Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2113 (886384998d*) started at 2026-05-03T23:56:38.674 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.68s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.5.2 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.24.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[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 To see why use `status --outdated -m` Installation completed after 6.13s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.4 s ✓ BGEN 7.9 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`. 28.0 s ✓ MendelIHT 3 dependencies successfully precompiled in 45 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 69.6s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_veUqpU/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 16.9s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.6s Test Summary: | Pass Total Time _choose! | 7 7 10.7s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.6s Test Summary: | Pass Total Time project_k! | 2 2 1.3s 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 = -1548.1242695918265, backtracks = 0, tol = 1.617028843584502 Iteration 2: loglikelihood = -1416.2123617973089, backtracks = 0, tol = 0.11316895643531266 Iteration 3: loglikelihood = -1406.981267550935, backtracks = 0, tol = 0.055597444827953604 Iteration 4: loglikelihood = -1406.719271728585, backtracks = 0, tol = 0.00422052328791275 Iteration 5: loglikelihood = -1406.7149839550307, backtracks = 0, tol = 0.0005092284514783901 Iteration 6: loglikelihood = -1406.7148769972225, backtracks = 0, tol = 9.702133034775172e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05579113960266113 Final loglikelihood: -1406.7148769972225 SNP PVE: 0.8675167644266715 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 189 0.491218 2 │ 379 -1.80759 3 │ 480 -1.21487 4 │ 718 0.140697 5 │ 2589 0.588568 6 │ 4099 -0.587381 7 │ 4823 0.688046 8 │ 5083 -0.265791 9 │ 8849 -0.311234 10 │ 9758 -0.194987 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0268224Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.0s **** 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 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 6.0s **** 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 = -1406.5940232363437, backtracks = 0, tol = 0.2756153448339419 Iteration 2: loglikelihood = -1375.9370725737242, backtracks = 0, tol = 0.04737797174623365 Iteration 3: loglikelihood = -1355.8786104651138, backtracks = 0, tol = 0.06575773546484674 Iteration 4: loglikelihood = -1344.7666861484026, backtracks = 1, tol = 0.06311582769889536 Iteration 5: loglikelihood = -1339.748759279601, backtracks = 0, tol = 0.061046229876017336 Iteration 6: loglikelihood = -1334.0574248575044, backtracks = 1, tol = 0.033648438376905 Iteration 7: loglikelihood = -1332.7983386480594, backtracks = 2, tol = 0.009035859698121452 Iteration 8: loglikelihood = -1331.9877395271171, backtracks = 2, tol = 0.007351560707338905 Iteration 9: loglikelihood = -1331.4805424348006, backtracks = 2, tol = 0.006412622455317695 Iteration 10: loglikelihood = -1331.170603104902, backtracks = 2, tol = 0.0054061197486434814 Iteration 11: loglikelihood = -1330.9858691858374, backtracks = 2, tol = 0.004374431883388979 Iteration 12: loglikelihood = -1330.8779950831076, backtracks = 2, tol = 0.003430361374454019 Iteration 13: loglikelihood = -1330.8158771177318, backtracks = 2, tol = 0.0026375778740256 Iteration 14: loglikelihood = -1330.7804143309486, backtracks = 2, tol = 0.0020054783582545907 Iteration 15: loglikelihood = -1330.760272885127, backtracks = 2, tol = 0.0015156966003716103 Iteration 16: loglikelihood = -1330.7488690355244, backtracks = 2, tol = 0.0011418385965250317 Iteration 17: loglikelihood = -1330.7424250065933, backtracks = 2, tol = 0.0008586799135815479 Iteration 18: loglikelihood = -1330.738788365263, backtracks = 2, tol = 0.0006450947896589385 Iteration 19: loglikelihood = -1330.7367378756169, backtracks = 2, tol = 0.00048434879912787293 Iteration 20: loglikelihood = -1330.7355824500876, backtracks = 2, tol = 0.00036352429526663086 Iteration 21: loglikelihood = -1330.7349316772895, backtracks = 2, tol = 0.0002727760124089597 Iteration 22: loglikelihood = -1330.734565262858, backtracks = 2, tol = 0.00020464972610019158 Iteration 23: loglikelihood = -1330.7343590056441, backtracks = 2, tol = 0.00015352195113259515 Iteration 24: loglikelihood = -1330.7342429232149, backtracks = 2, tol = 0.00011515919069571122 Iteration 25: loglikelihood = -1330.734177600416, backtracks = 2, tol = 8.637842448155306e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.4s **** 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 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 = -1478.1178588273806, backtracks = 0, tol = 0.3251086737108626 Iteration 2: loglikelihood = -1453.4919602379525, backtracks = 0, tol = 0.13411559632106332 Iteration 3: loglikelihood = -1450.2920030186976, backtracks = 0, tol = 0.09013276403222732 Iteration 4: loglikelihood = -1445.9219649269628, backtracks = 0, tol = 0.08302477568022752 Iteration 5: loglikelihood = -1445.7049768066897, backtracks = 1, tol = 0.007743035494822871 Iteration 6: loglikelihood = -1445.626682058436, backtracks = 1, tol = 0.0051739888988188 Iteration 7: loglikelihood = -1445.6030230891556, backtracks = 1, tol = 0.003031654287735685 Iteration 8: loglikelihood = -1445.5966277248522, backtracks = 1, tol = 0.0016410236314304844 Iteration 9: loglikelihood = -1445.5949726605268, backtracks = 1, tol = 0.0008362444827594269 Iteration 10: loglikelihood = -1445.5945506930018, backtracks = 1, tol = 0.00042154121516334563 Iteration 11: loglikelihood = -1445.5944435019749, backtracks = 1, tol = 0.00021163120689653942 Iteration 12: loglikelihood = -1445.5944163233712, backtracks = 1, tol = 0.00010639796950156717 Iteration 13: loglikelihood = -1445.5944094354131, backtracks = 1, tol = 5.348582944584022e-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 = -1721.9574883592334, backtracks = 0, tol = 0.7849033978816284 Iteration 2: loglikelihood = -1424.1764554226427, backtracks = 0, tol = 0.14624928655174532 Iteration 3: loglikelihood = -1392.7313819825667, backtracks = 0, tol = 0.0424281686123544 Iteration 4: loglikelihood = -1391.5011504294682, backtracks = 0, tol = 0.006392734565889969 Iteration 5: loglikelihood = -1390.1691223226019, backtracks = 0, tol = 0.027033579800321155 Iteration 6: loglikelihood = -1390.087591087292, backtracks = 0, tol = 0.0013937847996845201 Iteration 7: loglikelihood = -1389.8527932317068, backtracks = 0, tol = 0.028206359148238273 Iteration 8: loglikelihood = -1389.7631559215104, backtracks = 0, tol = 0.0015530508414401073 Iteration 9: loglikelihood = -1389.7626945555144, backtracks = 0, tol = 0.00013747900154549605 Iteration 10: loglikelihood = -1389.7626837363205, backtracks = 0, tol = 2.0317769220095337e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1710.0285533818421, backtracks = 0, tol = 0.6046294422780032 Iteration 2: loglikelihood = -1426.601690030175, backtracks = 0, tol = 0.11317515761235726 Iteration 3: loglikelihood = -1390.900019008803, backtracks = 0, tol = 0.05136671955826362 Iteration 4: loglikelihood = -1389.788445529782, backtracks = 0, tol = 0.006335936760441621 Iteration 5: loglikelihood = -1389.7679861838285, backtracks = 0, tol = 0.0009033658625973223 Iteration 6: loglikelihood = -1389.7676128841927, backtracks = 1, tol = 6.94583579956398e-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 = -1525.2527989126152, backtracks = 0, tol = 0.20373481276056632 Iteration 2: loglikelihood = -1487.8225539971406, backtracks = 0, tol = 0.09894799956519433 Iteration 3: loglikelihood = -1443.499456970337, backtracks = 1, tol = 0.06087164964974862 Iteration 4: loglikelihood = -1372.9605548244033, backtracks = 0, tol = 0.14973713277101702 Iteration 5: loglikelihood = -1348.1104055066094, backtracks = 0, tol = 0.10687103991265978 Iteration 6: loglikelihood = -1342.1370573987376, backtracks = 0, tol = 0.038314902069376724 Iteration 7: loglikelihood = -1340.499745894773, backtracks = 0, tol = 0.01624887014015021 Iteration 8: loglikelihood = -1339.7830452592616, backtracks = 0, tol = 0.017239163434911088 Iteration 9: loglikelihood = -1339.435970736137, backtracks = 0, tol = 0.007801604691340535 Iteration 10: loglikelihood = -1339.2692443322603, backtracks = 0, tol = 0.008121348187145501 Iteration 11: loglikelihood = -1339.1867800717012, backtracks = 0, tol = 0.0038739837558255654 Iteration 12: loglikelihood = -1339.146274602485, backtracks = 0, tol = 0.003938491705958339 Iteration 13: loglikelihood = -1339.1261619239933, backtracks = 0, tol = 0.0019347948925498867 Iteration 14: loglikelihood = -1339.1162089784054, backtracks = 0, tol = 0.0019337911137512114 Iteration 15: loglikelihood = -1339.1112652182574, backtracks = 0, tol = 0.000965733959586878 Iteration 16: loglikelihood = -1339.1088121605694, backtracks = 0, tol = 0.0009544546295586542 Iteration 17: loglikelihood = -1339.1075942874334, backtracks = 0, tol = 0.0004813589645927729 Iteration 18: loglikelihood = -1339.1069894663215, backtracks = 0, tol = 0.0004720783207661126 Iteration 19: loglikelihood = -1339.106689391428, backtracks = 0, tol = 0.00023963573870954585 Iteration 20: loglikelihood = -1339.1065403564435, backtracks = 0, tol = 0.0002336511182258928 Iteration 21: loglikelihood = -1339.10646646659, backtracks = 0, tol = 0.0001191815995583226 Iteration 22: loglikelihood = -1339.10642977916, backtracks = 0, tol = 0.00011564351261975843 Iteration 23: loglikelihood = -1339.106411602644, backtracks = 0, tol = 5.922529747712909e-5 1.055043 seconds (2.43 M allocations: 48.166 MiB, 2.53% gc time, 61.95% 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 = -1565.2428403943004, backtracks = 0, tol = 0.20373481276056632 Iteration 2: loglikelihood = -1513.217114911911, backtracks = 0, tol = 0.12075323580121666 Iteration 3: loglikelihood = -1471.123336279555, backtracks = 0, tol = 0.1325990360432654 Iteration 4: loglikelihood = -1445.522437755213, backtracks = 0, tol = 0.10804087511539981 Iteration 5: loglikelihood = -1430.301401927915, backtracks = 0, tol = 0.06914241854261688 Iteration 6: loglikelihood = -1418.3995828244117, backtracks = 0, tol = 0.02656259171233648 Iteration 7: loglikelihood = -1408.9118314238901, backtracks = 0, tol = 0.0753135923001167 Iteration 8: loglikelihood = -1402.8593720583228, backtracks = 0, tol = 0.0772656502998522 Iteration 9: loglikelihood = -1394.856611875633, backtracks = 0, tol = 0.07728349093529807 Iteration 10: loglikelihood = -1389.8069421508824, backtracks = 0, tol = 0.00747290709910225 Iteration 11: loglikelihood = -1385.3512524501257, backtracks = 0, tol = 0.003295076442944223 Iteration 12: loglikelihood = -1381.6187783950593, backtracks = 0, tol = 0.0011046205717350679 Iteration 13: loglikelihood = -1378.3097663471117, backtracks = 0, tol = 0.001187591022486013 Iteration 14: loglikelihood = -1375.4537659522377, backtracks = 0, tol = 0.0004858013109708712 Iteration 15: loglikelihood = -1373.3434837074658, backtracks = 0, tol = 0.07114339018499624 Iteration 16: loglikelihood = -1370.84148456899, backtracks = 0, tol = 0.007366407779989194 Iteration 17: loglikelihood = -1368.7838749318082, backtracks = 0, tol = 0.000867833920899033 Iteration 18: loglikelihood = -1366.915250529768, backtracks = 0, tol = 0.07301642449810147 Iteration 19: loglikelihood = -1365.2284714153125, backtracks = 0, tol = 0.006778491465158993 Iteration 20: loglikelihood = -1363.7798957206492, backtracks = 0, tol = 0.000803560027333506 Iteration 21: loglikelihood = -1362.48149540253, backtracks = 0, tol = 0.0003614077560942826 Iteration 22: loglikelihood = -1361.4601646848107, backtracks = 0, tol = 0.06769151226259479 Iteration 23: loglikelihood = -1360.1717600049658, backtracks = 0, tol = 0.004383032695628719 Iteration 24: loglikelihood = -1359.1193609358938, backtracks = 0, tol = 0.0008768528494048561 Iteration 25: loglikelihood = -1358.1424008223664, backtracks = 0, tol = 0.00028742244161241847 Iteration 26: loglikelihood = -1357.2531625777744, backtracks = 0, tol = 0.0002357217036906493 Iteration 27: loglikelihood = -1356.6073453618512, backtracks = 0, tol = 0.06943034440040197 Iteration 28: loglikelihood = -1355.8090635849283, backtracks = 0, tol = 0.005089594773611208 Iteration 29: loglikelihood = -1355.1361137244328, backtracks = 0, tol = 0.0008590399817274849 Iteration 30: loglikelihood = -1354.5227605196321, backtracks = 0, tol = 0.00032881273411505205 Iteration 31: loglikelihood = -1353.9372841694787, backtracks = 0, tol = 0.00037431257931048106 Iteration 32: loglikelihood = -1353.3958742975672, backtracks = 0, tol = 0.00015413203038188767 Iteration 33: loglikelihood = -1352.8635965067217, backtracks = 0, tol = 0.06980097242944908 Iteration 34: loglikelihood = -1352.1724357741748, backtracks = 0, tol = 0.005972491320577476 Iteration 35: loglikelihood = -1351.6823704893063, backtracks = 0, tol = 0.0010076943025091546 Iteration 36: loglikelihood = -1351.2147286604504, backtracks = 0, tol = 0.00033391230491307755 Iteration 37: loglikelihood = -1350.7848799826222, backtracks = 0, tol = 0.0002909717568854187 Iteration 38: loglikelihood = -1350.0200444923598, backtracks = 1, tol = 7.31115445955604e-5 0.385388 seconds (1.41 M allocations: 25.597 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3528.633, backtracks = 0, tol = 0.09550056811794551 Iteration 2: loglikelihood = -3480.741, backtracks = 0, tol = 0.049463954902123415 Iteration 3: loglikelihood = -3474.573, backtracks = 1, tol = 0.015736403281330153 Iteration 4: loglikelihood = -3472.8044, backtracks = 1, tol = 0.009698340325884342 Iteration 5: loglikelihood = -3472.3276, backtracks = 1, tol = 0.004937802726882621 Iteration 6: loglikelihood = -3472.203, backtracks = 1, tol = 0.0026731160308479966 Iteration 7: loglikelihood = -3472.1726, backtracks = 1, tol = 0.0013227239225210123 Iteration 8: loglikelihood = -3472.167, backtracks = 1, tol = 0.0006931191799976569 Iteration 9: loglikelihood = -3472.163, backtracks = 1, tol = 0.0003414949070006166 Iteration 10: loglikelihood = -3472.165, backtracks = 3, tol = 4.42529073957164e-5 26.983288 seconds (14.74 M allocations: 678.510 MiB, 4.42% gc time, 94.77% 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 = -3420.5322, backtracks = 0, tol = 0.09550056811794551 Iteration 2: loglikelihood = -3304.331, backtracks = 0, tol = 0.05116120626679555 Iteration 3: loglikelihood = -3115.3584, backtracks = 1, tol = 0.015000869375893521 Iteration 4: loglikelihood = -2899.4148, backtracks = 1, tol = 0.009401382060941425 Iteration 5: loglikelihood = -2669.7292, backtracks = 1, tol = 0.004878190900866644 Iteration 6: loglikelihood = -2461.6177, backtracks = 1, tol = 0.0025368057717441877 Iteration 7: loglikelihood = -2307.7678, backtracks = 1, tol = 0.0012717807312551412 Iteration 8: loglikelihood = -2278.432, backtracks = 0, tol = 0.09951506792364764 Iteration 9: loglikelihood = -2217.8372, backtracks = 0, tol = 0.11934784308287844 Iteration 10: loglikelihood = -2188.952, backtracks = 0, tol = 0.11879578581710845 Iteration 11: loglikelihood = -2176.855, backtracks = 0, tol = 0.10268935439617684 Iteration 12: loglikelihood = -2165.1536, backtracks = 0, tol = 0.10469607881648772 Iteration 13: loglikelihood = -2156.3296, backtracks = 1, tol = 0.01735850348849155 Iteration 14: loglikelihood = -2154.0354, backtracks = 1, tol = 0.00808317616335214 Iteration 15: loglikelihood = -2153.4673, backtracks = 1, tol = 0.003702424969165929 Iteration 16: loglikelihood = -2153.327, backtracks = 1, tol = 0.001647842847745133 Iteration 17: loglikelihood = -2153.293, backtracks = 1, tol = 0.0007125596268566713 Iteration 18: loglikelihood = -2153.2847, backtracks = 1, tol = 0.0003320417142171139 Iteration 19: loglikelihood = -2153.2844, backtracks = 1, tol = 0.00019696867383153885 Iteration 20: loglikelihood = -2153.2837, backtracks = 1, tol = 0.0001144133165057673 Iteration 21: loglikelihood = -2153.2827, backtracks = 1, tol = 6.577165887992046e-5 0.182159 seconds (1.29 M allocations: 21.607 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.3s **** 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 = -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 4.949934 seconds (1.15 M allocations: 137.149 MiB, 1.61% gc time, 89.53% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.4s 11.313428 seconds (4.00 M allocations: 82.500 MiB, 0.17% gc time, 0.58% compilation time) 5.983555 seconds (3.98 M allocations: 91.674 MiB, 0.39% gc time) 11.789404 seconds (20.41 M allocations: 439.458 MiB, 0.82% gc time, 16.89% compilation time: 80% of which was recompilation) 9.586108 seconds (20.18 M allocations: 434.187 MiB, 1.01% gc time) 40.617577 seconds (3.85 M allocations: 4.244 GiB, 10.61% gc time, 28.36% compilation time) 59.018639 seconds (70.38 k allocations: 183.440 MiB, 0.28% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m37.0s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.231 ms (78 allocations: 4.56 KiB) 4.446 μs (0 allocations: 0 bytes) 131.839 μs (4 allocations: 288 bytes) 7.210 μs (0 allocations: 0 bytes) 50.389 μs (2 allocations: 64 bytes) 31.290 μs (0 allocations: 0 bytes) 27.749 μs (0 allocations: 0 bytes) 34.210 μs (0 allocations: 0 bytes) 113.469 μs (0 allocations: 0 bytes) 38.731 ms (78 allocations: 4.56 KiB) 18.960 μs (0 allocations: 0 bytes) 169.239 μs (4 allocations: 288 bytes) 35.410 μs (0 allocations: 0 bytes) 235.078 μs (2 allocations: 64 bytes) 84.219 μs (0 allocations: 0 bytes) 157.928 μs (0 allocations: 0 bytes) 196.259 μs (0 allocations: 0 bytes) 204.818 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m20.7s **** 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 **** **** 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 0.446972 seconds (49.47 k allocations: 5.503 MiB, 58.79% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 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 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.767850 seconds (282.46 k allocations: 168.160 MiB, 38.02% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 3.4s **** 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: 0:03:51 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... 32%|██████████▏ | ETA: 0:00:20 Cross validating... 35%|███████████▏ | ETA: 0:00:17 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:14 Cross validating... 44%|██████████████▎ | ETA: 0:00:12 Cross validating... 48%|███████████████▎ | ETA: 0:00:11 Cross validating... 51%|████████████████▎ | ETA: 0:00:10 Cross validating... 54%|█████████████████▎ | ETA: 0:00:09 Cross validating... 57%|██████████████████▎ | ETA: 0:00:08 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 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: 0:00:12 Crossvalidation Results: k MSE 0 2467.623816988689 1 1366.87142001839 2 885.7477117048794 3 715.8819930226905 4 616.8009886480976 5 488.22319609121234 6 403.93871567845173 7 369.7525823020734 8 347.069170379114 9 340.48021229329413 10 344.7206554155367 11 339.2170122012623 12 340.8382193986268 13 344.5353257443031 14 343.6158872344123 15 340.5775215625214 16 343.3311444853565 17 348.0038814778861 18 358.9828526584391 19 371.8136038037419 20 372.4629596542888 Best k = 11 12.297795 seconds (11.63 M allocations: 307.888 MiB, 0.93% gc time, 62.95% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:04 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... 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... 73%|███████████████████████▍ | 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... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 2467.623816988689 1 1368.1559337854028 2 886.6853916362913 3 717.6257306084653 4 621.8010165103656 5 494.2648533450655 6 407.739861001945 7 373.4846927975609 8 354.1524248655736 9 348.88465265924077 10 361.4805519215895 11 357.33438363971 12 363.91078427616577 13 373.5812225673292 14 375.9808735297292 15 374.24033640356856 16 380.74599806413653 17 387.2131116622582 18 391.0204962139585 19 399.81707928025287 20 410.4578362211611 Best k = 9 5.766525 seconds (10.54 M allocations: 221.690 MiB, 0.76% gc time, 0.80% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.9s **** 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: 0:06:13 Cross validating... 8%|██▌ | ETA: 0:02:23 Cross validating... 13%|████▏ | ETA: 0:01:26 Cross validating... 19%|██████▏ | ETA: 0:00:54 Cross validating... 24%|███████▋ | ETA: 0:00:41 Cross validating... 29%|█████████▏ | ETA: 0:00:32 Cross validating... 33%|██████████▋ | ETA: 0:00:26 Cross validating... 38%|████████████▎ | ETA: 0:00:21 Cross validating... 43%|█████████████▊ | ETA: 0:00:18 Cross validating... 48%|███████████████▎ | ETA: 0:00:15 Cross validating... 52%|████████████████▊ | ETA: 0:00:12 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 62%|███████████████████▊ | ETA: 0:00:08 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1560.6925229492188 1 1318.2134267578124 2 1033.235053955078 3 797.7888846435546 4 614.3588548583984 5 489.06260070800784 6 413.2853767089844 7 353.95357318115236 8 326.07892315673826 9 326.1332276611328 10 328.8020057373047 11 330.6857949829101 12 331.2008981933594 13 329.74860766601563 14 349.8833353881836 15 339.6344838867187 16 337.9799130859375 17 343.652542175293 18 357.0484574584961 19 395.5823734741211 20 346.36659338378905 Best k = 8 15.702844 seconds (12.85 M allocations: 319.929 MiB, 0.62% gc time, 83.29% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:00 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1560.6925229492188 1 1318.7379997558594 2 1034.4031137695313 3 808.6926264648437 4 621.8698026123047 5 497.78954736328126 6 419.232450012207 7 359.7937537231445 8 332.5026404418945 9 334.7508194580078 10 342.5298471069336 11 347.82481335449216 12 350.8321638183594 13 346.28251446533204 14 373.92444696044925 15 365.01119598388675 16 365.35089642333986 17 385.25084686279297 18 370.0743847045899 19 394.1681088256836 20 397.5069052734375 Best k = 8 2.748428 seconds (11.48 M allocations: 211.567 MiB, 2.44% gc time, 1.53% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.8s **** 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: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 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: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 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... 52%|████████████████▊ | ETA: 0:00:04 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: 0:00:01 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: 0:00:07 Crossvalidation Results: k MSE 0 464.9354109881525 1 384.62988350009084 2 341.38810131559865 3 328.2425773578508 4 314.292345327673 5 305.8765654619325 6 303.898878631638 7 291.34140058779514 8 295.5381420712946 9 310.4626195189631 10 317.8498101517416 11 311.5180659287305 12 314.9102214494461 13 299.2524853955739 14 306.63548841923705 15 328.122286550741 16 308.54902034362544 17 335.87875914655007 18 310.03767275095186 19 339.03813901454237 20 342.2452759458561 Best k = 7 8.221827 seconds (17.24 M allocations: 406.372 MiB, 1.18% gc time, 32.65% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 14%|████▋ | 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: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 464.9354109881525 1 385.0087526512573 2 342.5421250946972 3 330.6116776704817 4 317.35396218508987 5 311.50030363137654 6 311.4580119510874 7 304.400709476098 8 314.6239992305591 9 314.546758813074 10 331.05294278890904 11 333.62903909026375 12 342.47677883636027 13 332.42364103141125 14 351.98380701344894 15 348.5693784500054 16 369.4112275714847 17 376.7025872288233 18 373.2829010643542 19 390.7019091553574 20 375.90456769387026 Best k = 7 5.397533 seconds (17.19 M allocations: 354.238 MiB, 1.69% gc time, 1.11% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.0s **** 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: 0:00:46 Cross validating... 6%|██ | ETA: 0:00:24 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 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: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.65897509351544 1 444.6271695492662 2 411.8720274404684 3 390.55502948980626 4 373.84853310450444 5 362.53944086274095 6 348.6861270005995 7 340.97557847363635 8 343.2861940399623 9 344.4281926614177 10 342.095565120696 11 346.20429597106465 12 348.198336273985 13 361.5309385503099 14 357.65445770799107 15 360.3367184476823 16 364.12259811422444 17 363.69725911742455 18 401.75135532941965 19 384.2019173999798 20 411.3311799089241 Best k = 7 7.651490 seconds (15.86 M allocations: 373.747 MiB, 13.18% gc time, 34.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:04 Cross validating... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:04 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 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: 0:00:01 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 0 463.65897509351544 1 446.7391121464169 2 414.6170423638389 3 393.20706450822667 4 377.0308084301272 5 363.94778659085046 6 355.048505216781 7 343.24967397918715 8 351.00348991900375 9 355.8847120441157 10 358.21935002379365 11 366.00230553851424 12 377.1343419735391 13 367.970233165325 14 391.4117800889986 15 394.15831234282217 16 395.4151176924737 17 422.51933263706644 18 431.55730645389554 19 427.3919202629089 20 438.16316205687565 Best k = 7 4.354405 seconds (16.81 M allocations: 343.813 MiB, 1.89% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 11%|███▌ | ETA: 0:00:21 Cross validating... 14%|████▋ | ETA: 0:00:17 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:11 Cross validating... 27%|████████▋ | ETA: 0:00:10 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 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validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 571.3572106871319 1 489.1336760904712 2 445.55765665532726 3 434.9407726777119 4 431.5235085597483 5 416.2582641416004 6 414.8815761602287 7 416.81425898252434 8 419.2404675331649 9 412.6678696671033 10 417.76672865349315 11 422.52563145594377 12 418.21353312398804 13 432.3775690596152 14 422.99065796935963 15 417.23763289633064 16 425.447372685465 17 441.13774033726395 18 430.6769618393407 19 452.8798977389643 20 454.31064507280206 Best k = 9 8.486541 seconds (16.58 M allocations: 408.089 MiB, 0.86% gc time, 32.47% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 5%|█▌ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | 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... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross 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100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 571.3572106871319 1 486.81104226304774 2 444.0307523244135 3 436.9170268645114 4 435.59875774989075 5 420.84243999832603 6 423.1741363660613 7 427.6640916537346 8 432.05115146147847 9 436.44697179616594 10 435.59389295478115 11 457.928516164043 12 449.827881858697 13 466.2218019638835 14 463.29514283150087 15 493.21195544833165 16 491.0411488893833 17 483.85718273642556 18 482.25669945603033 19 502.87347200165664 20 499.75464383590645 Best k = 5 5.905645 seconds (15.94 M allocations: 332.094 MiB, 0.97% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.8s **** 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: 0:01:04 Cross validating... 5%|█▌ | ETA: 0:00:58 Cross validating... 8%|██▌ | ETA: 0:00:44 Cross validating... 10%|███ | ETA: 0:00:44 Cross validating... 11%|███▌ | ETA: 0:00:38 Cross validating... 13%|████▏ | ETA: 0:00:33 Cross validating... 16%|█████▏ | ETA: 0:00:27 Cross validating... 17%|█████▋ | ETA: 0:00:28 Cross validating... 19%|██████▏ | ETA: 0:00:26 Cross validating... 21%|██████▋ | ETA: 0:00:25 Cross validating... 22%|███████▏ | ETA: 0:00:26 Cross validating... 24%|███████▋ | ETA: 0:00:27 Cross validating... 25%|████████▏ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:27 Cross validating... 29%|█████████▏ | ETA: 0:00:28 Cross validating... 30%|█████████▋ | ETA: 0:00:28 Cross validating... 32%|██████████▏ | ETA: 0:00:28 Cross validating... 33%|██████████▋ | ETA: 0:00:28 Cross validating... 37%|███████████▋ | ETA: 0:00:25 Cross validating... 40%|████████████▊ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:23 Cross validating... 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0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:39 Crossvalidation Results: k MSE 0 300.10160884787916 1 250.0695103951507 2 229.9483021049486 3 224.7720336373044 4 214.02215391365115 5 214.64317887135985 6 213.33703406693388 7 215.0291153079342 8 215.8966975197959 9 217.39964585370797 10 218.45342151750543 11 216.4638249531183 12 218.61447649104798 13 222.0740296000518 14 221.7125749491903 15 219.20965755344918 16 221.29149115560847 17 222.25926175748015 18 226.34035349148917 19 223.9495461584263 20 226.90602539669294 Best k = 6 39.439651 seconds (126.79 M allocations: 3.264 GiB, 1.14% gc time, 5.96% 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 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 300.10160884787916 1 250.17470501635677 2 231.10469383961632 3 226.6651450067839 4 216.14487793872172 5 218.84213132873572 6 218.0399568323898 7 221.39774076265394 8 227.48913323464134 9 228.3707745261206 10 233.76832840333017 11 235.10737461993264 12 236.47418674829095 13 237.83981140847158 14 235.91939844414972 15 244.2298657232245 16 249.548849732208 17 252.28601320406645 18 254.85030223861745 19 263.8620017582122 20 270.900056175413 Best k = 4 12.416439 seconds (36.78 M allocations: 765.576 MiB, 0.92% gc time, 0.48% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 52.3s **** 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: 0:01:14 Cross validating... 6%|██ | ETA: 0:00:38 Cross validating... 10%|███ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 0:00:19 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: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 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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 6.452225 seconds (17.01 M allocations: 337.916 MiB, 1.12% gc time, 47.67% 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... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 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94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.324454 seconds (16.17 M allocations: 286.711 MiB, 1.55% gc time, 1.88% 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 **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:23 Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 4%|█▎ | ETA: 0:00:49 Cross validating... 5%|█▋ | ETA: 0:00:42 Cross validating... 6%|█▉ | ETA: 0:00:38 Cross validating... 7%|██▎ | ETA: 0:00:34 Cross validating... 8%|██▌ | ETA: 0:00:32 Cross validating... 9%|██▉ | ETA: 0:00:30 Cross validating... 10%|███▎ | ETA: 0:00:28 Cross validating... 11%|███▌ | ETA: 0:00:27 Cross validating... 12%|███▉ | ETA: 0:00:25 Cross validating... 13%|████▏ | ETA: 0:00:24 Cross validating... 14%|████▌ | ETA: 0:00:24 Cross validating... 15%|████▊ | ETA: 0:00:23 Cross validating... 16%|█████▏ | ETA: 0:00:22 Cross validating... 17%|█████▌ | ETA: 0:00:22 Cross validating... 18%|█████▊ | ETA: 0:00:21 Cross validating... 19%|██████▏ | ETA: 0:00:20 Cross validating... 20%|██████▍ | ETA: 0:00:20 Cross validating... 21%|██████▊ 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2158.652587730973 11 2157.282549933401 12 2185.9471137466057 13 2200.3881446065643 14 2204.2947702028578 15 2222.2518152127723 16 2235.9774284460286 17 2253.6530757014953 18 2250.574491879549 19 2281.101255572019 20 2283.2788190850397 Best k = 8 20.002902 seconds (348.92 k allocations: 231.586 MiB, 0.50% gc time, 7.81% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 25.3s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m43.0s **** 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... 2%|▋ | ETA: 0:00:09 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:11 Cross validating... 7%|██▎ | ETA: 0:00:11 Cross validating... 8%|██▌ | ETA: 0:00:11 Cross 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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 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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: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 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: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross 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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 1m25.5s 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(0x86e8abe1964b5e5d, 0x931f8f091c2b0c00, 0x779c69687be3a00c, 0x4553893e63d61351, 0x7b9e28bc111929d0) 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 1086.61s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1212.21s: package tests unexpectedly errored