Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1730 (9c1e1fa299*) started at 2026-02-17T22:54:52.540 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 12.31s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [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 v0.10.15 [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 v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.56s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4286.3 ms ✓ BGEN 6272.7 ms ✓ VCFTools 24400.8 ms ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 23106.1 ms ✓ MendelIHT 4 dependencies successfully precompiled in 62 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 81.92s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_rbTn16/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.1 [2913bbd2] StatsBase v0.34.10 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v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 17.7s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.3s 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 1.4s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** 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 = -1984.4495566949865, backtracks = 0, tol = 2.362732585066664 Iteration 2: loglikelihood = -1494.6368550877094, backtracks = 0, tol = 0.15634715974321448 Iteration 3: loglikelihood = -1405.0659033431755, backtracks = 0, tol = 0.07086612507748125 Iteration 4: loglikelihood = -1403.7513088131268, backtracks = 0, tol = 0.007589399158803912 Iteration 5: loglikelihood = -1403.7443758469506, backtracks = 0, tol = 0.0006132589017304335 Iteration 6: loglikelihood = -1403.7443063384178, backtracks = 0, tol = 5.4104494891298246e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.052290916442871094 Final loglikelihood: -1403.7443063384178 SNP PVE: 0.9624677885642183 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 440 -2.41497 2 │ 1679 2.76463 3 │ 2258 1.61511 4 │ 3032 0.172355 5 │ 3836 -0.517981 6 │ 4339 0.427782 7 │ 4731 2.61545 8 │ 6477 -0.601948 9 │ 8455 -0.482996 10 │ 9517 -0.159025 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.060676Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.3s **** 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 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 3.4s **** 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 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 = -20493.063457273533, backtracks = 0, tol = 0.5120700070330378 Iteration 2: loglikelihood = -8371.831844661485, backtracks = 0, tol = 0.07584301283999846 Iteration 3: loglikelihood = -3728.0798457176766, backtracks = 0, tol = 0.07968184957496761 Iteration 4: loglikelihood = -2113.5516069390555, backtracks = 0, tol = 0.07422762626836667 Iteration 5: loglikelihood = -1824.7194112641605, backtracks = 0, tol = 0.048909685812297356 Iteration 6: loglikelihood = -1758.1158118715034, backtracks = 0, tol = 0.0422318826370328 Iteration 7: loglikelihood = -1703.6901540417944, backtracks = 0, tol = 0.059788865720594754 Iteration 8: loglikelihood = -1667.0264037389622, backtracks = 0, tol = 0.028270001317487945 Iteration 9: loglikelihood = -1595.7549312675067, backtracks = 0, tol = 0.05521533627340496 Iteration 10: loglikelihood = -1575.223179309107, backtracks = 0, tol = 0.023326122625654172 Iteration 11: loglikelihood = -1560.1550133945773, backtracks = 1, tol = 0.026317371900435562 Iteration 12: loglikelihood = -1552.5013072922393, backtracks = 0, tol = 0.025744433148134252 Iteration 13: loglikelihood = -1546.6919619128498, backtracks = 0, tol = 0.018719623229926496 Iteration 14: loglikelihood = -1542.4579991343242, backtracks = 0, tol = 0.016495227534428163 Iteration 15: loglikelihood = -1539.0645655986025, backtracks = 0, tol = 0.014275157611618176 Iteration 16: loglikelihood = -1536.4526790444652, backtracks = 0, tol = 0.01165136874290497 Iteration 17: loglikelihood = -1534.3149192206192, backtracks = 0, tol = 0.011365459216869522 Iteration 18: loglikelihood = -1532.6486912116438, backtracks = 0, tol = 0.00856066856561176 Iteration 19: loglikelihood = -1531.27820378674, backtracks = 0, tol = 0.009147692026605222 Iteration 20: loglikelihood = -1530.2141105190033, backtracks = 0, tol = 0.006389105134731628 Iteration 21: loglikelihood = -1520.8825839460972, backtracks = 0, tol = 0.04353436302572361 Iteration 22: loglikelihood = -1517.5473752324317, backtracks = 1, tol = 0.012997682794968974 Iteration 23: loglikelihood = -1516.3179726989415, backtracks = 0, tol = 0.009176899510411264 Iteration 24: loglikelihood = -1515.5185093456143, backtracks = 0, tol = 0.006210179306237146 Iteration 25: loglikelihood = -1514.9606042643886, backtracks = 0, tol = 0.007176134437641455 Iteration 26: loglikelihood = -1514.53745920459, backtracks = 0, tol = 0.004568494454769461 Iteration 27: loglikelihood = -1514.2182552487513, backtracks = 0, tol = 0.005480617066039771 Iteration 28: loglikelihood = -1513.966931529942, backtracks = 0, tol = 0.0035393978954596774 Iteration 29: loglikelihood = -1513.7715073564682, backtracks = 0, tol = 0.004228320592744883 Iteration 30: loglikelihood = -1513.6154036195667, backtracks = 0, tol = 0.002797526118726656 Iteration 31: loglikelihood = -1513.492061900984, backtracks = 0, tol = 0.0033012349233034217 Iteration 32: loglikelihood = -1513.392776339345, backtracks = 0, tol = 0.0022351373919329296 Iteration 33: loglikelihood = -1513.3135471634919, backtracks = 0, tol = 0.0026034981331585247 Iteration 34: loglikelihood = -1513.2494611343302, backtracks = 0, tol = 0.001798017760887533 Iteration 35: loglikelihood = -1513.1979789631177, backtracks = 0, tol = 0.00206971785303411 Iteration 36: loglikelihood = -1513.156199058956, backtracks = 0, tol = 0.0014531234830336922 Iteration 37: loglikelihood = -1513.1224777255543, backtracks = 0, tol = 0.001655709280283447 Iteration 38: loglikelihood = -1513.0950472750744, backtracks = 0, tol = 0.0011782760880807396 Iteration 39: loglikelihood = -1513.0728315963227, backtracks = 0, tol = 0.001331016549177047 Iteration 40: loglikelihood = -1513.0547294741725, backtracks = 0, tol = 0.0009577245811473169 Iteration 41: loglikelihood = -1513.0400312040936, backtracks = 0, tol = 0.0010741161146724317 Iteration 42: loglikelihood = -1513.0280393405924, backtracks = 0, tol = 0.0007798577637282925 Iteration 43: loglikelihood = -1513.0182834882614, backtracks = 0, tol = 0.0008694290316827673 Iteration 44: loglikelihood = -1513.0103163881595, backtracks = 0, tol = 0.0006358881716470152 Iteration 45: loglikelihood = -1513.0038251730016, backtracks = 0, tol = 0.0007054379042431367 Iteration 46: loglikelihood = -1512.9985202742946, backtracks = 0, tol = 0.0005190368007204807 Iteration 47: loglikelihood = -1512.9941930842408, backtracks = 0, tol = 0.0005734723923645459 Iteration 48: loglikelihood = -1512.9906547366047, backtracks = 0, tol = 0.00042399939233872416 Iteration 49: loglikelihood = -1512.987765892322, backtracks = 0, tol = 0.00046690538403381846 Iteration 50: loglikelihood = -1512.9854026519288, backtracks = 0, tol = 0.0003465813895806824 Iteration 51: loglikelihood = -1512.9834718238376, backtracks = 0, tol = 0.0003806071060152265 Iteration 52: loglikelihood = -1512.981891756259, backtracks = 0, tol = 0.00028343919090895425 Iteration 53: loglikelihood = -1512.980600062292, backtracks = 0, tol = 0.0003105652554734376 Iteration 54: loglikelihood = -1512.9795427368397, backtracks = 0, tol = 0.00023189132635709163 Iteration 55: loglikelihood = -1512.9786779856252, backtracks = 0, tol = 0.0002536146507791075 Iteration 56: loglikelihood = -1512.97796998587, backtracks = 0, tol = 0.0001897773646660439 Iteration 57: loglikelihood = -1512.9773907238723, backtracks = 0, tol = 0.00020724087359284658 Iteration 58: loglikelihood = -1512.9769163824371, backtracks = 0, tol = 0.0001553504638372593 Iteration 59: loglikelihood = -1512.9765281771008, backtracks = 0, tol = 0.0001694350456085743 Iteration 60: loglikelihood = -1512.9762102431491, backtracks = 0, tol = 0.00012719429452437265 Iteration 61: loglikelihood = -1512.9759499808772, backtracks = 0, tol = 0.00013858470104539865 Iteration 62: loglikelihood = -1512.9757368068006, backtracks = 0, tol = 0.00010415803286491732 Iteration 63: loglikelihood = -1512.9755622676478, backtracks = 0, tol = 0.00011339064198011108 Iteration 64: loglikelihood = -1512.9754192944642, backtracks = 0, tol = 8.530500892520814e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1805.3331787732823, backtracks = 0, tol = 0.49395125550941893 Iteration 2: loglikelihood = -1637.3071596104264, backtracks = 0, tol = 0.18753637887170863 Iteration 3: loglikelihood = -1566.7258963530326, backtracks = 0, tol = 0.13828303211304302 Iteration 4: loglikelihood = -1531.6344707957774, backtracks = 0, tol = 0.14188403955663884 Iteration 5: loglikelihood = -1527.7300743632693, backtracks = 0, tol = 0.08930100645412736 Iteration 6: loglikelihood = -1527.2247707382514, backtracks = 0, tol = 0.06750669692322053 Iteration 7: loglikelihood = -1526.9051452908084, backtracks = 0, tol = 0.011469828891265205 Iteration 8: loglikelihood = -1526.823467052864, backtracks = 0, tol = 0.07478878170239656 Iteration 9: loglikelihood = -1526.5969341322104, backtracks = 0, tol = 0.011164617233647742 Iteration 10: loglikelihood = -1526.5858324650108, backtracks = 0, tol = 0.002033472723769914 Iteration 11: loglikelihood = -1526.5837872489321, backtracks = 0, tol = 0.0011372382698296242 Iteration 12: loglikelihood = -1526.5833209669634, backtracks = 1, tol = 0.0003670592376356185 Iteration 13: loglikelihood = -1526.5830999702507, backtracks = 1, tol = 0.00024482696874500074 Iteration 14: loglikelihood = -1526.5830227287768, backtracks = 1, tol = 0.0001707284955632548 Iteration 15: loglikelihood = -1526.5830009515416, backtracks = 1, tol = 8.061677950719729e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** 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 = -1745.3615086143845, backtracks = 0, tol = 0.8047352874454117 Iteration 2: loglikelihood = -1424.378983975844, backtracks = 0, tol = 0.11864710654565497 Iteration 3: loglikelihood = -1396.995727131057, backtracks = 0, tol = 0.03831670215988597 Iteration 4: loglikelihood = -1393.8895820733585, backtracks = 0, tol = 0.028946358826500852 Iteration 5: loglikelihood = -1393.7786773322869, backtracks = 0, tol = 0.0016734215395206326 Iteration 6: loglikelihood = -1393.7781304927219, backtracks = 0, tol = 0.00013393466012085153 Iteration 7: loglikelihood = -1393.7781251247673, backtracks = 0, tol = 1.542577273128484e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1517.825411761103, backtracks = 0, tol = 0.37339166119818284 Iteration 2: loglikelihood = -1400.1497661696942, backtracks = 0, tol = 0.0896804469497695 Iteration 3: loglikelihood = -1395.397114289336, backtracks = 0, tol = 0.03284855482475236 Iteration 4: loglikelihood = -1395.3192806764664, backtracks = 0, tol = 0.02819007780991118 Iteration 5: loglikelihood = -1394.7155087994777, backtracks = 0, tol = 0.02819007780991118 Iteration 6: loglikelihood = -1394.5408563890846, backtracks = 0, tol = 0.03121987418029656 Iteration 7: loglikelihood = -1394.2836033309022, backtracks = 0, tol = 0.0024582174128661193 Iteration 8: loglikelihood = -1394.2830143667254, backtracks = 1, tol = 0.00010770954933773995 Iteration 9: loglikelihood = -1394.2828610119402, backtracks = 1, tol = 5.574093500487726e-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 10.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1530.4339753391002, backtracks = 0, tol = 0.2089053143375084 Iteration 2: loglikelihood = -1458.81443165902, backtracks = 0, tol = 0.09126634069644227 Iteration 3: loglikelihood = -1409.9427721731906, backtracks = 0, tol = 0.07716134909975471 Iteration 4: loglikelihood = -1386.9214900298575, backtracks = 0, tol = 0.07964808930620208 Iteration 5: loglikelihood = -1373.1702072981702, backtracks = 0, tol = 0.07618896196095312 Iteration 6: loglikelihood = -1356.6076073910533, backtracks = 0, tol = 0.037927744400369966 Iteration 7: loglikelihood = -1348.9949436184102, backtracks = 0, tol = 0.042644212826492243 Iteration 8: loglikelihood = -1342.684133980029, backtracks = 0, tol = 0.022845148880703277 Iteration 9: loglikelihood = -1328.5305951601333, backtracks = 0, tol = 0.05752174520236889 Iteration 10: loglikelihood = -1325.7433834867777, backtracks = 0, tol = 0.0836361478699892 Iteration 11: loglikelihood = -1316.6524767469605, backtracks = 0, tol = 0.08105611696926057 Iteration 12: loglikelihood = -1316.0526574268222, backtracks = 0, tol = 0.00906421732482684 Iteration 13: loglikelihood = -1315.9015630138256, backtracks = 0, tol = 0.00449668408128782 Iteration 14: loglikelihood = -1315.8513887076901, backtracks = 0, tol = 0.0027434161254910406 Iteration 15: loglikelihood = -1315.8299579139532, backtracks = 0, tol = 0.0023763846461751594 Iteration 16: loglikelihood = -1315.8196626512042, backtracks = 0, tol = 0.0013146091030744123 Iteration 17: loglikelihood = -1315.8143773578256, backtracks = 0, tol = 0.001282082347197992 Iteration 18: loglikelihood = -1315.811598324442, backtracks = 0, tol = 0.0006920331525898667 Iteration 19: loglikelihood = -1315.8101240273347, backtracks = 0, tol = 0.0006847463984216144 Iteration 20: loglikelihood = -1315.8093372500696, backtracks = 0, tol = 0.00036912562592084986 Iteration 21: loglikelihood = -1315.8089171186436, backtracks = 0, tol = 0.0003657317080332551 Iteration 22: loglikelihood = -1315.808692258875, backtracks = 0, tol = 0.00019746686435689935 Iteration 23: loglikelihood = -1315.8085718924765, backtracks = 0, tol = 0.0001956185927901683 Iteration 24: loglikelihood = -1315.8085073562945, backtracks = 0, tol = 0.00010575080351227035 Iteration 25: loglikelihood = -1315.8084726996228, backtracks = 0, tol = 0.0001047393309089189 Iteration 26: loglikelihood = -1315.8084542207357, backtracks = 0, tol = 5.6663062126375106e-5 0.883208 seconds (4.07 M allocations: 73.180 MiB, 6.08% gc time, 47.24% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1556.012648754953, backtracks = 0, tol = 0.2089053143375084 Iteration 2: loglikelihood = -1513.2806534229617, backtracks = 0, tol = 0.09126634069644227 Iteration 3: loglikelihood = -1488.460127183178, backtracks = 0, tol = 0.10033360371530384 Iteration 4: loglikelihood = -1465.734022591757, backtracks = 0, tol = 0.08290983411789128 Iteration 5: loglikelihood = -1447.5092131959416, backtracks = 0, tol = 0.059257984037522894 Iteration 6: loglikelihood = -1427.3524008145946, backtracks = 0, tol = 0.0434120618983558 Iteration 7: loglikelihood = -1408.7128954000125, backtracks = 0, tol = 0.06310593672417757 Iteration 8: loglikelihood = -1398.2856639598986, backtracks = 0, tol = 0.09303501466215768 Iteration 9: loglikelihood = -1385.5479668290236, backtracks = 0, tol = 0.09075640337303847 Iteration 10: loglikelihood = -1378.2971842122172, backtracks = 0, tol = 0.01006469950469248 Iteration 11: loglikelihood = -1371.9420839794495, backtracks = 0, tol = 0.06070572167462227 Iteration 12: loglikelihood = -1366.3483383704718, backtracks = 0, tol = 0.06450642301244995 Iteration 13: loglikelihood = -1362.211015924309, backtracks = 0, tol = 0.005750631101665269 Iteration 14: loglikelihood = -1358.5375116763796, backtracks = 0, tol = 0.0024236312687988 Iteration 15: loglikelihood = -1355.3748693884627, backtracks = 0, tol = 0.000572772577475262 Iteration 16: loglikelihood = -1352.5705855476217, backtracks = 0, tol = 0.0003732340304251659 Iteration 17: loglikelihood = -1350.0903946523695, backtracks = 0, tol = 0.0004696168643497241 Iteration 18: loglikelihood = -1347.8764595406094, backtracks = 0, tol = 0.0003000573674440928 Iteration 19: loglikelihood = -1344.4172544302019, backtracks = 1, tol = 0.0001897992771148662 Iteration 20: loglikelihood = -1342.7706163010432, backtracks = 0, tol = 0.000667677471590715 Iteration 21: loglikelihood = -1340.272665738795, backtracks = 1, tol = 0.00015192098435815932 Iteration 22: loglikelihood = -1337.8646157588064, backtracks = 1, tol = 0.000267074014044889 Iteration 23: loglikelihood = -1335.9563191487289, backtracks = 1, tol = 0.0003505898427442658 Iteration 24: loglikelihood = -1334.419669398425, backtracks = 1, tol = 0.0003561136831694882 Iteration 25: loglikelihood = -1333.100391279175, backtracks = 1, tol = 0.0003295153634075905 Iteration 26: loglikelihood = -1331.9562094038288, backtracks = 1, tol = 0.0002979531137878161 Iteration 27: loglikelihood = -1330.9551592653636, backtracks = 1, tol = 0.0002675501818490371 Iteration 28: loglikelihood = -1330.0719270012394, backtracks = 1, tol = 0.000240086089052956 Iteration 29: loglikelihood = -1329.2864873159153, backtracks = 1, tol = 0.00021611820809360572 Iteration 30: loglikelihood = -1328.5829678056723, backtracks = 1, tol = 0.0001955430168356898 Iteration 31: loglikelihood = -1327.9487784069072, backtracks = 1, tol = 0.00017798594974864504 Iteration 32: loglikelihood = -1327.373895003611, backtracks = 1, tol = 0.0001629843144243497 Iteration 33: loglikelihood = -1326.850276166782, backtracks = 1, tol = 0.00015008440421362693 Iteration 34: loglikelihood = -1326.371398006609, backtracks = 1, tol = 0.0001388863239099428 Iteration 35: loglikelihood = -1325.9318946306366, backtracks = 1, tol = 0.00012905970636974514 Iteration 36: loglikelihood = -1325.527287921704, backtracks = 1, tol = 0.00012034303163576649 Iteration 37: loglikelihood = -1325.153788561991, backtracks = 1, tol = 0.00011253490317880013 Iteration 38: loglikelihood = -1324.808150932658, backtracks = 1, tol = 0.00010548246392044385 Iteration 39: loglikelihood = -1324.487567120027, backtracks = 1, tol = 9.906996275059646e-5 0.351214 seconds (1.77 M allocations: 32.755 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 = -3548.454, backtracks = 0, tol = 0.09339850976778775 Iteration 2: loglikelihood = -3505.214, backtracks = 0, tol = 0.04532349079667222 Iteration 3: loglikelihood = -3483.2397, backtracks = 1, tol = 0.06275403594643533 Iteration 4: loglikelihood = -3479.556, backtracks = 1, tol = 0.010515267485865724 Iteration 5: loglikelihood = -3478.3572, backtracks = 1, tol = 0.0060001704486704 Iteration 6: loglikelihood = -3478.0146, backtracks = 1, tol = 0.0038214425162003745 Iteration 7: loglikelihood = -3477.9263, backtracks = 1, tol = 0.002139512196529873 Iteration 8: loglikelihood = -3477.8997, backtracks = 1, tol = 0.001126716663646007 Iteration 9: loglikelihood = -3477.8977, backtracks = 1, tol = 0.0005706828399133284 Iteration 10: loglikelihood = -3477.894, backtracks = 2, tol = 0.0001429549903286632 Iteration 11: loglikelihood = -3477.8984, backtracks = 3, tol = 5.3492631259644826e-5 21.676721 seconds (15.03 M allocations: 668.347 MiB, 4.49% gc time, 94.24% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -3448.7644, backtracks = 0, tol = 0.09339850976778775 Iteration 2: loglikelihood = -3339.2983, backtracks = 0, tol = 0.04644678652308664 Iteration 3: loglikelihood = -3109.2686, backtracks = 1, tol = 0.0610780849484284 Iteration 4: loglikelihood = -3091.754, backtracks = 0, tol = 0.11320807989453388 Iteration 5: loglikelihood = -2907.1047, backtracks = 0, tol = 0.10556536963523004 Iteration 6: loglikelihood = -2783.673, backtracks = 0, tol = 0.09293448943884947 Iteration 7: loglikelihood = -2670.4841, backtracks = 0, tol = 0.009313940766709147 Iteration 8: loglikelihood = -2557.3293, backtracks = 0, tol = 0.083166080100655 Iteration 9: loglikelihood = -2449.2786, backtracks = 0, tol = 0.09137641058392022 Iteration 10: loglikelihood = -2369.3652, backtracks = 0, tol = 0.08823255235937158 Iteration 11: loglikelihood = -2279.4717, backtracks = 0, tol = 0.10107852973151964 Iteration 12: loglikelihood = -2217.192, backtracks = 0, tol = 0.09876569348624152 Iteration 13: loglikelihood = -2174.066, backtracks = 0, tol = 0.09489517979007084 Iteration 14: loglikelihood = -2143.3503, backtracks = 0, tol = 0.0932830345255897 Iteration 15: loglikelihood = -2122.0933, backtracks = 0, tol = 0.10464418844342005 Iteration 16: loglikelihood = -2114.228, backtracks = 0, tol = 0.10189308546072313 Iteration 17: loglikelihood = -2106.9468, backtracks = 0, tol = 0.11096198414968556 Iteration 18: loglikelihood = -2105.374, backtracks = 0, tol = 0.10931717843778159 Iteration 19: loglikelihood = -2102.8848, backtracks = 0, tol = 0.11146831350524938 Iteration 20: loglikelihood = -2100.2495, backtracks = 1, tol = 0.01818562696425102 Iteration 21: loglikelihood = -2099.703, backtracks = 1, tol = 0.008174214804851573 Iteration 22: loglikelihood = -2099.5864, backtracks = 1, tol = 0.003454710407346471 Iteration 23: loglikelihood = -2099.56, backtracks = 1, tol = 0.001389836755600162 Iteration 24: loglikelihood = -2099.549, backtracks = 1, tol = 0.0005297983364545959 Iteration 25: loglikelihood = -2099.547, backtracks = 1, tol = 0.0002781933307357933 Iteration 26: loglikelihood = -2099.5369, backtracks = 2, tol = 8.040371305683246e-5 0.217766 seconds (1.38 M allocations: 22.858 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 25.8s **** 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 = -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 4.585568 seconds (1.17 M allocations: 138.590 MiB, 1.47% gc time, 91.83% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.0s 9.334825 seconds (4.00 M allocations: 82.481 MiB, 0.71% gc time, 0.63% compilation time) 5.205241 seconds (3.98 M allocations: 91.675 MiB, 0.09% gc time) 10.214736 seconds (20.40 M allocations: 439.321 MiB, 1.04% gc time, 16.43% compilation time: 78% of which was recompilation) 8.160959 seconds (20.18 M allocations: 434.188 MiB, 0.84% gc time) 48.724792 seconds (3.71 M allocations: 4.237 GiB, 8.88% gc time, 20.85% compilation time) 50.070451 seconds (71.97 k allocations: 183.461 MiB, 0.11% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m26.9s Test Summary: | Pass Total Time update_support! | 10 10 0.4s 14.291 ms (78 allocations: 4.56 KiB) 4.863 μs (0 allocations: 0 bytes) 147.879 μs (4 allocations: 288 bytes) 5.575 μs (0 allocations: 0 bytes) 45.929 μs (2 allocations: 64 bytes) 29.569 μs (0 allocations: 0 bytes) 22.379 μs (0 allocations: 0 bytes) 29.669 μs (0 allocations: 0 bytes) 70.109 μs (0 allocations: 0 bytes) 37.283 ms (78 allocations: 4.56 KiB) 27.000 μs (0 allocations: 0 bytes) 170.059 μs (4 allocations: 288 bytes) 32.660 μs (0 allocations: 0 bytes) 199.448 μs (2 allocations: 64 bytes) 73.440 μs (0 allocations: 0 bytes) 125.368 μs (0 allocations: 0 bytes) 143.778 μs (0 allocations: 0 bytes) 197.509 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m28.6s **** 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 **** **** 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 0.386333 seconds (49.12 k allocations: 5.471 MiB, 59.62% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 11.3s **** 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 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 1.972543 seconds (312.53 k allocations: 169.961 MiB, 58.97% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:34 Cross validating... 13%|████▏ | ETA: 0:00:52 Cross validating... 16%|█████▏ | ETA: 0:00:41 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: 0:00:21 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: 0:00:13 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... 70%|██████████████████████▍ | ETA: 0:00:04 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 8632.688081433887 1 5675.368795043741 2 3532.0766209320036 3 1537.4162083285232 4 683.1567940195075 5 575.3988654817001 6 501.68405841502886 7 426.15210181820777 8 345.78896932867644 9 338.20196195140824 10 333.39985274213177 11 337.49458875298876 12 346.98101260637907 13 342.9642435600725 14 361.9145343620972 15 355.5098599021613 16 358.84913215935063 17 345.14122163939794 18 355.31021245252043 19 348.2087056899106 20 368.3932788023967 Best k = 10 11.614096 seconds (11.60 M allocations: 305.911 MiB, 1.04% gc time, 61.85% 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: 0:00:02 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: 0:00:01 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | 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 8632.688081433887 1 5676.487461495896 2 3546.181834096634 3 1550.554839706543 4 695.99546562839 5 585.2556523642492 6 510.474733817509 7 431.6337375677748 8 351.8428623053886 9 345.36985205431006 10 340.7054458710985 11 348.31255676748304 12 355.94853263961875 13 364.27268655057753 14 366.27745800681294 15 376.24692276305063 16 379.53084955219174 17 376.38129538969656 18 377.09501174599217 19 381.16448645289563 20 386.2909660525303 Best k = 10 4.417442 seconds (10.65 M allocations: 224.232 MiB, 1.30% gc time, 0.97% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 16.9s **** 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: 0:06:54 Cross validating... 8%|██▌ | ETA: 0:02:39 Cross validating... 14%|████▋ | ETA: 0:01:23 Cross validating... 17%|█████▋ | ETA: 0:01:06 Cross validating... 22%|███████▏ | ETA: 0:00:49 Cross validating... 27%|████████▋ | ETA: 0:00:38 Cross validating... 32%|██████████▏ | ETA: 0:00:31 Cross validating... 37%|███████████▋ | ETA: 0:00:25 Cross validating... 41%|█████████████▎ | ETA: 0:00:21 Cross validating... 48%|███████████████▎ | ETA: 0:00:16 Cross validating... 52%|████████████████▊ | ETA: 0:00:13 Cross validating... 57%|██████████████████▎ | ETA: 0:00:11 Cross validating... 62%|███████████████████▊ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:08 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 0 1694.452186767578 1 1356.1945419921876 2 1162.5265681152343 3 915.3109379882812 4 667.8880091552734 5 543.6906439208984 6 451.237893737793 7 391.14543682861324 8 366.1477322998047 9 348.6432731933594 10 350.76212341308593 11 353.7364600219727 12 355.84931329345704 13 358.058528137207 14 359.41246643066404 15 363.44650341796876 16 368.4591153564453 17 369.82505377197265 18 393.55209912109376 19 374.3729580078125 20 395.28286431884766 Best k = 9 17.130529 seconds (12.44 M allocations: 308.084 MiB, 0.68% gc time, 85.03% 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... 19%|██████▏ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:01 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | 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... 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 1694.452186767578 1 1356.1945419921876 2 1163.997685546875 3 917.1675889892579 4 673.3060443115235 5 549.9482755126953 6 460.03933557128903 7 399.18915496826173 8 371.171366394043 9 355.70291796875 10 362.8569338378906 11 370.1710475463867 12 373.91849011230465 13 379.89318084716797 14 385.5511328125 15 393.9856080932617 16 397.9471029052735 17 416.05593658447265 18 410.2556178588867 19 402.39774841308594 20 420.30392065429686 Best k = 9 2.558017 seconds (10.90 M allocations: 200.349 MiB, 2.76% gc time, 1.56% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 21.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:49 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 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95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.56782139890856 1 392.1336496608169 2 315.41220911362007 3 244.60999339513762 4 185.4567849210446 5 174.6094205550909 6 185.80616130144458 7 192.59591175192747 8 191.29454179067608 9 202.39081342371557 10 196.27777006888567 11 222.66956923398357 12 211.00532728539378 13 217.4327676272125 14 233.7899089893379 15 245.6862351975377 16 234.6049858642528 17 230.54261360206885 18 267.45236391530904 19 233.76059324143006 20 291.22716836827465 Best k = 5 6.883902 seconds (17.38 M allocations: 395.765 MiB, 1.33% gc time, 29.26% 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... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.56782139890856 1 392.43837328269484 2 315.7433076245635 3 245.59227170159025 4 187.33274847918705 5 190.6213581858418 6 201.39433524504543 7 207.29104007533846 8 214.94564867911123 9 225.6978678105965 10 234.68663960078243 11 238.16307615449648 12 248.7698007176628 13 251.66277775794055 14 258.78110866627804 15 256.80778223901933 16 266.954512236641 17 265.5050087059973 18 273.7203404093896 19 274.4400285886019 20 294.414969979041 Best k = 4 5.647521 seconds (17.74 M allocations: 367.207 MiB, 1.53% gc time, 1.01% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, 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: 0:00:47 Cross validating... 8%|██▌ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:13 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 22%|███████▏ | ETA: 0:00:08 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 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: 0:00:06 Crossvalidation Results: k MSE 0 464.07684540661216 1 428.2586760620954 2 401.6382154860762 3 368.68317441941645 4 344.12405080266035 5 337.92978225328136 6 325.6849257122176 7 322.3454724138786 8 326.02042400668944 9 324.6906788243691 10 330.25521819033986 11 330.73502126831147 12 337.01928767036634 13 354.12896735764593 14 342.50687001041797 15 355.85824841729766 16 332.894575732146 17 334.4986379971898 18 346.6085316183185 19 370.86339321848556 20 337.3516490161296 Best k = 7 7.550119 seconds (16.32 M allocations: 387.615 MiB, 12.59% gc time, 34.12% 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: 0:00:05 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: 0:00:01 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 0 464.07684540661216 1 430.05927482002687 2 403.4377857904931 3 370.93483287893054 4 349.2021668332628 5 344.35947581115875 6 332.0880235382855 7 332.4022214492279 8 341.03871396961745 9 347.86915199806873 10 351.6654850490432 11 356.90055871855344 12 365.91958871565896 13 372.048208128473 14 378.11601515782394 15 390.7059562513171 16 404.72838773679405 17 406.48802153444865 18 418.8373345317765 19 431.59651335443937 20 414.79348912896603 Best k = 6 4.528971 seconds (17.60 M allocations: 363.880 MiB, 2.23% gc time, 0.95% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:56 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:12 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 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: 0:00:06 Crossvalidation Results: k MSE 0 1951.5342859844454 1 1356.4968911443996 2 1142.0340386269131 3 922.2260945095347 4 770.2736404056727 5 702.0979139019214 6 855.4750502332857 7 800.1044521503146 8 921.4204991166325 9 842.8157043820338 10 756.7545939189563 11 632.2092950674053 12 636.434197731091 13 620.5643646777745 14 708.9837242671097 15 768.5863252620807 16 678.1597802573127 17 599.3261710143569 18 607.7368815365098 19 701.5276490488287 20 593.4246430971484 Best k = 20 7.710198 seconds (15.44 M allocations: 361.204 MiB, 0.86% gc time, 31.47% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 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: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1951.5342859844454 1 1173.8091931462998 2 895.3250680516353 3 710.9946226482754 4 628.439106131586 5 633.0665056349121 6 605.499863237731 7 637.041406106191 8 642.1002203388143 9 655.3800235317651 10 670.6272225806131 11 689.8165215758569 12 700.7903760829998 13 685.395602768818 14 666.1146531686836 15 734.8133486165325 16 698.9333759391043 17 673.1733095106497 18 711.5485206787934 19 708.2471413874141 20 647.030255046465 Best k = 6 5.283458 seconds (13.96 M allocations: 278.272 MiB, 1.05% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:28 Cross validating... 5%|█▌ | ETA: 0:01:17 Cross validating... 8%|██▌ | ETA: 0:00:46 Cross validating... 11%|███▌ | ETA: 0:00:33 Cross validating... 13%|████▏ | ETA: 0:00:29 Cross validating... 14%|████▋ | ETA: 0:00:32 Cross validating... 16%|█████▏ | ETA: 0:00:29 Cross validating... 17%|█████▋ | ETA: 0:00:31 Cross validating... 19%|██████▏ | ETA: 0:00:32 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross 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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: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:40 Crossvalidation Results: k MSE 0 577.3604985643053 1 420.9118078196085 2 318.7614667103759 3 236.59588036419945 4 201.06495396646505 5 200.1089615854757 6 201.17992082726067 7 204.1540255415768 8 201.91763449222526 9 203.30778387492134 10 205.15287392980997 11 205.69381093080642 12 205.63378005546963 13 207.43408690667383 14 203.96332169445077 15 204.4928076787585 16 205.87907503529146 17 203.83776378950725 18 207.40235281169214 19 210.55677831452294 20 208.43485402030814 Best k = 5 41.220341 seconds (130.65 M allocations: 3.337 GiB, 1.26% gc time, 5.39% 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... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:07 Cross validating... 16%|█████▏ | ETA: 0:00:07 Cross validating... 17%|█████▋ | ETA: 0:00:07 Cross validating... 19%|██████▏ | ETA: 0:00:07 Cross validating... 21%|██████▋ | ETA: 0:00:07 Cross validating... 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220.19203928479521 11 222.63694235649191 12 226.75599560880164 13 232.85875863690734 14 227.90521741433275 15 227.44260156872951 16 231.82469112681557 17 240.57880543631956 18 235.70070446429094 19 254.2540928738315 20 237.6244334112174 Best k = 4 11.422282 seconds (38.02 M allocations: 787.861 MiB, 1.26% gc time, 0.55% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 53.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:59 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:20 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:13 Cross validating... 19%|██████▏ | ETA: 0:00:11 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | 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: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | 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 5.837019 seconds (17.00 M allocations: 337.780 MiB, 2.71% gc time, 40.90% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 24%|███████▋ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 63%|████████████████████▍ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 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 3.153699 seconds (16.17 M allocations: 286.688 MiB, 1.88% gc time, 1.64% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 9.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:27 Cross validating... 3%|█ | ETA: 0:01:03 Cross validating... 4%|█▎ | ETA: 0:00:51 Cross validating... 5%|█▋ | ETA: 0:00:44 Cross validating... 6%|█▉ | ETA: 0:00:39 Cross validating... 7%|██▎ | ETA: 0:00:35 Cross validating... 8%|██▌ | ETA: 0:00:33 Cross validating... 9%|██▉ | ETA: 0:00:31 Cross validating... 10%|███▎ | ETA: 0:00:29 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross validating... 12%|███▉ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:26 Cross validating... 14%|████▌ | ETA: 0:00:25 Cross validating... 15%|████▊ | ETA: 0:00:24 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100%|████████████████████████████████| Time: 0:00:20 Crossvalidation Results: k MSE 1 4815.972081109889 2 4283.637286805842 3 3612.0237564483623 4 3027.1237790785553 5 2416.710842028691 6 2187.9234268733767 7 2183.416639320232 8 2196.2871127303406 9 2223.98547030529 10 2222.2960416460082 11 2221.2973557529845 12 2254.2189081235956 13 2253.3113575750554 14 2294.1637575088457 15 2266.9210237248003 16 2299.575365134334 17 2307.6524093199937 18 2330.558348054582 19 2323.4054242779603 20 2340.379735353091 Best k = 7 20.383331 seconds (358.00 k allocations: 244.854 MiB, 0.31% gc time, 8.13% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 25.2s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m40.4s **** 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... 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: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 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 validating... 17%|█████▌ | ETA: 0:00:23 Cross validating... 18%|█████▊ | ETA: 0:00:22 Cross validating... 19%|██████▏ | ETA: 0:00:22 Cross validating... 20%|██████▍ | ETA: 0:00:22 Cross validating... 21%|██████▊ | ETA: 0:00:21 Cross validating... 22%|███████ | ETA: 0:00:20 Cross validating... 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60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:10 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross 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Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:10 Cross validating... 56%|█████████████████▉ | ETA: 0:00:10 Cross validating... 57%|██████████████████▎ | ETA: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:09 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 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99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** 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: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 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 validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:17 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | ETA: 0:00:16 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:15 Cross validating... 27%|████████▋ | 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validating... 64%|████████████████████▌ | ETA: 0:00:08 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:07 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:06 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:05 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:04 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 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 1m25.6s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [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:310 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:489 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.7s RNG of the outermost testset: Xoshiro(0x88270894e1fb9ef0, 0x24e16f4a2d2d4163, 0x43edec0367580068, 0xa4e51522f32328c2, 0xccb486791431826f) 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 1096.81s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1219.43s: package tests unexpectedly errored