s RNG of the outermost testset: Xoshiro(0x8e619a18e47ef4c7, 0x51a1804da866ddbc, 0x25501bdf0d93d50b, 0xf3584ad907102a46, 0xe540b24c5307df1c) 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 1088.63s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1212.05s: package tests unexpectedly errored