Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2362 (adf6a0d284*) started at 2026-06-16T02:36:29.683 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.26s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.6.1 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.25.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.7 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.2+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.4+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.7+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.77s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 4.6 s ✓ BGEN 7.7 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 23.1 s ✓ MendelIHT 3 dependencies successfully precompiled in 40 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 63.89s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_pAzSHF/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.126 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.11 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nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:219 └ @ Distributions ~/.julia/packages/Distributions/nfRUl/src/multivariate/mvnormal.jl:219 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 15.9s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.3s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.4s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** 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 = -1842.965978070162, backtracks = 0, tol = 1.9895363431793844 Iteration 2: loglikelihood = -1444.275027609549, backtracks = 0, tol = 0.1808163058006514 Iteration 3: loglikelihood = -1399.8926295218505, backtracks = 0, tol = 0.06469882066599235 Iteration 4: loglikelihood = -1399.5488625373346, backtracks = 0, tol = 0.004115705293452169 Iteration 5: loglikelihood = -1399.5470813234865, backtracks = 0, tol = 0.0003818187815217102 Iteration 6: loglikelihood = -1399.5470634729668, backtracks = 0, tol = 2.9358374710619425e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05336809158325195 Final loglikelihood: -1399.5470634729668 SNP PVE: 0.9439059809549784 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 547 0.122101 2 │ 1208 -0.860997 3 │ 1686 2.14756 4 │ 3368 -0.630909 5 │ 3408 -0.497901 6 │ 4282 2.43214 7 │ 4688 -0.293697 8 │ 5616 2.04605 9 │ 6978 -0.305201 10 │ 9455 0.307573 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0315202Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -102687.08211389337, backtracks = 0, tol = 0.7612506324845698 Iteration 2: loglikelihood = -39116.674971899476, backtracks = 0, tol = 0.06423525388193205 Iteration 3: loglikelihood = -14636.971739824148, backtracks = 0, tol = 0.07335584226292145 Iteration 4: loglikelihood = -5596.738754265493, backtracks = 0, tol = 0.08156387147504307 Iteration 5: loglikelihood = -2461.272412920584, backtracks = 0, tol = 0.08530799536618844 Iteration 6: loglikelihood = -1692.1846213721876, backtracks = 0, tol = 0.07606408499963538 Iteration 7: loglikelihood = -1581.246348855896, backtracks = 0, tol = 0.04502602886436185 Iteration 8: loglikelihood = -1524.272941894614, backtracks = 0, tol = 0.04800863927699842 Iteration 9: loglikelihood = -1498.5053063370922, backtracks = 0, tol = 0.042651661635125876 Iteration 10: loglikelihood = -1480.4805720462746, backtracks = 0, tol = 0.021608043837327128 Iteration 11: loglikelihood = -1452.9653207783786, backtracks = 0, tol = 0.03601500412053442 Iteration 12: loglikelihood = -1441.9867220276374, backtracks = 0, tol = 0.017699054723595033 Iteration 13: loglikelihood = -1415.6863932872568, backtracks = 0, tol = 0.04692175402210833 Iteration 14: loglikelihood = -1405.8237736192602, backtracks = 0, tol = 0.04490788484921617 Iteration 15: loglikelihood = -1401.5680409679308, backtracks = 0, tol = 0.016062605800734483 Iteration 16: loglikelihood = -1398.6451782163624, backtracks = 0, tol = 0.012669817341391705 Iteration 17: loglikelihood = -1396.3141099506668, backtracks = 0, tol = 0.011818669210358663 Iteration 18: loglikelihood = -1394.496743755697, backtracks = 0, tol = 0.009224820572893484 Iteration 19: loglikelihood = -1392.9766561956933, backtracks = 0, tol = 0.00956461049396467 Iteration 20: loglikelihood = -1391.7423120603598, backtracks = 0, tol = 0.007073350931625554 Iteration 21: loglikelihood = -1390.6888698082578, backtracks = 0, tol = 0.007997065791571334 Iteration 22: loglikelihood = -1389.8208725128334, backtracks = 0, tol = 0.005554672049978561 Iteration 23: loglikelihood = -1389.0741299209512, backtracks = 0, tol = 0.006767218858271515 Iteration 24: loglikelihood = -1388.457144813609, backtracks = 0, tol = 0.004412520316778831 Iteration 25: loglikelihood = -1387.9259203734182, backtracks = 0, tol = 0.005737801272050785 Iteration 26: loglikelihood = -1387.4886017463964, backtracks = 0, tol = 0.003718599425193523 Iteration 27: loglikelihood = -1387.1136598594255, backtracks = 0, tol = 0.004845574070050812 Iteration 28: loglikelihood = -1386.8072714601813, backtracks = 0, tol = 0.0031492421601477544 Iteration 29: loglikelihood = -1386.546692630546, backtracks = 0, tol = 0.004059687983821972 Iteration 30: loglikelihood = -1386.3357891850387, backtracks = 0, tol = 0.0026386610760303023 Iteration 31: loglikelihood = -1386.1583773847374, backtracks = 0, tol = 0.003537701817748784 Iteration 32: loglikelihood = -1386.0163171821366, backtracks = 0, tol = 0.002183613263873183 Iteration 33: loglikelihood = -1385.8983653069943, backtracks = 0, tol = 0.003051099378278844 Iteration 34: loglikelihood = -1385.8049542406484, backtracks = 0, tol = 0.0017830299181539886 Iteration 35: loglikelihood = -1385.7474369602908, backtracks = 1, tol = 0.0012873756729304326 Iteration 36: loglikelihood = -1385.6937220071152, backtracks = 0, tol = 0.002400931807298492 Iteration 37: loglikelihood = -1385.6500340031364, backtracks = 0, tol = 0.0014969006386012444 Iteration 38: loglikelihood = -1385.61494425826, backtracks = 0, tol = 0.0019025096484713503 Iteration 39: loglikelihood = -1385.5862384376733, backtracks = 0, tol = 0.0012137934856624865 Iteration 40: loglikelihood = -1385.5629795652467, backtracks = 0, tol = 0.0015246778835785607 Iteration 41: loglikelihood = -1385.5438697920401, backtracks = 0, tol = 0.0009906572089940348 Iteration 42: loglikelihood = -1385.5282861478565, backtracks = 0, tol = 0.001232263100098077 Iteration 43: loglikelihood = -1385.515440259389, backtracks = 0, tol = 0.0008124539771405131 Iteration 44: loglikelihood = -1385.504913722319, backtracks = 0, tol = 0.0010023966495855783 Iteration 45: loglikelihood = -1385.4962143840874, backtracks = 0, tol = 0.0006687529246215492 Iteration 46: loglikelihood = -1385.4890590710834, backtracks = 0, tol = 0.0008195268656453657 Iteration 47: loglikelihood = -1385.4831339555847, backtracks = 0, tol = 0.0005520297549372103 Iteration 48: loglikelihood = -1385.47824625, backtracks = 0, tol = 0.0006726854141418012 Iteration 49: loglikelihood = -1385.4741924589296, backtracks = 0, tol = 0.0004566917290250861 Iteration 50: loglikelihood = -1385.4708407210385, backtracks = 0, tol = 0.0005539058929397208 Iteration 51: loglikelihood = -1385.4680573116273, backtracks = 0, tol = 0.0003784842174661682 Iteration 52: loglikelihood = -1385.465751709883, backtracks = 0, tol = 0.000457262284497774 Iteration 53: loglikelihood = -1385.4638350931327, backtracks = 0, tol = 0.0003141112446997072 Iteration 54: loglikelihood = -1385.4622451379912, backtracks = 0, tol = 0.0003782591462487548 Iteration 55: loglikelihood = -1385.46092233286, backtracks = 0, tol = 0.00026098264828068097 Iteration 56: loglikelihood = -1385.4598236670554, backtracks = 0, tol = 0.0003134307370520338 Iteration 57: loglikelihood = -1385.4589089853432, backtracks = 0, tol = 0.00021703963308299982 Iteration 58: loglikelihood = -1385.4581485485285, backtracks = 0, tol = 0.00026006920777417496 Iteration 59: loglikelihood = -1385.4575151054416, backtracks = 0, tol = 0.00018063080015123952 Iteration 60: loglikelihood = -1385.4569880614122, backtracks = 0, tol = 0.00021603526780804142 Iteration 61: loglikelihood = -1385.456548834961, backtracks = 0, tol = 0.00015042180025007912 Iteration 62: loglikelihood = -1385.4561831460314, backtracks = 0, tol = 0.00017962314834781882 Iteration 63: loglikelihood = -1385.455878275317, backtracks = 0, tol = 0.00012532806731008333 Iteration 64: loglikelihood = -1385.4556243109528, backtracks = 0, tol = 0.00014946226729337968 Iteration 65: loglikelihood = -1385.4554125184231, backtracks = 0, tol = 0.00010446381675126384 Iteration 66: loglikelihood = -1385.4552360119874, backtracks = 0, tol = 0.00012444429541316732 Iteration 67: loglikelihood = -1385.455088777621, backtracks = 0, tol = 8.710277521995962e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1755.7802881991342, backtracks = 0, tol = 0.6859018834695224 Iteration 2: loglikelihood = -1630.0859682024545, backtracks = 0, tol = 0.11695908891621666 Iteration 3: loglikelihood = -1545.3703089034789, backtracks = 0, tol = 0.08469536745074281 Iteration 4: loglikelihood = -1498.1281541789901, backtracks = 0, tol = 0.08924634744216611 Iteration 5: loglikelihood = -1483.9681720697527, backtracks = 0, tol = 0.06394995466367386 Iteration 6: loglikelihood = -1479.9735299542729, backtracks = 0, tol = 0.07128604825165695 Iteration 7: loglikelihood = -1479.0107761370732, backtracks = 0, tol = 0.020223327728407858 Iteration 8: loglikelihood = -1478.7988237111301, backtracks = 0, tol = 0.012298936267268393 Iteration 9: loglikelihood = -1478.739565418421, backtracks = 0, tol = 0.005231886000406735 Iteration 10: loglikelihood = -1478.7225354619864, backtracks = 0, tol = 0.0036575246707181816 Iteration 11: loglikelihood = -1478.718859138563, backtracks = 1, tol = 0.0009342318987495107 Iteration 12: loglikelihood = -1478.717012084245, backtracks = 1, tol = 0.0008456055795507915 Iteration 13: loglikelihood = -1478.7164927355175, backtracks = 1, tol = 0.00046319402852439595 Iteration 14: loglikelihood = -1478.716359524751, backtracks = 1, tol = 0.0002248993515497652 Iteration 15: loglikelihood = -1478.7163214470154, backtracks = 1, tol = 0.0001255731115761458 Iteration 16: loglikelihood = -1478.716311755247, backtracks = 1, tol = 6.0003049306405694e-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 = -1852.032371816296, backtracks = 0, tol = 0.7699783321675481 Iteration 2: loglikelihood = -1481.930930813247, backtracks = 0, tol = 0.14597901393120924 Iteration 3: loglikelihood = -1390.8018675239275, backtracks = 0, tol = 0.0486059292965358 Iteration 4: loglikelihood = -1383.7961957869209, backtracks = 0, tol = 0.02950255582119762 Iteration 5: loglikelihood = -1383.7133201165625, backtracks = 0, tol = 0.025085823662760166 Iteration 6: loglikelihood = -1383.46132751361, backtracks = 0, tol = 0.0024227323399268284 Iteration 7: loglikelihood = -1382.513356450538, backtracks = 0, tol = 0.023500812677293197 Iteration 8: loglikelihood = -1382.395761904966, backtracks = 0, tol = 0.0019136619767586795 Iteration 9: loglikelihood = -1382.3938514932279, backtracks = 0, tol = 0.0002340458644211453 Iteration 10: loglikelihood = -1382.3938124741514, backtracks = 0, tol = 3.757650882430804e-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 = -1664.2703367503577, backtracks = 0, tol = 0.42857190444293664 Iteration 2: loglikelihood = -1416.6490225941236, backtracks = 0, tol = 0.08634938825290314 Iteration 3: loglikelihood = -1385.477833318675, backtracks = 0, tol = 0.039699274657743325 Iteration 4: loglikelihood = -1384.421076673344, backtracks = 0, tol = 0.03240913498351941 Iteration 5: loglikelihood = -1384.233938087515, backtracks = 1, tol = 0.002007594599255695 Iteration 6: loglikelihood = -1383.5140182208422, backtracks = 0, tol = 0.026452430997483595 Iteration 7: loglikelihood = -1383.4332258575205, backtracks = 0, tol = 0.0018434335691080498 Iteration 8: loglikelihood = -1383.4322255877694, backtracks = 0, tol = 0.00021371161428560166 Iteration 9: loglikelihood = -1383.4322098546652, backtracks = 0, tol = 2.6159191234289e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.5s **** 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 = -1602.414168173386, backtracks = 0, tol = 0.1549262943518412 Iteration 2: loglikelihood = -1523.767093357155, backtracks = 0, tol = 0.09713960344269741 Iteration 3: loglikelihood = -1486.6861352680007, backtracks = 0, tol = 0.08641800623656072 Iteration 4: loglikelihood = -1444.0947374900165, backtracks = 0, tol = 0.06729127921796815 Iteration 5: loglikelihood = -1426.2306225212174, backtracks = 0, tol = 0.04190281764241287 Iteration 6: loglikelihood = -1411.9586662119525, backtracks = 0, tol = 0.04753472983216967 Iteration 7: loglikelihood = -1403.3029330488985, backtracks = 0, tol = 0.031701520169128417 Iteration 8: loglikelihood = -1399.1903986117702, backtracks = 0, tol = 0.024886731529115573 Iteration 9: loglikelihood = -1390.5206764310394, backtracks = 0, tol = 0.06074850134757634 Iteration 10: loglikelihood = -1388.5000690286347, backtracks = 0, tol = 0.017816494835399106 Iteration 11: loglikelihood = -1387.570933729302, backtracks = 0, tol = 0.012115971707784908 Iteration 12: loglikelihood = -1386.9731080050826, backtracks = 0, tol = 0.010860240680382181 Iteration 13: loglikelihood = -1386.5675594428992, backtracks = 0, tol = 0.008713390331410227 Iteration 14: loglikelihood = -1386.285383123125, backtracks = 0, tol = 0.006782257426352983 Iteration 15: loglikelihood = -1386.08428574593, backtracks = 0, tol = 0.006358109256784985 Iteration 16: loglikelihood = -1382.0611332219692, backtracks = 0, tol = 0.0405589499695844 Iteration 17: loglikelihood = -1379.9090689376442, backtracks = 0, tol = 0.0225266112823348 Iteration 18: loglikelihood = -1379.524037852998, backtracks = 0, tol = 0.005569608829606237 Iteration 19: loglikelihood = -1379.422148599035, backtracks = 0, tol = 0.004577226975016506 Iteration 20: loglikelihood = -1379.3870057675454, backtracks = 0, tol = 0.0024157596445080975 Iteration 21: loglikelihood = -1379.366542751432, backtracks = 0, tol = 0.0023756023974350698 Iteration 22: loglikelihood = -1379.3532148629165, backtracks = 0, tol = 0.0013835078056252175 Iteration 23: loglikelihood = -1379.3429903108424, backtracks = 0, tol = 0.0019506497853745202 Iteration 24: loglikelihood = -1379.3349506935897, backtracks = 0, tol = 0.0011843893906090574 Iteration 25: loglikelihood = -1378.9232342477746, backtracks = 0, tol = 0.060563496343338734 Iteration 26: loglikelihood = -1378.704355114788, backtracks = 0, tol = 0.005919475548841167 Iteration 27: loglikelihood = -1378.6913984646771, backtracks = 0, tol = 0.0012241027228662078 Iteration 28: loglikelihood = -1378.6850052535005, backtracks = 0, tol = 0.0011561108147295053 Iteration 29: loglikelihood = -1378.6810307884234, backtracks = 0, tol = 0.0008860609854515648 Iteration 30: loglikelihood = -1378.6778288264438, backtracks = 0, tol = 0.001040006094276956 Iteration 31: loglikelihood = -1378.6752025617186, backtracks = 0, tol = 0.0007367093409926622 Iteration 32: loglikelihood = -1378.6729159358604, backtracks = 0, tol = 0.000946714420401855 Iteration 33: loglikelihood = -1378.6709457235052, backtracks = 0, tol = 0.000640594444882331 Iteration 34: loglikelihood = -1378.669194584944, backtracks = 0, tol = 0.000850029851873786 Iteration 35: loglikelihood = -1378.6676648998514, backtracks = 0, tol = 0.0005634414885276878 Iteration 36: loglikelihood = -1378.6662967808718, backtracks = 0, tol = 0.0007590943268446749 Iteration 37: loglikelihood = -1378.665096791641, backtracks = 0, tol = 0.0004980982208744899 Iteration 38: loglikelihood = -1378.6640214156846, backtracks = 0, tol = 0.0006759245494605691 Iteration 39: loglikelihood = -1378.6630769997196, backtracks = 0, tol = 0.00044130384277435355 Iteration 40: loglikelihood = -1378.6622300340046, backtracks = 0, tol = 0.0006010657527470684 Iteration 41: loglikelihood = -1378.6614858767816, backtracks = 0, tol = 0.0003914060305060898 Iteration 42: loglikelihood = -1378.6608182634177, backtracks = 0, tol = 0.0005342082774512627 Iteration 43: loglikelihood = -1378.66023156524, backtracks = 0, tol = 0.00034734061411985633 Iteration 44: loglikelihood = -1378.6597050884989, backtracks = 0, tol = 0.0004747214886553418 Iteration 45: loglikelihood = -1378.659242364501, backtracks = 0, tol = 0.00030832305836413925 Iteration 46: loglikelihood = -1378.6588270562877, backtracks = 0, tol = 0.00042188332180387517 Iteration 47: loglikelihood = -1378.6584620123601, backtracks = 0, tol = 0.0002737255354726498 Iteration 48: loglikelihood = -1378.6581343231421, backtracks = 0, tol = 0.0003749785984295327 Iteration 49: loglikelihood = -1378.65784628309, backtracks = 0, tol = 0.00024302183311887242 Iteration 50: loglikelihood = -1378.6575876837992, backtracks = 0, tol = 0.00033334443935206207 Iteration 51: loglikelihood = -1378.6573603729623, backtracks = 0, tol = 0.00021576057032101473 Iteration 52: loglikelihood = -1378.6571562728166, backtracks = 0, tol = 0.00029638247676767496 Iteration 53: loglikelihood = -1378.6569768724341, backtracks = 0, tol = 0.00019154837495820851 Iteration 54: loglikelihood = -1378.6568157756672, backtracks = 0, tol = 0.0002635588335386089 Iteration 55: loglikelihood = -1378.6566741830989, backtracks = 0, tol = 0.0001700402504828101 Iteration 56: loglikelihood = -1378.656547027374, backtracks = 0, tol = 0.00023440055912242946 Iteration 57: loglikelihood = -1378.656435276551, backtracks = 0, tol = 0.00015093207662364926 Iteration 58: loglikelihood = -1378.6563349141563, backtracks = 0, tol = 0.00020849017988278936 Iteration 59: loglikelihood = -1378.656246721084, backtracks = 0, tol = 0.00013395492551433456 Iteration 60: loglikelihood = -1378.6561675123737, backtracks = 0, tol = 0.00018545899880571714 Iteration 61: loglikelihood = -1378.656097918017, backtracks = 0, tol = 0.00011887085791385221 Iteration 62: loglikelihood = -1378.65603541166, backtracks = 0, tol = 0.00016498162568227636 Iteration 63: loglikelihood = -1378.6559805015363, backtracks = 0, tol = 0.00010546880128755107 Iteration 64: loglikelihood = -1378.6559311832111, backtracks = 0, tol = 0.0001467707338382674 Iteration 65: loglikelihood = -1378.655887866827, backtracks = 0, tol = 9.3561388660254e-5 1.644830 seconds (5.10 M allocations: 91.977 MiB, 3.34% gc time, 39.57% 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 **** 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 = -1622.4239995890885, backtracks = 0, tol = 0.1549262943518412 Iteration 2: loglikelihood = -1574.21900662176, backtracks = 0, tol = 0.1102724305993382 Iteration 3: loglikelihood = -1545.6225140675278, backtracks = 0, tol = 0.10189852081953923 Iteration 4: loglikelihood = -1517.1788236760244, backtracks = 0, tol = 0.07550883682835355 Iteration 5: loglikelihood = -1499.640653937301, backtracks = 0, tol = 0.05148715419610298 Iteration 6: loglikelihood = -1481.004724564979, backtracks = 0, tol = 0.05000750069858344 Iteration 7: loglikelihood = -1465.3168144257234, backtracks = 0, tol = 0.07428504321963432 Iteration 8: loglikelihood = -1454.0551534554402, backtracks = 0, tol = 0.022340366383932518 Iteration 9: loglikelihood = -1443.4774177391398, backtracks = 0, tol = 0.06996969581222488 Iteration 10: loglikelihood = -1435.3457066810317, backtracks = 0, tol = 0.04829238599328447 Iteration 11: loglikelihood = -1429.928620099879, backtracks = 0, tol = 0.010024080073804748 Iteration 12: loglikelihood = -1425.2577320574258, backtracks = 0, tol = 0.004138022633036405 Iteration 13: loglikelihood = -1421.438426450697, backtracks = 0, tol = 0.0034158442751410097 Iteration 14: loglikelihood = -1418.039919297654, backtracks = 0, tol = 0.002198062885144464 Iteration 15: loglikelihood = -1413.2784260230176, backtracks = 1, tol = 0.0015186080206526242 Iteration 16: loglikelihood = -1409.0249154150654, backtracks = 1, tol = 0.0012177803068717638 Iteration 17: loglikelihood = -1406.122401078352, backtracks = 1, tol = 0.0012233539588187895 Iteration 18: loglikelihood = -1404.072947249, backtracks = 1, tol = 0.0013285070592815704 Iteration 19: loglikelihood = -1402.5881448807374, backtracks = 2, tol = 0.000877047640375103 Iteration 20: loglikelihood = -1400.6394227590015, backtracks = 2, tol = 0.0008417687144286516 Iteration 21: loglikelihood = -1399.4261931726476, backtracks = 1, tol = 0.06439221024269036 Iteration 22: loglikelihood = -1398.3646815753289, backtracks = 0, tol = 0.006922459421983656 Iteration 23: loglikelihood = -1397.5203740435977, backtracks = 0, tol = 0.0012267831700984832 Iteration 24: loglikelihood = -1396.7852155150256, backtracks = 0, tol = 0.0005474368098328505 Iteration 25: loglikelihood = -1396.096209582426, backtracks = 0, tol = 0.00044961856566766553 Iteration 26: loglikelihood = -1395.0184048412061, backtracks = 1, tol = 0.00025562387436068603 Iteration 27: loglikelihood = -1394.0356580845475, backtracks = 0, tol = 0.06373616842932019 Iteration 28: loglikelihood = -1393.28020831026, backtracks = 0, tol = 0.007270065774177226 Iteration 29: loglikelihood = -1392.7761515118975, backtracks = 0, tol = 0.0014695155736378297 Iteration 30: loglikelihood = -1392.2927942865565, backtracks = 0, tol = 0.001351773858896536 Iteration 31: loglikelihood = -1391.8768077351647, backtracks = 0, tol = 0.0009593543518100926 Iteration 32: loglikelihood = -1391.4692710733461, backtracks = 0, tol = 0.0009740534767074181 Iteration 33: loglikelihood = -1391.113276539845, backtracks = 0, tol = 0.000984179808010386 Iteration 34: loglikelihood = -1390.761673304054, backtracks = 0, tol = 0.000772934821602122 Iteration 35: loglikelihood = -1390.4782327952169, backtracks = 1, tol = 0.0005512084628903959 Iteration 36: loglikelihood = -1390.3565545331815, backtracks = 1, tol = 0.0006367944924644036 Iteration 37: loglikelihood = -1390.1957928376235, backtracks = 2, tol = 0.00032996425014426557 Iteration 38: loglikelihood = -1399.6369336873913, backtracks = 3, tol = 0.0004015397028670726 Iteration 39: loglikelihood = -1398.6470843995783, backtracks = 0, tol = 0.0033914300651409868 Iteration 40: loglikelihood = -1397.7339555679202, backtracks = 0, tol = 0.0006002994872158084 Iteration 41: loglikelihood = -1396.676214004191, backtracks = 1, tol = 0.00021408758006345797 Iteration 42: loglikelihood = -1395.2157781532874, backtracks = 1, tol = 0.00022611379539587428 Iteration 43: loglikelihood = -1394.8807205517576, backtracks = 0, tol = 0.06487776619973955 Iteration 44: loglikelihood = -1394.1371784437783, backtracks = 0, tol = 0.004095678839823315 Iteration 45: loglikelihood = -1393.5719911817923, backtracks = 0, tol = 0.0009260480198496308 Iteration 46: loglikelihood = -1393.036705320218, backtracks = 0, tol = 0.0005092847774370018 Iteration 47: loglikelihood = -1392.5500414609292, backtracks = 0, tol = 0.0003476538141169683 Iteration 48: loglikelihood = -1392.0910521129817, backtracks = 0, tol = 0.00020474641444764196 Iteration 49: loglikelihood = -1391.7311886097782, backtracks = 0, tol = 0.061720196529162094 Iteration 50: loglikelihood = -1391.1019524430678, backtracks = 0, tol = 0.005648568986086912 Iteration 51: loglikelihood = -1390.6380502181548, backtracks = 0, tol = 0.0018654130507788217 Iteration 52: loglikelihood = -1390.2586856440898, backtracks = 0, tol = 0.0013070012595863042 Iteration 53: loglikelihood = -1389.8785119652243, backtracks = 0, tol = 0.0011747770085184536 Iteration 54: loglikelihood = -1389.3613249930295, backtracks = 0, tol = 0.06800595214012556 Iteration 55: loglikelihood = -1388.823324204334, backtracks = 0, tol = 0.006272494029475718 Iteration 56: loglikelihood = -1388.4851141008444, backtracks = 0, tol = 0.0013819413058706563 Iteration 57: loglikelihood = -1388.154592746323, backtracks = 0, tol = 0.000811701699334322 Iteration 58: loglikelihood = -1387.859322956351, backtracks = 0, tol = 0.0004381844685525535 Iteration 59: loglikelihood = -1387.5714618638629, backtracks = 0, tol = 0.0005041265403916366 Iteration 60: loglikelihood = -1387.3079248532479, backtracks = 0, tol = 0.0003577497339769947 Iteration 61: loglikelihood = -1387.051039199858, backtracks = 0, tol = 0.00038181080929130894 Iteration 62: loglikelihood = -1386.814280302457, backtracks = 0, tol = 0.00032247312922063066 Iteration 63: loglikelihood = -1386.5834180052116, backtracks = 0, tol = 0.00029769047274566404 Iteration 64: loglikelihood = -1385.8464213463226, backtracks = 0, tol = 0.06263136419098597 Iteration 65: loglikelihood = -1385.4281505820802, backtracks = 0, tol = 0.004110741298572805 Iteration 66: loglikelihood = -1385.1999853604284, backtracks = 0, tol = 0.0020013482195752443 Iteration 67: loglikelihood = -1384.9717073978716, backtracks = 0, tol = 0.0012730899241562418 Iteration 68: loglikelihood = -1384.7848149916333, backtracks = 0, tol = 0.0010028738082027133 Iteration 69: loglikelihood = -1384.5915192210289, backtracks = 0, tol = 0.0009333630250763858 Iteration 70: loglikelihood = -1384.4252216404698, backtracks = 0, tol = 0.0008812018266028685 Iteration 71: loglikelihood = -1384.252797553945, backtracks = 0, tol = 0.000761142545916894 Iteration 72: loglikelihood = -1383.9344045961936, backtracks = 1, tol = 0.00041974938607415796 Iteration 73: loglikelihood = -1384.7823149402693, backtracks = 3, tol = 0.00027872507676669224 Iteration 74: loglikelihood = -1385.529098899863, backtracks = 3, tol = 0.00025058207155971535 Iteration 75: loglikelihood = -1385.493076334983, backtracks = 1, tol = 0.06553747222058473 Iteration 76: loglikelihood = -1385.220231345612, backtracks = 0, tol = 0.0041959044198760466 Iteration 77: loglikelihood = -1385.022087045368, backtracks = 0, tol = 0.0016503071477900328 Iteration 78: loglikelihood = -1384.822723575919, backtracks = 1, tol = 0.0008569721257801189 Iteration 79: loglikelihood = -1384.7431728686727, backtracks = 2, tol = 0.0007750297549178998 Iteration 80: loglikelihood = -1392.715388738213, backtracks = 3, tol = 0.0006685259852057707 Iteration 81: loglikelihood = -1392.1215777440818, backtracks = 0, tol = 0.001513474686181483 Iteration 82: loglikelihood = -1391.5471875372652, backtracks = 0, tol = 0.001103930658425811 Iteration 83: loglikelihood = -1390.9780739061152, backtracks = 0, tol = 0.06334772188959821 Iteration 84: loglikelihood = -1390.3543216926244, backtracks = 0, tol = 0.0032294884768745077 Iteration 85: loglikelihood = -1389.8905204405141, backtracks = 0, tol = 0.0012535695605841225 Iteration 86: loglikelihood = -1389.4384838477097, backtracks = 0, tol = 0.0005670194606267628 Iteration 87: loglikelihood = -1389.0257647990404, backtracks = 0, tol = 0.0003068198196118273 Iteration 88: loglikelihood = -1388.6286449772886, backtracks = 0, tol = 0.00024273035063700676 Iteration 89: loglikelihood = -1388.257332403156, backtracks = 0, tol = 0.000171263153353149 Iteration 90: loglikelihood = -1387.9033047702007, backtracks = 0, tol = 9.666328261859672e-5 0.947741 seconds (4.00 M allocations: 72.349 MiB, 1.79% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3700.6245, backtracks = 0, tol = 0.08843169223018361 Iteration 2: loglikelihood = -3631.8267, backtracks = 0, tol = 0.052538936159625814 Iteration 3: loglikelihood = -3623.849, backtracks = 1, tol = 0.020262884939834174 Iteration 4: loglikelihood = -3621.5537, backtracks = 1, tol = 0.010538952715898104 Iteration 5: loglikelihood = -3620.9377, backtracks = 1, tol = 0.005998642689853277 Iteration 6: loglikelihood = -3620.7786, backtracks = 1, tol = 0.0029041031122665527 Iteration 7: loglikelihood = -3620.737, backtracks = 1, tol = 0.0015934734207483268 Iteration 8: loglikelihood = -3620.728, backtracks = 1, tol = 0.0007483929910085056 Iteration 9: loglikelihood = -3620.7214, backtracks = 1, tol = 0.0004126292633934151 Iteration 10: loglikelihood = -3620.726, backtracks = 3, tol = 4.750335606642979e-5 26.047009 seconds (13.38 M allocations: 643.593 MiB, 0.87% gc time, 98.42% 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 = -3566.4558, backtracks = 0, tol = 0.08843169223018361 Iteration 2: loglikelihood = -3415.6907, backtracks = 0, tol = 0.05452917931366207 Iteration 3: loglikelihood = -3207.417, backtracks = 1, tol = 0.019188719177952274 Iteration 4: loglikelihood = -2969.3584, backtracks = 1, tol = 0.00999655749835714 Iteration 5: loglikelihood = -2725.871, backtracks = 1, tol = 0.004709971257115854 Iteration 6: loglikelihood = -2644.0496, backtracks = 0, tol = 0.091477881687372 Iteration 7: loglikelihood = -2535.74, backtracks = 0, tol = 0.11698975344845892 Iteration 8: loglikelihood = -2434.3752, backtracks = 0, tol = 0.1157536868957757 Iteration 9: loglikelihood = -2402.7722, backtracks = 0, tol = 0.13379190930090207 Iteration 10: loglikelihood = -2332.0056, backtracks = 0, tol = 0.1312542988711703 Iteration 11: loglikelihood = -2273.251, backtracks = 0, tol = 0.11567340193618014 Iteration 12: loglikelihood = -2249.488, backtracks = 0, tol = 0.11349287998881663 Iteration 13: loglikelihood = -2239.3064, backtracks = 0, tol = 0.11067189507113045 Iteration 14: loglikelihood = -2226.5764, backtracks = 0, tol = 0.10916113944794517 Iteration 15: loglikelihood = -2196.518, backtracks = 1, tol = 0.09214980542423781 Iteration 16: loglikelihood = -2188.5664, backtracks = 1, tol = 0.06020957482544064 Iteration 17: loglikelihood = -2186.291, backtracks = 1, tol = 0.02718377951930141 Iteration 18: loglikelihood = -2183.1814, backtracks = 1, tol = 0.0482872826525228 Iteration 19: loglikelihood = -2180.694, backtracks = 0, tol = 0.08266857223516126 Iteration 20: loglikelihood = -2180.129, backtracks = 1, tol = 0.010385930270751765 Iteration 21: loglikelihood = -2179.972, backtracks = 1, tol = 0.005350431840086003 Iteration 22: loglikelihood = -2179.9238, backtracks = 1, tol = 0.0027337574953203063 Iteration 23: loglikelihood = -2179.909, backtracks = 1, tol = 0.0013900097205374051 Iteration 24: loglikelihood = -2179.9036, backtracks = 1, tol = 0.0008349149578173183 Iteration 25: loglikelihood = -2179.9006, backtracks = 1, tol = 0.0004998506881084788 Iteration 26: loglikelihood = -2179.8987, backtracks = 1, tol = 0.00029972248589708417 Iteration 27: loglikelihood = -2179.9011, backtracks = 3, tol = 4.441613237344216e-5 0.600275 seconds (1.67 M allocations: 27.779 MiB, 64.91% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 32.0s **** 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 4.862799 seconds (1.03 M allocations: 133.295 MiB, 1.25% gc time, 90.07% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.4s 9.668342 seconds (4.00 M allocations: 82.408 MiB, 0.77% gc time, 0.69% compilation time) 5.167846 seconds (3.98 M allocations: 91.674 MiB, 0.24% gc time) 10.457294 seconds (20.38 M allocations: 438.740 MiB, 1.07% gc time, 17.67% compilation time: 78% of which was recompilation) 8.331442 seconds (20.18 M allocations: 434.187 MiB, 0.92% gc time) 37.321011 seconds (3.41 M allocations: 4.230 GiB, 6.56% gc time, 30.82% compilation time) 56.235134 seconds (72.50 k allocations: 183.667 MiB, 0.18% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m26.4s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.490 ms (78 allocations: 4.56 KiB) 4.574 μs (0 allocations: 0 bytes) 144.820 μs (4 allocations: 288 bytes) 6.707 μs (0 allocations: 0 bytes) 47.040 μs (2 allocations: 64 bytes) 30.110 μs (0 allocations: 0 bytes) 25.410 μs (0 allocations: 0 bytes) 28.590 μs (0 allocations: 0 bytes) 104.650 μs (0 allocations: 0 bytes) 39.834 ms (78 allocations: 4.56 KiB) 18.830 μs (0 allocations: 0 bytes) 180.430 μs (4 allocations: 288 bytes) 34.300 μs (0 allocations: 0 bytes) 267.800 μs (2 allocations: 64 bytes) 87.430 μs (0 allocations: 0 bytes) 137.830 μs (0 allocations: 0 bytes) 154.250 μs (0 allocations: 0 bytes) 220.250 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m11.2s **** 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 **** **** 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 0.463721 seconds (44.58 k allocations: 5.362 MiB, 60.13% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.988811 seconds (258.77 k allocations: 167.555 MiB, 56.23% 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 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:50 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:26 Cross validating... 29%|█████████▏ | ETA: 0:00:22 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross 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Results: k MSE 0 5708.8833851082745 1 3831.2687267691463 2 2383.5493236835805 3 869.1813141481346 4 632.5902762065947 5 496.3057838813105 6 415.69111440873337 7 394.0635751846628 8 365.68894800713247 9 327.0473050543742 10 330.9206139645005 11 338.8511264212981 12 335.532228082627 13 340.19842935959036 14 349.819922642317 15 344.59345840892024 16 365.3333511190564 17 372.85882522675547 18 350.7507519665382 19 384.46659884870013 20 383.20995719869893 Best k = 9 12.721976 seconds (11.51 M allocations: 300.308 MiB, 0.97% gc time, 60.56% 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: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 5708.8833851082745 1 3840.5498360744177 2 2392.3366351795976 3 870.6397392017186 4 635.2411490636403 5 498.3789482134461 6 417.8718540512642 7 396.74783586179495 8 368.30454991937796 9 331.06951720455777 10 340.5389349232081 11 349.8863992921069 12 355.42181620266405 13 365.3826717823134 14 370.3653059411388 15 378.12401682498006 16 385.87854941948905 17 395.2006096272118 18 404.417415600018 19 398.88230881775576 20 396.67491507243835 Best k = 9 5.139668 seconds (10.60 M allocations: 222.259 MiB, 0.92% gc time, 1.09% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.7s **** 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: 0:06:15 Cross validating... 8%|██▌ | ETA: 0:02:24 Cross validating... 13%|████▏ | ETA: 0:01:26 Cross validating... 17%|█████▋ | ETA: 0:01:00 Cross validating... 22%|███████▏ | ETA: 0:00:45 Cross validating... 27%|████████▋ | ETA: 0:00:35 Cross validating... 32%|██████████▏ | ETA: 0:00:28 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:19 Cross validating... 46%|██████████████▊ | ETA: 0:00:16 Cross validating... 51%|████████████████▎ | ETA: 0:00:13 Cross validating... 56%|█████████████████▊ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 63%|████████████████████▍ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 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: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1671.2878907470704 1 1220.2885777587892 2 994.2689850463868 3 789.5823989868164 4 645.9335342407227 5 532.1569346923828 6 445.4571947937012 7 385.5202791137695 8 351.1435467224121 9 351.28041708374025 10 348.4304236450196 11 346.35761447143557 12 348.979108001709 13 352.7684463195801 14 350.5004925231934 15 353.0086018981934 16 380.40536730957035 17 359.7294331665039 18 376.59666723632813 19 360.0476993408203 20 376.11968106079104 Best k = 11 16.137117 seconds (12.24 M allocations: 304.509 MiB, 0.56% gc time, 83.40% 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... 11%|███▌ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:02 Cross validating... 21%|██████▋ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:01 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1671.2878907470704 1 1220.2885777587892 2 1030.8582207641603 3 792.6531129150392 4 647.20258392334 5 535.7929687194825 6 451.7797106323243 7 392.4790656433105 8 360.02368075561526 9 365.4017101135254 10 363.0062937011719 11 374.99565625 12 372.78501434326176 13 382.07620935058594 14 388.61976174926764 15 389.0903238220215 16 398.7063748779297 17 405.270005279541 18 404.9261014709473 19 411.61900827026375 20 411.07265682983405 Best k = 8 2.774012 seconds (10.58 M allocations: 193.559 MiB, 1.70% gc time, 1.62% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:11 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:09 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.2645060202092 1 378.73460891852255 2 283.374657136027 3 240.20669928624937 4 232.25826932981252 5 226.06022948979603 6 226.25222379635935 7 230.07974941833447 8 228.8987088246012 9 242.37520249102957 10 242.85944302746609 11 232.09221908800066 12 249.85657912887388 13 259.4091678133989 14 256.6650200514611 15 258.08484221420963 16 264.42137932596086 17 274.4822198038405 18 239.82001735961 19 263.9199041941605 20 270.093743489855 Best k = 5 8.507685 seconds (17.16 M allocations: 393.415 MiB, 0.91% gc time, 31.83% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:04 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... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.2645060202092 1 378.71170821391286 2 283.920709911763 3 241.3716657039935 4 233.4279249935443 5 229.3623225447285 6 235.13953098067674 7 234.25165723024838 8 242.61195345432327 9 252.29709560042062 10 247.18386713254915 11 263.6523210338219 12 264.9607582691639 13 264.1698514850084 14 266.316844551701 15 282.50180727057443 16 303.3566384874624 17 302.810877040084 18 292.6690282557102 19 289.78034171727205 20 300.3856382873492 Best k = 5 6.274527 seconds (17.16 M allocations: 351.575 MiB, 1.29% gc time, 1.04% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:46 Cross validating... 6%|██ | ETA: 0:00:24 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 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... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.14728898861944 1 419.54953298644364 2 408.5761671420613 3 391.5155213506273 4 362.3496357640757 5 335.31843650181906 6 336.8550310842228 7 337.2768955589869 8 333.1052709668335 9 343.839071879775 10 344.93732632587455 11 335.23057079432937 12 353.3458377117688 13 356.4842275523795 14 368.31142068839665 15 354.7265195988802 16 375.5690127642703 17 381.1503307981676 18 349.0912479123655 19 357.59923415893724 20 356.6843261839432 Best k = 8 7.266104 seconds (16.23 M allocations: 380.438 MiB, 7.78% gc time, 36.07% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 462.14728898861944 1 421.0540061062427 2 412.40131973362406 3 396.19404474677674 4 366.99818665543404 5 340.9203791129533 6 346.21495910130244 7 353.10796103174425 8 357.34089559457425 9 356.2714349411639 10 371.4654170881082 11 370.40887408394144 12 382.447044580149 13 386.6063466159118 14 418.4853798596016 15 415.25689295820206 16 432.57243566777436 17 418.8393155291873 18 436.25103103324 19 450.90094602094103 20 451.928400205549 Best k = 5 4.305612 seconds (16.72 M allocations: 342.123 MiB, 1.12% gc time, 1.32% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 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: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:05 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1613.9498512968516 1 933.1119891535034 2 742.7401601136585 3 609.7104244348675 4 612.5915394571402 5 612.8844169385936 6 628.1331004313723 7 590.8721938394546 8 567.1914395956425 9 531.3187110476913 10 560.5193945080116 11 602.2834426061257 12 600.0651187756541 13 625.3849370196604 14 587.6456686581375 15 528.8147262934542 16 616.8282084426646 17 563.2732524747075 18 635.9916051748687 19 592.1337304386618 20 600.1113408756319 Best k = 15 8.563273 seconds (14.69 M allocations: 335.450 MiB, 0.96% gc time, 31.91% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 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 1613.9498512968516 1 846.564437122269 2 661.3750639717757 3 539.3718538404887 4 520.579391159014 5 518.9632187315767 6 514.0227600919666 7 531.3520304422485 8 517.1651234773906 9 542.5926786688683 10 558.3592927620291 11 553.906038774963 12 558.7511847574466 13 538.23489039915 14 567.1396592169139 15 562.642922810186 16 567.7367181383427 17 573.1710473152884 18 607.4314141266626 19 601.9331057095555 20 607.3995428979415 Best k = 6 5.894690 seconds (13.74 M allocations: 271.962 MiB, 0.86% gc time, 1.11% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 5%|█▌ | ETA: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:49 Cross validating... 8%|██▌ | ETA: 0:00:39 Cross validating... 10%|███ | ETA: 0:00:34 Cross validating... 11%|███▌ | ETA: 0:00:29 Cross validating... 13%|████▏ | ETA: 0:00:33 Cross validating... 14%|████▋ | ETA: 0:00:35 Cross validating... 16%|█████▏ | ETA: 0:00:37 Cross validating... 17%|█████▋ | ETA: 0:00:39 Cross validating... 19%|██████▏ | ETA: 0:00:36 Cross 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validating... 81%|█████████████████████████▉ | ETA: 0:00:07 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:07 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:41 Crossvalidation Results: k MSE 0 517.4126651310485 1 381.02969112113203 2 292.2380263185304 3 226.84361887737944 4 221.66622290953154 5 216.29246877466335 6 213.915779204294 7 217.2687694007892 8 216.23823991515616 9 217.55000618289927 10 216.60712257444078 11 214.35394858102072 12 221.7235198489943 13 221.14291588926278 14 221.29767047037558 15 219.42458799043936 16 221.69819840642955 17 223.05778745317713 18 221.7998763518396 19 223.00899066010925 20 222.69712436850023 Best k = 6 41.850537 seconds (119.83 M allocations: 3.097 GiB, 1.22% gc time, 5.53% 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: 0:00:06 Cross validating... 8%|██▌ | ETA: 0:00:07 Cross validating... 10%|███ | ETA: 0:00:07 Cross validating... 11%|███▌ | ETA: 0:00:07 Cross validating... 13%|████▏ | ETA: 0:00:07 Cross 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0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 517.4126651310485 1 380.04719060537684 2 292.0898828878642 3 227.37927011976143 4 222.57244847039277 5 217.59775724725847 6 216.8288007323175 7 224.20389082708428 8 220.6628909605119 9 225.9780764485379 10 229.96604875366484 11 231.4977533618054 12 243.688796512344 13 244.69610289970683 14 245.54497042127122 15 241.81446659904364 16 248.99992023001124 17 250.33477665968005 18 256.5495938030657 19 259.2412800204326 20 259.1892119670254 Best k = 6 13.093158 seconds (37.01 M allocations: 753.564 MiB, 1.12% gc time, 0.53% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 55.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:09 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 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... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 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 0 709.7238911132813 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 6.296227 seconds (16.96 M allocations: 336.603 MiB, 1.28% gc time, 45.67% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 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92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.376339 seconds (16.17 M allocations: 286.704 MiB, 1.46% gc time, 1.89% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:21 Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 4%|█▎ | ETA: 0:00:50 Cross validating... 5%|█▋ | ETA: 0:00:43 Cross validating... 6%|█▉ | ETA: 0:00:39 Cross validating... 7%|██▎ | ETA: 0:00:35 Cross validating... 8%|██▌ | ETA: 0:00:33 Cross validating... 9%|██▉ | ETA: 0:00:31 Cross validating... 10%|███▎ | ETA: 0:00:29 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross validating... 12%|███▉ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:26 Cross validating... 14%|████▌ | ETA: 0:00:25 Cross validating... 15%|████▊ | ETA: 0:00:24 Cross validating... 16%|█████▏ | ETA: 0:00:24 Cross validating... 17%|█████▌ | ETA: 0:00:23 Cross validating... 18%|█████▊ | ETA: 0:00:23 Cross validating... 19%|██████▏ | ETA: 0:00:22 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2338.4550388735106 8 2320.772999308408 9 2318.96967255692 10 2315.291532254543 11 2333.1008034531997 12 2343.9051765395507 13 2347.0029189600264 14 2368.1193971315247 15 2383.8009614309303 16 2411.944800699673 17 2416.9887904789966 18 2420.2366763259283 19 2432.070591639391 20 2447.8520661039856 Best k = 10 21.421894 seconds (345.28 k allocations: 323.708 MiB, 0.33% gc time, 7.89% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 26.3s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m07.7s **** 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... 2%|▋ | ETA: 0:00:09 Cross validating... 4%|█▎ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:11 Cross validating... 7%|██▎ | ETA: 0:00:11 Cross validating... 8%|██▌ | 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| ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 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: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 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2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m23.4s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:522 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.8s RNG of the outermost testset: Xoshiro(0x7872c2d8f70807ed, 0x7a63fd12f270383c, 0x13b4d034b629d48f, 0xfee9e59e28000ceb, 0x428c126c752a31d9) 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 1103.42s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1211.77s: package tests unexpectedly errored