Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2064 (1d5dcac2d2*) started at 2026-04-21T23:37:42.030 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.83s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.5.2 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.24.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.4 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.125 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [38e38edf] + GLM v1.9.4 [c27321d9] + Glob v1.4.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.7 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 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[bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 6.11s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.5 s ✓ BGEN 8.0 s ✓ VCFTools 28.9 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 26.5 s ✓ MendelIHT 4 dependencies successfully precompiled in 72 seconds. 170 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 99.12s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_ZRpzKC/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.125 [38e38edf] GLM v1.9.4 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.2 [2913bbd2] StatsBase v0.34.10 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v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = cholesky!(A::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}, ::Val{true}; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:215 └ @ LinearAlgebra ./deprecated.jl:215 Test Summary: | Pass Total Time loglikelihood | 4 4 23.9s Test Summary: | Pass Total Time deviance | 1 1 0.3s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 8.9s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.0s Test Summary: | Pass Total Time maf_weights | 6 6 1.8s **** 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) = 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 = -1662.00776303776, backtracks = 0, tol = 1.5278929904704752 Iteration 2: loglikelihood = -1426.5369346940593, backtracks = 0, tol = 0.15188503044590837 Iteration 3: loglikelihood = -1414.7719610222068, backtracks = 0, tol = 0.030274639214410076 Iteration 4: loglikelihood = -1414.6423722105903, backtracks = 0, tol = 0.00309523477634398 Iteration 5: loglikelihood = -1414.6400864889356, backtracks = 0, tol = 0.00045464474854874196 Iteration 6: loglikelihood = -1414.640036670724, backtracks = 0, tol = 6.715450368968229e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.046430110931396484 Final loglikelihood: -1414.640036670724 SNP PVE: 0.9101941777532438 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 285 1.80689 2 │ 1664 0.231402 3 │ 1870 1.26571 4 │ 4537 -1.42465 5 │ 4851 -0.348762 6 │ 5914 0.561323 7 │ 6484 -1.1075 8 │ 7013 -0.651104 9 │ 7299 -0.339952 10 │ 9799 -0.7859 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0472026Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 21.7s **** 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 logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.7s **** 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 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 = -1640.1387928720314, backtracks = 0, tol = 0.4339733884377949 Iteration 2: loglikelihood = -1409.87193303459, backtracks = 0, tol = 0.06798309116452826 Iteration 3: loglikelihood = -1367.7902997086237, backtracks = 0, tol = 0.053008754996036474 Iteration 4: loglikelihood = -1354.7898050079025, backtracks = 0, tol = 0.11274999645726744 Iteration 5: loglikelihood = -1325.2568438530225, backtracks = 0, tol = 0.044772970590704994 Iteration 6: loglikelihood = -1319.711865546929, backtracks = 0, tol = 0.07446318784660312 Iteration 7: loglikelihood = -1313.4726649502581, backtracks = 1, tol = 0.05215615156104057 Iteration 8: loglikelihood = -1312.6310523191123, backtracks = 2, tol = 0.007423866548597807 Iteration 9: loglikelihood = -1312.0153052994676, backtracks = 2, tol = 0.007548374159857796 Iteration 10: loglikelihood = -1311.6165964009615, backtracks = 2, tol = 0.00648076727242435 Iteration 11: loglikelihood = -1311.3766079390348, backtracks = 2, tol = 0.005106364752678506 Iteration 12: loglikelihood = -1311.235705493911, backtracks = 2, tol = 0.003908976629041104 Iteration 13: loglikelihood = -1311.1228161007236, backtracks = 2, tol = 0.05244525518800583 Iteration 14: loglikelihood = -1310.1435962306741, backtracks = 1, tol = 0.0090776362996252 Iteration 15: loglikelihood = -1309.153587268813, backtracks = 1, tol = 0.0531648944396213 Iteration 16: loglikelihood = -1308.8035942999497, backtracks = 0, tol = 0.006468066747070342 Iteration 17: loglikelihood = -1308.7245076943718, backtracks = 1, tol = 0.0015812038639423875 Iteration 18: loglikelihood = -1308.6846435785533, backtracks = 2, tol = 0.00124389506659088 Iteration 19: loglikelihood = -1307.0886015572667, backtracks = 1, tol = 0.058997892361822346 Iteration 20: loglikelihood = -1306.5502345482857, backtracks = 1, tol = 0.005018509033066175 Iteration 21: loglikelihood = -1306.3271125790693, backtracks = 1, tol = 0.0033996999594704982 Iteration 22: loglikelihood = -1306.2719239430878, backtracks = 2, tol = 0.0011731744696607586 Iteration 23: loglikelihood = -1306.2323876319485, backtracks = 2, tol = 0.001280209313440148 Iteration 24: loglikelihood = -1306.2036769214233, backtracks = 2, tol = 0.0013795344513672391 Iteration 25: loglikelihood = -1306.1837572324844, backtracks = 2, tol = 0.0013541845695492901 Iteration 26: loglikelihood = -1306.1769282188602, backtracks = 3, tol = 0.0005877504540201941 Iteration 27: loglikelihood = -1306.17154446997, backtracks = 3, tol = 0.0005288030631150043 Iteration 28: loglikelihood = -1306.1673275483922, backtracks = 3, tol = 0.00047136644886626976 Iteration 29: loglikelihood = -1306.16404138271, backtracks = 3, tol = 0.0004172108027912231 Iteration 30: loglikelihood = -1306.1614905367244, backtracks = 3, tol = 0.0003673645916575811 Iteration 31: loglikelihood = -1306.1595163133509, backtracks = 3, tol = 0.00032226947222839156 Iteration 32: loglikelihood = -1306.1579917503507, backtracks = 3, tol = 0.00028196710038316624 Iteration 33: loglikelihood = -1306.1568163932138, backtracks = 3, tol = 0.00024625466869129743 Iteration 34: loglikelihood = -1306.155911402097, backtracks = 3, tol = 0.000216056709639739 Iteration 35: loglikelihood = -1306.155215263488, backtracks = 3, tol = 0.00019281806067340023 Iteration 36: loglikelihood = -1306.1546801863472, backtracks = 3, tol = 0.0001717086719551415 Iteration 37: loglikelihood = -1306.1542691559296, backtracks = 3, tol = 0.00015262848085550505 Iteration 38: loglikelihood = -1306.1539535693103, backtracks = 3, tol = 0.00013545186538743595 Iteration 39: loglikelihood = -1306.1537113615298, backtracks = 3, tol = 0.00012004044923762712 Iteration 40: loglikelihood = -1306.1535255333335, backtracks = 3, tol = 0.00010625161721927787 Iteration 41: loglikelihood = -1306.1533830014616, backtracks = 3, tol = 9.394408220205729e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1499.4977389862215, backtracks = 0, tol = 0.37450338146963813 Iteration 2: loglikelihood = -1464.0358964318184, backtracks = 0, tol = 0.16256071822811574 Iteration 3: loglikelihood = -1454.1188005092934, backtracks = 0, tol = 0.1189916209298202 Iteration 4: loglikelihood = -1451.396054377377, backtracks = 0, tol = 0.1036289776974597 Iteration 5: loglikelihood = -1451.2101449841296, backtracks = 0, tol = 0.075292571136238 Iteration 6: loglikelihood = -1450.24536475649, backtracks = 0, tol = 0.0757104544506198 Iteration 7: loglikelihood = -1450.1824708453566, backtracks = 1, tol = 0.00390639222748573 Iteration 8: loglikelihood = -1450.1623871947813, backtracks = 1, tol = 0.0022993670703281744 Iteration 9: loglikelihood = -1450.1559747363824, backtracks = 1, tol = 0.0012547599066593685 Iteration 10: loglikelihood = -1450.1539590567575, backtracks = 1, tol = 0.000637770985573494 Iteration 11: loglikelihood = -1450.1533292878667, backtracks = 1, tol = 0.0003548706571949994 Iteration 12: loglikelihood = -1450.1531339616304, backtracks = 1, tol = 0.0002334136973372154 Iteration 13: loglikelihood = -1450.1530749819099, backtracks = 1, tol = 0.00014329448415552576 Iteration 14: loglikelihood = -1450.1530580263577, backtracks = 1, tol = 8.153749092518318e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1903.1517455796236, backtracks = 0, tol = 0.7060181123325177 Iteration 2: loglikelihood = -1493.470788916196, backtracks = 0, tol = 0.13822484866780607 Iteration 3: loglikelihood = -1407.533873190449, backtracks = 0, tol = 0.05721885823917924 Iteration 4: loglikelihood = -1404.6200476108595, backtracks = 0, tol = 0.01158173653227885 Iteration 5: loglikelihood = -1404.5708179705196, backtracks = 0, tol = 0.0011466329141914882 Iteration 6: loglikelihood = -1404.5698099070748, backtracks = 0, tol = 0.00019677186886767555 Iteration 7: loglikelihood = -1404.5697873032632, backtracks = 0, tol = 2.2447045450969706e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1640.081017492044, backtracks = 0, tol = 0.5419998796528435 Iteration 2: loglikelihood = -1430.146414228329, backtracks = 0, tol = 0.10333552479803992 Iteration 3: loglikelihood = -1404.970649456555, backtracks = 0, tol = 0.04183924717876881 Iteration 4: loglikelihood = -1404.6767801040316, backtracks = 0, tol = 0.003339169042363224 Iteration 5: loglikelihood = -1404.67380837647, backtracks = 0, tol = 0.0003297609385453731 Iteration 6: loglikelihood = -1404.6737643295826, backtracks = 0, tol = 4.66953333483145e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 9.6s **** 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 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 = -1644.7907542668725, backtracks = 0, tol = 0.1635188022412941 Iteration 2: loglikelihood = -1542.130322907812, backtracks = 0, tol = 0.11683889615345644 Iteration 3: loglikelihood = -1445.8786672347621, backtracks = 0, tol = 0.14437786749943488 Iteration 4: loglikelihood = -1417.0708460914834, backtracks = 0, tol = 0.11371330984311505 Iteration 5: loglikelihood = -1408.4841867116236, backtracks = 0, tol = 0.09426057722783852 Iteration 6: loglikelihood = -1398.1026099058247, backtracks = 0, tol = 0.0344395848335314 Iteration 7: loglikelihood = -1392.6296990448304, backtracks = 0, tol = 0.09968095879953418 Iteration 8: loglikelihood = -1389.2866318997842, backtracks = 0, tol = 0.027536966397328937 Iteration 9: loglikelihood = -1388.7849192403519, backtracks = 0, tol = 0.010400378158347386 Iteration 10: loglikelihood = -1388.561606850628, backtracks = 0, tol = 0.009932035586626487 Iteration 11: loglikelihood = -1388.4506325585128, backtracks = 0, tol = 0.004193603521596763 Iteration 12: loglikelihood = -1388.3934792766763, backtracks = 0, tol = 0.005219541910210836 Iteration 13: loglikelihood = -1388.3641107037506, backtracks = 0, tol = 0.0019352622333464525 Iteration 14: loglikelihood = -1388.3487526045435, backtracks = 0, tol = 0.0027752954589381805 Iteration 15: loglikelihood = -1388.3408541386939, backtracks = 0, tol = 0.0009532527581838504 Iteration 16: loglikelihood = -1388.3367031859132, backtracks = 0, tol = 0.001485008780827409 Iteration 17: loglikelihood = -1388.334585884101, backtracks = 0, tol = 0.00047661743609883714 Iteration 18: loglikelihood = -1388.3334732972157, backtracks = 0, tol = 0.0007947310119672386 Iteration 19: loglikelihood = -1388.3329150308193, backtracks = 0, tol = 0.00023699840998257112 Iteration 20: loglikelihood = -1388.3326235531704, backtracks = 0, tol = 0.0004222528414934934 Iteration 21: loglikelihood = -1388.332481160142, backtracks = 0, tol = 0.00011573383113710258 Iteration 22: loglikelihood = -1388.3324263544205, backtracks = 1, tol = 0.00011030559765386296 Iteration 23: loglikelihood = -1388.3323954491977, backtracks = 2, tol = 5.077913446160786e-5 0.913259 seconds (2.25 M allocations: 45.485 MiB, 64.46% 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 = -1658.858361589203, backtracks = 0, tol = 0.1635188022412941 Iteration 2: loglikelihood = -1591.3049836287844, backtracks = 0, tol = 0.128661721567357 Iteration 3: loglikelihood = -1530.8760824573822, backtracks = 0, tol = 0.15237999539921185 Iteration 4: loglikelihood = -1503.44090959412, backtracks = 0, tol = 0.11249313193357531 Iteration 5: loglikelihood = -1480.7145523619618, backtracks = 0, tol = 0.08134183994168917 Iteration 6: loglikelihood = -1467.6188066739821, backtracks = 0, tol = 0.08531499908583426 Iteration 7: loglikelihood = -1456.6748836920892, backtracks = 0, tol = 0.021085348469931292 Iteration 8: loglikelihood = -1448.735650350287, backtracks = 0, tol = 0.005802118249897385 Iteration 9: loglikelihood = -1441.8165687290714, backtracks = 0, tol = 0.005144534319668672 Iteration 10: loglikelihood = -1436.1879370359397, backtracks = 0, tol = 0.002082645531042712 Iteration 11: loglikelihood = -1431.342188621833, backtracks = 0, tol = 0.0012044212127473063 Iteration 12: loglikelihood = -1427.2248823142247, backtracks = 0, tol = 0.0008024093558198706 Iteration 13: loglikelihood = -1423.6653201500867, backtracks = 0, tol = 0.0003956441731090554 Iteration 14: loglikelihood = -1420.5788529448357, backtracks = 0, tol = 0.00045903302060837776 Iteration 15: loglikelihood = -1417.8774644466278, backtracks = 0, tol = 0.00039506846332487477 Iteration 16: loglikelihood = -1415.501483246772, backtracks = 0, tol = 0.00037716888716101207 Iteration 17: loglikelihood = -1413.3976169536804, backtracks = 0, tol = 0.00033772285154546797 Iteration 18: loglikelihood = -1411.5260494897186, backtracks = 0, tol = 0.0003153222436258688 Iteration 19: loglikelihood = -1409.8521834206933, backtracks = 0, tol = 0.0002874493736310646 Iteration 20: loglikelihood = -1408.349044110264, backtracks = 0, tol = 0.00026908037137497867 Iteration 21: loglikelihood = -1406.9932579966473, backtracks = 0, tol = 0.0002484334368610615 Iteration 22: loglikelihood = -1405.7660967361098, backtracks = 0, tol = 0.0002336160416604208 Iteration 23: loglikelihood = -1404.6512611187788, backtracks = 0, tol = 0.00021751154609568377 Iteration 24: loglikelihood = -1403.635411759618, backtracks = 0, tol = 0.0002052829902872157 Iteration 25: loglikelihood = -1402.7068647311492, backtracks = 0, tol = 0.00019229730122023687 Iteration 26: loglikelihood = -1401.855892776787, backtracks = 0, tol = 0.00018205733660121948 Iteration 27: loglikelihood = -1401.0739182668342, backtracks = 0, tol = 0.00017136840501830994 Iteration 28: loglikelihood = -1400.3536990221503, backtracks = 0, tol = 0.00016270844426708562 Iteration 29: loglikelihood = -1399.6888069814559, backtracks = 0, tol = 0.00015377613930178183 Iteration 30: loglikelihood = -1399.0737509932435, backtracks = 0, tol = 0.00014639061006242626 Iteration 31: loglikelihood = -1398.503627043229, backtracks = 0, tol = 0.0001388337927939324 Iteration 32: loglikelihood = -1397.9742042883151, backtracks = 0, tol = 0.0001324863832148123 Iteration 33: loglikelihood = -1397.4816823938572, backtracks = 0, tol = 0.0001260257193347052 Iteration 34: loglikelihood = -1397.0227548830544, backtracks = 0, tol = 0.00012053128264353552 Iteration 35: loglikelihood = -1396.5944356853263, backtracks = 0, tol = 0.00011495691538171707 Iteration 36: loglikelihood = -1396.1941077605995, backtracks = 0, tol = 0.00011016913157371347 Iteration 37: loglikelihood = -1395.8193957509204, backtracks = 0, tol = 0.00010532035458381992 Iteration 38: loglikelihood = -1395.4682046058138, backtracks = 0, tol = 0.00010112264746872299 Iteration 39: loglikelihood = -1395.1386237860215, backtracks = 0, tol = 9.687440396726476e-5 0.395630 seconds (1.48 M allocations: 26.626 MiB, 12.34% 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 = -3781.7568, backtracks = 0, tol = 0.07412832883761236 Iteration 2: loglikelihood = -3751.1055, backtracks = 0, tol = 0.040338049690236404 Iteration 3: loglikelihood = -3747.5554, backtracks = 1, tol = 0.00883786422619296 Iteration 4: loglikelihood = -3746.445, backtracks = 1, tol = 0.007043153201207445 Iteration 5: loglikelihood = -3746.1543, backtracks = 1, tol = 0.003538555475188407 Iteration 6: loglikelihood = -3746.078, backtracks = 1, tol = 0.0018746887933835266 Iteration 7: loglikelihood = -3746.0618, backtracks = 1, tol = 0.0009367001541762902 Iteration 8: loglikelihood = -3746.0574, backtracks = 1, tol = 0.00047664661235344736 Iteration 9: loglikelihood = -3746.053, backtracks = 1, tol = 0.00023821551501026242 Iteration 10: loglikelihood = -3746.0574, backtracks = 3, tol = 2.995707665888558e-5 23.600144 seconds (14.67 M allocations: 676.382 MiB, 5.11% gc time, 94.40% 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 **** 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 = -3668.3984, backtracks = 0, tol = 0.07412832883761236 Iteration 2: loglikelihood = -3555.6514, backtracks = 0, tol = 0.041319590481302924 Iteration 3: loglikelihood = -3307.0, backtracks = 1, tol = 0.008703961206427245 Iteration 4: loglikelihood = -3016.5417, backtracks = 1, tol = 0.006119526726290359 Iteration 5: loglikelihood = -2933.4182, backtracks = 0, tol = 0.09017788809398662 Iteration 6: loglikelihood = -2733.766, backtracks = 0, tol = 0.08864276258585242 Iteration 7: loglikelihood = -2614.3071, backtracks = 0, tol = 0.0888202786206855 Iteration 8: loglikelihood = -2474.8467, backtracks = 0, tol = 0.09293477211118617 Iteration 9: loglikelihood = -2383.5173, backtracks = 0, tol = 0.09332665129806869 Iteration 10: loglikelihood = -2304.4985, backtracks = 0, tol = 0.08785728763435842 Iteration 11: loglikelihood = -2253.3987, backtracks = 0, tol = 0.08793477212268927 Iteration 12: loglikelihood = -2222.5967, backtracks = 0, tol = 0.08864039074393383 Iteration 13: loglikelihood = -2206.5298, backtracks = 0, tol = 0.08877451485276287 Iteration 14: loglikelihood = -2193.9155, backtracks = 0, tol = 0.1038413585099256 Iteration 15: loglikelihood = -2189.1753, backtracks = 0, tol = 0.10344902063655731 Iteration 16: loglikelihood = -2185.1047, backtracks = 0, tol = 0.10367229016701 Iteration 17: loglikelihood = -2184.6812, backtracks = 0, tol = 0.10343645963576048 Iteration 18: loglikelihood = -2182.9824, backtracks = 0, tol = 0.10361493604986811 Iteration 19: loglikelihood = -2179.1655, backtracks = 1, tol = 0.022305072631844777 Iteration 20: loglikelihood = -2178.3472, backtracks = 1, tol = 0.011034057534733003 Iteration 21: loglikelihood = -2178.1565, backtracks = 1, tol = 0.005633535871595518 Iteration 22: loglikelihood = -2178.1077, backtracks = 1, tol = 0.002935290740112875 Iteration 23: loglikelihood = -2178.0974, backtracks = 1, tol = 0.0015642979323225081 Iteration 24: loglikelihood = -2178.0923, backtracks = 1, tol = 0.0008513025625936155 Iteration 25: loglikelihood = -2178.0889, backtracks = 1, tol = 0.0004672343243950026 Iteration 26: loglikelihood = -2178.09, backtracks = 3, tol = 6.343167303277081e-5 0.183262 seconds (1.49 M allocations: 24.755 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 27.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 4.218789 seconds (1.09 M allocations: 136.209 MiB, 0.56% gc time, 91.23% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.6s 9.310249 seconds (4.00 M allocations: 82.500 MiB, 0.21% gc time, 0.68% compilation time) 5.004289 seconds (3.98 M allocations: 91.676 MiB, 0.48% gc time) 10.030362 seconds (20.41 M allocations: 439.468 MiB, 0.89% gc time, 16.05% compilation time: 79% of which was recompilation) 7.991507 seconds (20.18 M allocations: 434.191 MiB, 1.13% gc time) 36.673898 seconds (3.85 M allocations: 4.244 GiB, 11.90% gc time, 25.91% compilation time) 55.723338 seconds (70.38 k allocations: 183.442 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m21.1s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.494 ms (78 allocations: 4.56 KiB) 5.004 μs (0 allocations: 0 bytes) 135.029 μs (4 allocations: 288 bytes) 6.875 μs (0 allocations: 0 bytes) 49.960 μs (2 allocations: 64 bytes) 31.480 μs (0 allocations: 0 bytes) 25.260 μs (0 allocations: 0 bytes) 29.900 μs (0 allocations: 0 bytes) 104.469 μs (0 allocations: 0 bytes) 38.113 ms (78 allocations: 4.56 KiB) 26.410 μs (0 allocations: 0 bytes) 165.638 μs (4 allocations: 288 bytes) 34.210 μs (0 allocations: 0 bytes) 250.218 μs (2 allocations: 64 bytes) 91.969 μs (0 allocations: 0 bytes) 127.389 μs (0 allocations: 0 bytes) 148.539 μs (0 allocations: 0 bytes) 215.367 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m18.9s **** 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 **** **** 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 0.423816 seconds (49.46 k allocations: 5.502 MiB, 63.51% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 1.780194 seconds (282.39 k allocations: 168.156 MiB, 59.80% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.4s **** 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: 0:03:34 Cross validating... 13%|████▏ | ETA: 0:00:52 Cross validating... 16%|█████▏ | ETA: 0:00:40 Cross validating... 19%|██████▏ | ETA: 0:00:33 Cross validating... 22%|███████▏ | ETA: 0:00:28 Cross validating... 25%|████████▏ | ETA: 0:00:24 Cross validating... 29%|█████████▏ | ETA: 0:00:20 Cross validating... 32%|██████████▏ | ETA: 0:00:18 Cross validating... 35%|███████████▏ | ETA: 0:00:16 Cross validating... 38%|████████████▎ | ETA: 0:00:14 Cross validating... 41%|█████████████▎ | ETA: 0:00:12 Cross validating... 44%|██████████████▎ | ETA: 0:00:11 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:06 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 3685.2882634590896 1 2598.9276219959297 2 1809.1396018108987 3 1301.2577057212823 4 899.7070253969812 5 664.5585398945902 6 568.3301317362802 7 435.47044573026153 8 393.5847796699148 9 348.30984276938403 10 330.38638984712725 11 335.4794615683693 12 337.9521902031697 13 339.73473168073014 14 342.55063213515893 15 344.75799469302837 16 347.3924526077857 17 362.33952886547206 18 351.6057597146532 19 377.52259478433575 20 378.1391069933105 Best k = 10 11.353661 seconds (11.24 M allocations: 301.407 MiB, 0.96% gc time, 63.22% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 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... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 3685.2882634590896 1 2599.536550936569 2 1814.7847136313853 3 1308.1701756222112 4 904.1489000657139 5 668.3158151608211 6 574.0229876381375 7 443.80591009904197 8 403.26996143457654 9 359.36775677003374 10 339.6774517535327 11 351.00435251069473 12 359.79442551995726 13 363.3110756665908 14 371.5172843486944 15 378.3860742073765 16 381.8862379269758 17 392.1249785146643 18 400.34037272436973 19 401.78272477546824 20 412.4917319832068 Best k = 10 4.570584 seconds (10.37 M allocations: 219.190 MiB, 0.91% gc time, 1.01% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 16.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:04 Cross validating... 8%|██▌ | ETA: 0:02:20 Cross validating... 13%|████▏ | ETA: 0:01:23 Cross validating... 17%|█████▋ | ETA: 0:00:58 Cross validating... 22%|███████▏ | ETA: 0:00:43 Cross validating... 27%|████████▋ | ETA: 0:00:34 Cross validating... 32%|██████████▏ | ETA: 0:00:27 Cross validating... 37%|███████████▋ | ETA: 0:00:22 Cross validating... 41%|█████████████▎ | ETA: 0:00:18 Cross validating... 48%|███████████████▎ | ETA: 0:00:14 Cross validating... 52%|████████████████▊ | ETA: 0:00:12 Cross validating... 56%|█████████████████▊ | ETA: 0:00:11 Cross validating... 59%|██████████████████▊ | ETA: 0:00:09 Cross validating... 63%|████████████████████▍ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1508.5942687988281 1 1275.738251953125 2 985.973150390625 3 796.0502943115234 4 651.5366916503906 5 530.0277053222657 6 445.71009124755864 7 398.85961822509773 8 349.89329522705077 9 337.2043764648438 10 341.84284942626954 11 345.3317758789063 12 345.7155509033203 13 351.38828033447265 14 352.5186229858399 15 366.5859879150391 16 376.1489256591797 17 358.44975231933597 18 369.9345700683594 19 372.5328582763672 20 358.525208984375 Best k = 9 15.796882 seconds (12.71 M allocations: 315.579 MiB, 0.49% gc time, 83.05% 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... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 54%|█████████████████▎ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1508.5942687988281 1 1279.750272216797 2 991.5410809326173 3 805.177655883789 4 658.1817127685547 5 536.2065656738282 6 452.4565084228516 7 402.9616822509766 8 355.225683959961 9 343.60852783203126 10 355.91591510009766 11 364.4275029907227 12 367.1915301513672 13 381.28735638427736 14 387.27586169433596 15 384.7937032470703 16 395.12071734619144 17 403.07702069091795 18 400.68127465820317 19 403.29317449951174 20 400.4854467163086 Best k = 9 2.795326 seconds (11.13 M allocations: 204.031 MiB, 1.80% gc time, 1.37% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 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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 0 463.88455708996264 1 411.051135980582 2 370.2659544316619 3 337.2613160082527 4 294.12523262149944 5 282.3603022759219 6 269.02648484971644 7 260.10872084769966 8 258.24282828341217 9 250.99001561025466 10 256.8323603823367 11 260.94703342266433 12 257.65340154431146 13 259.0945174278271 14 266.1919679415572 15 263.05015412286696 16 275.33627883364505 17 288.09178113744844 18 291.270541176438 19 307.48760389916606 20 287.0124617198985 Best k = 9 7.914932 seconds (17.70 M allocations: 417.313 MiB, 1.15% gc time, 32.12% 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: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | 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87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.88455708996264 1 411.2353074523022 2 370.897777791848 3 338.74715334343114 4 296.48770595498524 5 285.58713725039365 6 272.9755999353329 7 262.54486040123453 8 270.95890791622656 9 259.57563979722005 10 275.5771569918196 11 278.2428351045014 12 273.43931955348614 13 282.08719181404734 14 296.0898487543253 15 288.10368975484147 16 294.1830978503776 17 313.87128740586974 18 319.2555137247151 19 334.38255154088023 20 318.9950164791141 Best k = 9 5.471779 seconds (17.71 M allocations: 367.818 MiB, 1.18% gc time, 0.99% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:46 Cross validating... 6%|██ | ETA: 0:00:24 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross 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100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.51321245081385 1 439.9725221382007 2 410.71480172479585 3 385.39148654387725 4 357.40356318094155 5 331.11600630145824 6 335.71679849914415 7 337.45883160768403 8 348.2689788179143 9 340.1586415551958 10 339.9959499878282 11 344.2209991945877 12 343.14665829603626 13 384.17512006098127 14 349.59885689243833 15 374.06589394946116 16 352.5230594547048 17 351.7504041100177 18 379.70710707668707 19 438.86682644979555 20 413.59540626616626 Best k = 5 7.507295 seconds (16.21 M allocations: 381.557 MiB, 11.87% gc time, 34.49% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 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: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 464.51321245081385 1 440.0417909933957 2 411.8636624156869 3 387.13367465658587 4 360.5981995489041 5 334.2412709052394 6 346.82408993512126 7 356.6765475313649 8 365.97305240918604 9 374.3192736195325 10 374.4503394418389 11 384.8181607288957 12 379.6699976159918 13 394.19816847398454 14 404.78161444562386 15 412.3091699014394 16 417.57713181799704 17 425.196355854156 18 466.2717162975614 19 461.47232097941867 20 450.1208718386483 Best k = 5 4.521441 seconds (17.55 M allocations: 361.765 MiB, 1.32% gc time, 0.84% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross 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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 0 774.9233553597145 1 569.2039512054915 2 522.8200602721579 3 473.5543488627254 4 413.6878248862187 5 382.95720379966474 6 373.56110279977645 7 366.29977475194835 8 368.2979463921514 9 366.5542499472293 10 375.7870110939664 11 370.3915281120237 12 372.90196997115476 13 372.6193819131757 14 381.94953296453883 15 395.5955649929128 16 390.643503125568 17 391.5861657213687 18 399.5938857066599 19 374.8521811695904 20 374.5668341459456 Best k = 7 7.924159 seconds (15.86 M allocations: 379.779 MiB, 1.06% gc time, 33.32% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 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Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 774.9233553597145 1 562.6479003997333 2 519.9515269589748 3 477.2618917479806 4 419.7537375189197 5 389.16549642418454 6 377.8910382410082 7 371.9686783054879 8 371.2035908966426 9 384.8017178681191 10 391.0353357766503 11 398.99939041887086 12 402.2922683409262 13 397.1872676537081 14 402.2051871460912 15 408.6153437501672 16 413.52076298286624 17 418.20574128126043 18 415.717637787659 19 409.997636521539 20 419.09174882354665 Best k = 8 5.300645 seconds (14.64 M allocations: 296.989 MiB, 1.02% gc time, 1.06% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.7s **** 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 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0:00:09 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:08 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:08 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:06 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:06 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:05 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:04 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:02 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: 0:00:37 Crossvalidation Results: k MSE 0 344.27657886277314 1 291.7050984300371 2 261.9703733111954 3 238.00614529711356 4 222.4818856876825 5 218.91647084833906 6 211.16810324850672 7 211.10186265922133 8 211.87614724216232 9 216.29903468298355 10 217.58934007339585 11 213.60170601922187 12 213.31263006494865 13 214.09002093678833 14 217.5144791909815 15 221.0831013378228 16 221.82763628092778 17 221.19913524090094 18 222.06322255985003 19 217.0715741700442 20 218.55210132830334 Best k = 7 37.839184 seconds (121.81 M allocations: 3.163 GiB, 1.22% gc time, 5.92% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 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ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 344.27657886277314 1 291.7087236850023 2 262.3009739899678 3 239.03525351078815 4 223.33162658132244 5 220.28629690676354 6 216.91554683097505 7 218.15610876099947 8 219.332939978424 9 225.72831086951396 10 229.6258301672466 11 224.74201754497028 12 224.86873572662165 13 229.86519589248127 14 234.07571074191821 15 242.45940595858156 16 248.25684109030612 17 249.0152647481739 18 251.49326931825786 19 252.36917971007927 20 252.78395336884154 Best k = 6 11.547238 seconds (37.24 M allocations: 772.964 MiB, 0.97% gc time, 0.53% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 49.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:13 Cross validating... 6%|██ | ETA: 0:00:37 Cross validating... 10%|███ | ETA: 0:00:25 Cross 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75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 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 6.392948 seconds (17.01 M allocations: 337.918 MiB, 1.21% gc time, 46.87% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | 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ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.475611 seconds (16.18 M allocations: 286.714 MiB, 1.85% gc time, 1.56% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange 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3132.014825593491 13 3164.848778722316 14 3193.1189876111966 15 3244.6989646454012 16 3237.982876971583 17 3250.10984648695 18 3281.3610077905046 19 3299.2116126157016 20 3332.06059528128 Best k = 4 18.573492 seconds (326.71 k allocations: 225.615 MiB, 0.61% gc time, 9.17% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.6s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m57.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross 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ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:20 Cross validating... 20%|██████▍ | ETA: 0:00:20 Cross validating... 21%|██████▊ | ETA: 0:00:19 Cross validating... 22%|███████ | ETA: 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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: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m30.7s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] getproperty(x::Nothing, f::Symbol) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] collect(itr::Base.Generator{UnitRange{Int64}, MendelIHT.var"#convert_bgen_gt##0#convert_bgen_gt##1"}) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [18] _start() @ Base ./client.jl:593 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.1s RNG of the outermost testset: Xoshiro(0xac10b6e3af2e13e5, 0x5b0d706aeb1ad93c, 0xdcb2abb421ff8d2e, 0x55df68d5fadfd95e, 0x65d24082f69b5311) 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 1084.23s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1230.76s: package tests unexpectedly errored