Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1877 (00654c1407*) started at 2026-03-10T22:36:34.114 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.31s ################################################################################ # 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 v4.5.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.23.0 [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+1 [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 v1.3.2+0 [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 5.79s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4603.2 ms ✓ BGEN 6800.9 ms ✓ VCFTools 26192.4 ms ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 24166.4 ms ✓ MendelIHT 4 dependencies successfully precompiled in 65 seconds. 170 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 87.39s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_QT5Rvu/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 13.3s 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 9.9s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.7s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1641.433514078013, backtracks = 0, tol = 1.7479636402734615 Iteration 2: loglikelihood = -1426.411930638877, backtracks = 0, tol = 0.13108278844442786 Iteration 3: loglikelihood = -1408.1071947627377, backtracks = 0, tol = 0.044216669600178296 Iteration 4: loglikelihood = -1407.737206176337, backtracks = 0, tol = 0.004550000582346926 Iteration 5: loglikelihood = -1407.7280552646685, backtracks = 0, tol = 0.0010635700421517671 Iteration 6: loglikelihood = -1407.7278133441291, backtracks = 0, tol = 0.0001335741128206048 Iteration 7: loglikelihood = -1407.7278067456552, backtracks = 0, tol = 2.6711914363511483e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.06330990791320801 Final loglikelihood: -1407.7278067456552 SNP PVE: 0.9099351069749557 Iterations: 7 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1550 1.28767 2 │ 1768 -1.19802 3 │ 4497 0.930706 4 │ 5682 -0.864843 5 │ 5743 -0.894498 6 │ 5938 -0.312223 7 │ 6035 0.413131 8 │ 6144 0.130938 9 │ 8233 0.263759 10 │ 8884 -2.05131 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0667651Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.8s **** 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 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 3.6s **** 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 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 = -19924.83251506826, backtracks = 0, tol = 0.3505853637900018 Iteration 2: loglikelihood = -8213.838003604824, backtracks = 0, tol = 0.022722274973324852 Iteration 3: loglikelihood = -3883.167554985562, backtracks = 0, tol = 0.02316204300333576 Iteration 4: loglikelihood = -2280.8786491301453, backtracks = 0, tol = 0.023553719924952837 Iteration 5: loglikelihood = -1691.8397903235239, backtracks = 0, tol = 0.023662650822630322 Iteration 6: loglikelihood = -1446.4618398165542, backtracks = 0, tol = 0.03568729798295838 Iteration 7: loglikelihood = -1395.3392287498637, backtracks = 0, tol = 0.038303789859052334 Iteration 8: loglikelihood = -1360.3574772648667, backtracks = 0, tol = 0.06241752104678737 Iteration 9: loglikelihood = -1342.1965932348587, backtracks = 0, tol = 0.046339739486170886 Iteration 10: loglikelihood = -1329.456350100964, backtracks = 0, tol = 0.028442574422591564 Iteration 11: loglikelihood = -1313.0126671708888, backtracks = 1, tol = 0.055832994219441386 Iteration 12: loglikelihood = -1309.2940111002024, backtracks = 0, tol = 0.026700713464572912 Iteration 13: loglikelihood = -1307.2453428218437, backtracks = 0, tol = 0.014903174545283901 Iteration 14: loglikelihood = -1306.1454540884527, backtracks = 1, tol = 0.007814485457543633 Iteration 15: loglikelihood = -1305.4058578515192, backtracks = 1, tol = 0.009755141136712407 Iteration 16: loglikelihood = -1304.9465978663204, backtracks = 1, tol = 0.005241097609618941 Iteration 17: loglikelihood = -1304.63909759563, backtracks = 1, tol = 0.0061793706612919665 Iteration 18: loglikelihood = -1304.4402980398468, backtracks = 1, tol = 0.0035594873576756266 Iteration 19: loglikelihood = -1304.3087562841445, backtracks = 1, tol = 0.003967668938365631 Iteration 20: loglikelihood = -1304.2205800486001, backtracks = 1, tol = 0.002432669534361415 Iteration 21: loglikelihood = -1304.163707607734, backtracks = 1, tol = 0.002557795876803165 Iteration 22: loglikelihood = -1304.1236347906397, backtracks = 1, tol = 0.0016877420940053496 Iteration 23: loglikelihood = -1302.9307459450856, backtracks = 0, tol = 0.06372908497298713 Iteration 24: loglikelihood = -1302.6889021073846, backtracks = 0, tol = 0.006491956590822385 Iteration 25: loglikelihood = -1302.66111970651, backtracks = 0, tol = 0.0025268900184323667 Iteration 26: loglikelihood = -1302.6465945999287, backtracks = 0, tol = 0.0014116076016348466 Iteration 27: loglikelihood = -1302.637127842437, backtracks = 0, tol = 0.0012843648535162402 Iteration 28: loglikelihood = -1302.6308059915634, backtracks = 0, tol = 0.0008929778425968856 Iteration 29: loglikelihood = -1302.6265702891983, backtracks = 0, tol = 0.0008367033864348207 Iteration 30: loglikelihood = -1302.623707858347, backtracks = 0, tol = 0.0005957136289212666 Iteration 31: loglikelihood = -1302.621774616408, backtracks = 0, tol = 0.0005591800402007997 Iteration 32: loglikelihood = -1302.6204624779652, backtracks = 0, tol = 0.00040171078690970157 Iteration 33: loglikelihood = -1302.6195727020736, backtracks = 0, tol = 0.00037648832689913696 Iteration 34: loglikelihood = -1302.6189674617772, backtracks = 0, tol = 0.0002721919385219811 Iteration 35: loglikelihood = -1302.6185560854121, backtracks = 0, tol = 0.0002546108280951713 Iteration 36: loglikelihood = -1302.6182759138862, backtracks = 0, tol = 0.00018492426309578343 Iteration 37: loglikelihood = -1302.6180852137384, backtracks = 0, tol = 0.00017269224194485858 Iteration 38: loglikelihood = -1302.6179552407764, backtracks = 0, tol = 0.00012583504257999268 Iteration 39: loglikelihood = -1302.6178666955022, backtracks = 0, tol = 0.00011735987135460894 Iteration 40: loglikelihood = -1302.61780632013, backtracks = 0, tol = 8.57108181759761e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 2.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1558.7655911899203, backtracks = 0, tol = 0.3334517420791768 Iteration 2: loglikelihood = -1494.5421069058855, backtracks = 0, tol = 0.13527140410194682 Iteration 3: loglikelihood = -1465.4066944561653, backtracks = 0, tol = 0.09081147030338046 Iteration 4: loglikelihood = -1462.6955499780834, backtracks = 0, tol = 0.08513881843353764 Iteration 5: loglikelihood = -1458.613017026859, backtracks = 0, tol = 0.07806095740095487 Iteration 6: loglikelihood = -1457.1237104309994, backtracks = 0, tol = 0.07378500265618207 Iteration 7: loglikelihood = -1456.8927356349327, backtracks = 1, tol = 0.004715040157679233 Iteration 8: loglikelihood = -1456.8146465645698, backtracks = 1, tol = 0.0035865181221124975 Iteration 9: loglikelihood = -1456.187223179297, backtracks = 1, tol = 0.05952402213079009 Iteration 10: loglikelihood = -1456.1171547342678, backtracks = 0, tol = 0.07366540032004537 Iteration 11: loglikelihood = -1455.7754631670498, backtracks = 0, tol = 0.0690210910068748 Iteration 12: loglikelihood = -1455.736627712861, backtracks = 0, tol = 0.0034826922343062336 Iteration 13: loglikelihood = -1455.7353140531447, backtracks = 1, tol = 0.0006493057257476586 Iteration 14: loglikelihood = -1455.7347171010892, backtracks = 1, tol = 0.0005416780348698362 Iteration 15: loglikelihood = -1455.7345968611978, backtracks = 2, tol = 0.0001525692472231014 Iteration 16: loglikelihood = -1455.7345278208957, backtracks = 2, tol = 0.00011523843495059146 Iteration 17: loglikelihood = -1455.7344883617802, backtracks = 2, tol = 8.604344118560257e-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 = -1827.2562557994304, backtracks = 0, tol = 0.7544219539684175 Iteration 2: loglikelihood = -1515.4247395862126, backtracks = 0, tol = 0.13134846908262035 Iteration 3: loglikelihood = -1438.3214580980834, backtracks = 0, tol = 0.051134337041244544 Iteration 4: loglikelihood = -1414.2671298808814, backtracks = 0, tol = 0.03617970785495477 Iteration 5: loglikelihood = -1409.2567336072898, backtracks = 0, tol = 0.029573313655527417 Iteration 6: loglikelihood = -1408.778415332163, backtracks = 0, tol = 0.0037988186025111367 Iteration 7: loglikelihood = -1408.0773760359925, backtracks = 0, tol = 0.02450394740877637 Iteration 8: loglikelihood = -1407.6146872167503, backtracks = 0, tol = 0.003904438247064476 Iteration 9: loglikelihood = -1407.3085913935618, backtracks = 0, tol = 0.024673843753267557 Iteration 10: loglikelihood = -1407.2095865597494, backtracks = 0, tol = 0.0013846659123864635 Iteration 11: loglikelihood = -1407.2091345431238, backtracks = 1, tol = 7.576896977364818e-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 = -1577.9672612331017, backtracks = 0, tol = 0.2734716496881814 Iteration 2: loglikelihood = -1441.8614186738316, backtracks = 0, tol = 0.06700106473350835 Iteration 3: loglikelihood = -1410.611978349092, backtracks = 0, tol = 0.03677619985177223 Iteration 4: loglikelihood = -1407.762465600004, backtracks = 0, tol = 0.029890036061303728 Iteration 5: loglikelihood = -1407.375592933108, backtracks = 0, tol = 0.004175384792234463 Iteration 6: loglikelihood = -1407.3713153263884, backtracks = 1, tol = 0.0003632148333278816 Iteration 7: loglikelihood = -1407.3701760755978, backtracks = 1, tol = 0.0001836073772883665 Iteration 8: loglikelihood = -1407.3698774810769, backtracks = 1, tol = 8.991376331504765e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 11.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1574.5764778055388, backtracks = 0, tol = 0.20407854732022165 Iteration 2: loglikelihood = -1511.2552708913827, backtracks = 0, tol = 0.09959299016057022 Iteration 3: loglikelihood = -1457.21482953032, backtracks = 0, tol = 0.11874255795103546 Iteration 4: loglikelihood = -1414.5608318460886, backtracks = 0, tol = 0.07871807524677865 Iteration 5: loglikelihood = -1403.8467809216716, backtracks = 0, tol = 0.05014300633698109 Iteration 6: loglikelihood = -1391.5404317580455, backtracks = 0, tol = 0.051067429563700424 Iteration 7: loglikelihood = -1384.952843851326, backtracks = 0, tol = 0.04155704536009199 Iteration 8: loglikelihood = -1382.303428639712, backtracks = 0, tol = 0.022611937641245528 Iteration 9: loglikelihood = -1380.7856524123656, backtracks = 0, tol = 0.02291046097847311 Iteration 10: loglikelihood = -1379.90216724839, backtracks = 0, tol = 0.011870037279516363 Iteration 11: loglikelihood = -1373.1506963105096, backtracks = 0, tol = 0.06323981061117397 Iteration 12: loglikelihood = -1371.7843443084832, backtracks = 0, tol = 0.023983386843703856 Iteration 13: loglikelihood = -1371.3971907193088, backtracks = 0, tol = 0.007984446850182415 Iteration 14: loglikelihood = -1371.3292323606806, backtracks = 0, tol = 0.06011297255129933 Iteration 15: loglikelihood = -1371.0050689285536, backtracks = 1, tol = 0.004476889819268381 Iteration 16: loglikelihood = -1370.8735369476792, backtracks = 1, tol = 0.003032651862516377 Iteration 17: loglikelihood = -1370.8383783048682, backtracks = 2, tol = 0.0015427835088658729 Iteration 18: loglikelihood = -1370.8161486676167, backtracks = 2, tol = 0.0013812449777708118 Iteration 19: loglikelihood = -1370.8026011637971, backtracks = 2, tol = 0.0011692595289503806 Iteration 20: loglikelihood = -1370.7946124041566, backtracks = 2, tol = 0.0009411101184243948 Iteration 21: loglikelihood = -1370.7900041196, backtracks = 2, tol = 0.0007331332336928693 Iteration 22: loglikelihood = -1370.7873778195094, backtracks = 2, tol = 0.0005604187672278672 Iteration 23: loglikelihood = -1370.785890073292, backtracks = 2, tol = 0.0004244146208613969 Iteration 24: loglikelihood = -1370.7850497761399, backtracks = 2, tol = 0.0003198293785493448 Iteration 25: loglikelihood = -1370.7845758756073, backtracks = 2, tol = 0.00024047034253937724 Iteration 26: loglikelihood = -1370.7843088272607, backtracks = 2, tol = 0.00018055801045879257 Iteration 27: loglikelihood = -1370.784158414841, backtracks = 2, tol = 0.00013549800398661639 Iteration 28: loglikelihood = -1370.7840737222919, backtracks = 2, tol = 0.00010163982447586222 Iteration 29: loglikelihood = -1370.7840260444061, backtracks = 2, tol = 7.623377517401328e-5 1.511626 seconds (8.33 M allocations: 140.946 MiB, 2.65% gc time, 39.65% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1603.3841040926113, backtracks = 0, tol = 0.20407854732022165 Iteration 2: loglikelihood = -1559.5929665761396, backtracks = 0, tol = 0.11602918246281546 Iteration 3: loglikelihood = -1528.9114269796614, backtracks = 0, tol = 0.0956543674550694 Iteration 4: loglikelihood = -1500.3654480328057, backtracks = 0, tol = 0.0815075108112075 Iteration 5: loglikelihood = -1475.7037597225165, backtracks = 0, tol = 0.08853370710941827 Iteration 6: loglikelihood = -1464.421471073913, backtracks = 0, tol = 0.0688412710944786 Iteration 7: loglikelihood = -1458.956437488946, backtracks = 0, tol = 0.07441294285813181 Iteration 8: loglikelihood = -1443.572634516885, backtracks = 0, tol = 0.06658962706616342 Iteration 9: loglikelihood = -1431.4373361958098, backtracks = 0, tol = 0.06106624767228289 Iteration 10: loglikelihood = -1429.8857945449477, backtracks = 0, tol = 0.0739749445475797 Iteration 11: loglikelihood = -1421.203437486478, backtracks = 1, tol = 0.006078337215490541 Iteration 12: loglikelihood = -1415.404018789047, backtracks = 1, tol = 0.0037653225453512297 Iteration 13: loglikelihood = -1406.6461492639328, backtracks = 1, tol = 0.062403384420469506 Iteration 14: loglikelihood = -1401.7184118605091, backtracks = 1, tol = 0.004450587420149062 Iteration 15: loglikelihood = -1398.2498074650216, backtracks = 1, tol = 0.002353626385459645 Iteration 16: loglikelihood = -1395.4060572719866, backtracks = 1, tol = 0.0013986509857750464 Iteration 17: loglikelihood = -1393.812740247547, backtracks = 1, tol = 0.0010682037085822651 Iteration 18: loglikelihood = -1392.3195646970914, backtracks = 1, tol = 0.060559682196933196 Iteration 19: loglikelihood = -1390.9298243336686, backtracks = 0, tol = 0.005622539302486544 Iteration 20: loglikelihood = -1389.6337862019923, backtracks = 0, tol = 0.0026482553918127025 Iteration 21: loglikelihood = -1388.507163872848, backtracks = 0, tol = 0.0011305069830199273 Iteration 22: loglikelihood = -1386.6728711002331, backtracks = 1, tol = 0.0006469598856791031 Iteration 23: loglikelihood = -1385.224833067738, backtracks = 1, tol = 0.0004053407441296417 Iteration 24: loglikelihood = -1384.2558543636646, backtracks = 1, tol = 0.00036401601544538325 Iteration 25: loglikelihood = -1383.7199244727708, backtracks = 1, tol = 0.00033519868692039506 Iteration 26: loglikelihood = -1383.6868693051852, backtracks = 1, tol = 0.00029211778212032895 Iteration 27: loglikelihood = -1383.254265705438, backtracks = 2, tol = 0.0001077417979423864 Iteration 28: loglikelihood = -1382.3289512504036, backtracks = 1, tol = 0.0001069527842534012 Iteration 29: loglikelihood = -1381.7180132252558, backtracks = 0, tol = 0.00020817258546320283 Iteration 30: loglikelihood = -1381.2959367832207, backtracks = 1, tol = 0.00015000729199957287 Iteration 31: loglikelihood = -1380.2988933604881, backtracks = 1, tol = 7.396428591313414e-5 0.325061 seconds (1.49 M allocations: 27.659 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 = -3597.6836, backtracks = 0, tol = 0.08650301667531679 Iteration 2: loglikelihood = -3545.3645, backtracks = 0, tol = 0.04778120130320671 Iteration 3: loglikelihood = -3513.2417, backtracks = 1, tol = 0.06408043049029642 Iteration 4: loglikelihood = -3509.2375, backtracks = 0, tol = 0.0851992120418093 Iteration 5: loglikelihood = -3506.25, backtracks = 1, tol = 0.007174168886098717 Iteration 6: loglikelihood = -3505.3572, backtracks = 1, tol = 0.004122469336743724 Iteration 7: loglikelihood = -3505.0872, backtracks = 1, tol = 0.002398832345795065 Iteration 8: loglikelihood = -3505.0022, backtracks = 1, tol = 0.001458917101324537 Iteration 9: loglikelihood = -3489.113, backtracks = 1, tol = 0.07683600029629618 Iteration 10: loglikelihood = -3487.227, backtracks = 1, tol = 0.009240898252032751 Iteration 11: loglikelihood = -3486.7188, backtracks = 1, tol = 0.004496778417495321 Iteration 12: loglikelihood = -3486.5864, backtracks = 1, tol = 0.0022110277746430406 Iteration 13: loglikelihood = -3486.5498, backtracks = 1, tol = 0.0010897650378893572 Iteration 14: loglikelihood = -3486.5405, backtracks = 1, tol = 0.0005296054576903827 Iteration 15: loglikelihood = -3486.538, backtracks = 1, tol = 0.00032910288257963807 Iteration 16: loglikelihood = -3486.5364, backtracks = 3, tol = 5.002804875015963e-5 25.830412 seconds (17.06 M allocations: 699.725 MiB, 4.28% gc time, 94.11% 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 = -3486.3518, backtracks = 0, tol = 0.08650301667531679 Iteration 2: loglikelihood = -3362.2363, backtracks = 0, tol = 0.049345977653836 Iteration 3: loglikelihood = -3150.0369, backtracks = 1, tol = 0.06268041616059551 Iteration 4: loglikelihood = -3062.036, backtracks = 0, tol = 0.09484620842502622 Iteration 5: loglikelihood = -2931.8796, backtracks = 0, tol = 0.08989004204000364 Iteration 6: loglikelihood = -2812.5925, backtracks = 0, tol = 0.08764568045735342 Iteration 7: loglikelihood = -2703.1633, backtracks = 0, tol = 0.09021443709722786 Iteration 8: loglikelihood = -2595.186, backtracks = 0, tol = 0.0866228850151223 Iteration 9: loglikelihood = -2487.1084, backtracks = 0, tol = 0.08792351011176931 Iteration 10: loglikelihood = -2394.6436, backtracks = 0, tol = 0.08761014832443342 Iteration 11: loglikelihood = -2311.1445, backtracks = 0, tol = 0.08642613915797334 Iteration 12: loglikelihood = -2246.2937, backtracks = 0, tol = 0.08603089523534523 Iteration 13: loglikelihood = -2199.192, backtracks = 0, tol = 0.08893278735705616 Iteration 14: loglikelihood = -2165.275, backtracks = 0, tol = 0.08861722019687557 Iteration 15: loglikelihood = -2143.661, backtracks = 0, tol = 0.010473305386489743 Iteration 16: loglikelihood = -2131.0383, backtracks = 0, tol = 0.0028461841395663796 Iteration 17: loglikelihood = -2125.8987, backtracks = 0, tol = 0.09579047000316224 Iteration 18: loglikelihood = -2120.2256, backtracks = 0, tol = 0.09580467663850482 Iteration 19: loglikelihood = -2117.767, backtracks = 0, tol = 0.011050319782944063 Iteration 20: loglikelihood = -2116.6885, backtracks = 0, tol = 0.002406867265282932 Iteration 21: loglikelihood = -2116.1472, backtracks = 0, tol = 0.0005921863888013814 Iteration 22: loglikelihood = -2115.8813, backtracks = 0, tol = 0.0002350558019756482 Iteration 23: loglikelihood = -2115.6716, backtracks = 1, tol = 6.90110573812342e-5 0.187955 seconds (1.07 M allocations: 17.798 MiB, 12.86% gc time) 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 **** 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 4.945238 seconds (1.18 M allocations: 138.749 MiB, 0.50% gc time, 92.07% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.3s 9.240404 seconds (4.00 M allocations: 82.493 MiB, 0.70% gc time, 0.76% compilation time) 5.486999 seconds (3.98 M allocations: 91.675 MiB, 0.30% gc time) 10.478068 seconds (20.41 M allocations: 439.521 MiB, 1.02% gc time, 18.18% compilation time: 80% of which was recompilation) 8.297571 seconds (20.18 M allocations: 434.188 MiB, 0.91% gc time) 44.236593 seconds (3.76 M allocations: 4.239 GiB, 10.07% gc time, 28.39% compilation time) 48.254706 seconds (71.97 k allocations: 183.459 MiB, 0.19% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m25.3s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 13.783 ms (78 allocations: 4.56 KiB) 4.977 μs (0 allocations: 0 bytes) 150.888 μs (4 allocations: 288 bytes) 6.580 μs (0 allocations: 0 bytes) 45.540 μs (2 allocations: 64 bytes) 38.050 μs (0 allocations: 0 bytes) 25.370 μs (0 allocations: 0 bytes) 28.320 μs (0 allocations: 0 bytes) 73.919 μs (0 allocations: 0 bytes) 38.866 ms (78 allocations: 4.56 KiB) 27.540 μs (0 allocations: 0 bytes) 169.689 μs (4 allocations: 288 bytes) 33.690 μs (0 allocations: 0 bytes) 240.047 μs (2 allocations: 64 bytes) 74.779 μs (0 allocations: 0 bytes) 119.919 μs (0 allocations: 0 bytes) 150.529 μs (0 allocations: 0 bytes) 203.478 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m30.5s **** 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 **** **** 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 0.399651 seconds (49.20 k allocations: 5.484 MiB, 60.81% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 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 **** 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 2.076911 seconds (312.25 k allocations: 169.924 MiB, 59.24% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:37 Cross validating... 11%|███▌ | ETA: 0:01:01 Cross validating... 14%|████▋ | ETA: 0:00:46 Cross validating... 17%|█████▋ | ETA: 0:00:37 Cross validating... 21%|██████▋ | ETA: 0:00:31 Cross validating... 24%|███████▋ | ETA: 0:00:26 Cross validating... 27%|████████▋ | ETA: 0:00:22 Cross validating... 30%|█████████▋ | ETA: 0:00:20 Cross validating... 33%|██████████▋ | ETA: 0:00:17 Cross validating... 37%|███████████▋ | ETA: 0:00:15 Cross validating... 40%|████████████▊ | ETA: 0:00:13 Cross validating... 43%|█████████████▊ | ETA: 0:00:12 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 62%|███████████████████▊ | ETA: 0:00:06 Cross validating... 65%|████████████████████▉ | ETA: 0:00:05 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | 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 3623.083502273918 1 2225.7990298721033 2 1723.058915776354 3 1285.9449971100548 4 1047.6891228773186 5 754.1211734750723 6 444.7284249286962 7 391.41759382987635 8 358.0118280356912 9 334.4356793646592 10 340.31154356611415 11 342.52189801959315 12 341.8435851951018 13 356.5290524809371 14 344.04580672277564 15 350.93897751437964 16 347.913953642102 17 374.8481715182363 18 408.6112985789756 19 357.99645701352637 20 379.79531424444315 Best k = 9 11.702934 seconds (11.45 M allocations: 302.569 MiB, 0.89% gc time, 62.15% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 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... 37%|███████████▋ | 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... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | 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 3623.083502273918 1 2231.4741894372787 2 1726.0616624831775 3 1291.6546032045542 4 1052.1811086586017 5 762.2144426748562 6 452.08457423690515 7 396.9112032523171 8 365.2728830053748 9 342.2665819836664 10 356.8334054876466 11 362.68538790926664 12 363.51713053718174 13 370.5128959337627 14 375.5641336543313 15 391.72512893893116 16 396.3605701172835 17 408.6550863238597 18 406.2561663524858 19 409.7605340481818 20 415.39983980877986 Best k = 9 4.540761 seconds (10.68 M allocations: 224.919 MiB, 1.02% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.2s **** 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: 0:06:44 Cross validating... 8%|██▌ | ETA: 0:02:35 Cross validating... 13%|████▏ | ETA: 0:01:32 Cross validating... 17%|█████▋ | ETA: 0:01:04 Cross validating... 22%|███████▏ | ETA: 0:00:48 Cross validating... 27%|████████▋ | ETA: 0:00:38 Cross validating... 32%|██████████▏ | ETA: 0:00:30 Cross validating... 37%|███████████▋ | ETA: 0:00:25 Cross validating... 41%|█████████████▎ | ETA: 0:00:20 Cross validating... 48%|███████████████▎ | ETA: 0:00:16 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 59%|██████████████████▊ | ETA: 0:00:10 Cross validating... 63%|████████████████████▍ | ETA: 0:00:09 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1646.511437011719 1 1289.9121602783202 2 1032.453024169922 3 804.1541405029296 4 662.4925261230469 5 515.7784745178222 6 457.7140184631348 7 383.02402017211915 8 367.8067526550293 9 347.6655906066895 10 352.46567633056645 11 354.78190621948244 12 356.9493793334961 13 356.5950637512207 14 360.4088636474609 15 370.2525203552246 16 364.1476680297851 17 378.15096087646486 18 387.5166734313965 19 390.00252770996093 20 388.54592416381837 Best k = 9 16.799853 seconds (12.59 M allocations: 311.616 MiB, 0.43% gc time, 84.76% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1646.511437011719 1 1289.9121602783202 2 1032.9837022705078 3 805.5133674926758 4 669.9844868774414 5 515.7755459899902 6 462.19321911621097 7 388.3599965515137 8 374.05478814697267 9 354.25109567260745 10 366.9839173278808 11 372.8608232116699 12 380.3535161437988 13 383.7267488098144 14 389.8890108642578 15 390.29092489624026 16 405.28809005737304 17 411.826527130127 18 423.99561846923825 19 417.65001385498044 20 424.16231005859373 Best k = 9 2.579678 seconds (10.85 M allocations: 199.365 MiB, 2.23% gc time, 1.49% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.7s **** 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: 0:00:57 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 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: 0:00:08 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: 0:00:04 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... 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... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.4594122086624 1 372.25831000067024 2 342.7567548330393 3 300.6429761748787 4 291.9346966938855 5 274.8444901903749 6 247.6126011227209 7 246.54357415476733 8 239.87560075392454 9 243.426909488969 10 255.43287288084207 11 257.38999178936183 12 250.34499446988008 13 253.85360413938997 14 266.15259524656113 15 265.5789700585916 16 252.8058838208711 17 260.7528634893917 18 255.58262080315887 19 280.5863521160379 20 293.0379400171012 Best k = 8 8.017897 seconds (17.41 M allocations: 412.541 MiB, 1.47% gc time, 31.29% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | 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 0 463.4594122086624 1 373.64814983961367 2 344.41933186921756 3 302.4273211683246 4 296.29516692428507 5 279.40437702344326 6 254.4598556188011 7 257.1861823852734 8 262.8947847638567 9 260.54330686076133 10 266.5645619584431 11 274.7416434227073 12 284.0149435656606 13 287.1984047247833 14 292.46845269373017 15 288.22752346600674 16 294.62802695153675 17 303.38047342924665 18 316.9814974967645 19 330.0711818231447 20 323.0061063395251 Best k = 6 5.660353 seconds (17.40 M allocations: 360.498 MiB, 1.28% gc time, 0.94% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:49 Cross validating... 8%|██▌ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:05 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 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... 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: 0:00:01 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 0 465.5865069716634 1 442.9492781698367 2 409.50408643698495 3 394.6100776380681 4 377.87235505912446 5 351.35792431582314 6 348.78378443068976 7 344.70558168109574 8 350.0373647520467 9 351.5507325083137 10 355.9946205568283 11 354.2663058724862 12 355.50376890974195 13 403.49125230147456 14 360.0786314091779 15 359.84895989158844 16 392.02659422914144 17 410.69900793972346 18 361.69739627366397 19 377.8883945945399 20 403.09817402202015 Best k = 7 7.498972 seconds (16.08 M allocations: 380.759 MiB, 13.16% gc time, 35.41% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 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: 0:00:02 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 0 465.5865069716634 1 443.39526685226633 2 410.9421651410139 3 397.33779897026886 4 381.54834584180713 5 355.6636878371192 6 360.3805012808434 7 361.59570796006903 8 377.55732720332196 9 385.23190646340043 10 391.6072572142167 11 392.8486331035549 12 398.27995566714316 13 420.6828873066224 14 410.33300728987996 15 425.08198946609866 16 421.46678848290304 17 443.27903486004175 18 436.77749057926655 19 446.4724030512358 20 444.8523325760166 Best k = 5 4.279825 seconds (17.11 M allocations: 351.504 MiB, 2.09% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross 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100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 735.0824858853306 1 651.784920785669 2 543.4556941451775 3 450.4364824375356 4 377.9545735198977 5 355.291668950493 6 360.0120207025581 7 364.0738858674149 8 369.5029188985353 9 386.10081820093586 10 379.225139908498 11 390.82787115951385 12 391.7540044949628 13 387.23551583329174 14 378.8366098141486 15 390.47266257723766 16 374.97584501536323 17 382.24008394081517 18 388.76539664043935 19 391.712297588909 20 393.29906678831355 Best k = 5 8.084512 seconds (15.25 M allocations: 359.348 MiB, 1.27% gc time, 32.47% 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... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 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: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 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: 0:00:05 Crossvalidation Results: k MSE 0 735.0824858853306 1 639.8839076644447 2 507.3515102309285 3 449.673301106437 4 380.3362237664659 5 358.9018995761721 6 370.6012710925639 7 376.7988374248141 8 394.54835834072185 9 399.9595619097742 10 402.9510360967872 11 421.8836392474964 12 424.8390488554319 13 430.81692316196 14 429.6005225898729 15 444.791031848595 16 443.64241825194097 17 452.59903121806786 18 451.3887223042534 19 455.0143855526113 20 459.73013914205654 Best k = 5 5.415622 seconds (14.22 M allocations: 285.406 MiB, 1.00% gc time, 1.04% 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: 0:01:00 Cross validating... 5%|█▌ | ETA: 0:00:43 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 8%|██▌ | ETA: 0:00:27 Cross validating... 10%|███ | ETA: 0:00:32 Cross validating... 11%|███▌ | ETA: 0:00:35 Cross validating... 13%|████▏ | ETA: 0:00:36 Cross validating... 14%|████▋ | ETA: 0:00:37 Cross validating... 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79%|█████████████████████████▍ | ETA: 0:00:11 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:10 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:09 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:07 Cross validating... 87%|███████████████████████████▉ | 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: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:47 Crossvalidation Results: k MSE 0 368.1877816228234 1 300.1729229258751 2 276.2270239203366 3 247.8732889827943 4 223.53579732308353 5 217.69858704298846 6 214.64016057877575 7 212.28693073627863 8 213.8946266139871 9 211.7426077900053 10 212.6885105648879 11 213.68784051656894 12 215.04127575251027 13 215.6911677373928 14 219.1316427447042 15 218.49392442495792 16 220.25947310470528 17 220.43155256602307 18 223.73771366486523 19 218.9593190037233 20 223.2898997894016 Best k = 9 48.015019 seconds (156.16 M allocations: 3.864 GiB, 1.25% gc time, 4.57% 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: 0:00:06 Cross validating... 5%|█▌ | ETA: 0:00:09 Cross validating... 6%|██ | ETA: 0:00:09 Cross validating... 8%|██▌ | ETA: 0:00:08 Cross validating... 10%|███ | ETA: 0:00:08 Cross validating... 11%|███▌ | ETA: 0:00:08 Cross validating... 13%|████▏ | 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Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 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: 0:00:12 Crossvalidation Results: k MSE 0 368.1877816228234 1 299.75557686206463 2 273.5515706607532 3 249.90863368249654 4 225.88495091491228 5 220.78612711441627 6 219.049755024227 7 220.36046741143548 8 222.01395216938556 9 222.07967058269264 10 233.2388400889332 11 226.20388934354014 12 232.63460076764594 13 241.9316393481165 14 240.02818459251426 15 258.21097156762744 16 255.27401452596354 17 247.49707450533757 18 252.18055346517724 19 265.4937575074798 20 262.28097386376317 Best k = 6 12.579776 seconds (41.14 M allocations: 865.171 MiB, 1.22% gc time, 0.49% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m01.0s **** 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: 0:01:05 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 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... 33%|██████████▋ | 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: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | 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 6.154775 seconds (17.00 M allocations: 337.857 MiB, 1.83% gc time, 44.58% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 25%|████████▏ | 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... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | 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... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 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 3.249930 seconds (16.17 M allocations: 286.698 MiB, 2.61% gc time, 1.65% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:21 Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 4%|█▎ | ETA: 0:00:47 Cross validating... 5%|█▋ | ETA: 0:00:39 Cross validating... 6%|█▉ | ETA: 0:00:34 Cross validating... 7%|██▎ | ETA: 0:00:30 Cross 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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: 0:00:17 Crossvalidation Results: k MSE 1 3758.611615507891 2 3093.7548561980066 3 2820.058116811069 4 2684.8716183133088 5 2528.6515678957785 6 2319.971652165281 7 2257.394904609205 8 2257.191504063887 9 2275.192398329502 10 2300.0293413231025 11 2314.2419860054947 12 2330.613931315333 13 2372.9959668319016 14 2374.6497768384675 15 2395.8969355736776 16 2425.270818243876 17 2437.644066912657 18 2434.1903374222616 19 2467.397285349349 20 2509.6285140393393 Best k = 8 17.640608 seconds (327.57 k allocations: 219.098 MiB, 0.40% gc time, 9.52% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 22.7s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m45.3s **** 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... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 Cross validating... 16%|█████▏ 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100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** 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: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 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: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 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 1m26.1s 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 5.5s RNG of the outermost testset: Xoshiro(0xb98e0d4cbf7b7be2, 0x682f380c1d7edb23, 0x541021b5a32cfa22, 0xfdbc5f787ca97060, 0x8692fa48b07b0295) 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 1131.7s 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 1260.18s: package tests unexpectedly errored