Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2086 (d19eac062f*) started at 2026-04-29T00:04:24.264 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.34s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [79e6a3ab] + Adapt v4.5.2 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.24.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.1+0 [deac9b47] + LibCURL_jll v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.32+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.8s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.0 s ✓ BGEN 7.5 s ✓ VCFTools 27.6 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 28.2 s ✓ MendelIHT 4 dependencies successfully precompiled in 78 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 97.27s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_PQEvZ3/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.125 [38e38edf] GLM v1.9.4 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.2 [2913bbd2] StatsBase v0.34.10 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v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = cholesky!(A::LinearAlgebra.Symmetric{Float64, Matrix{Float64}}, ::Val{true}; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:215 └ @ LinearAlgebra ./deprecated.jl:215 Test Summary: | Pass Total Time loglikelihood | 4 4 17.5s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.6s Test Summary: | Pass Total Time _choose! | 7 7 10.4s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.6s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.2s Test Summary: | Pass Total Time maf_weights | 6 6 2.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1556.791132787809, backtracks = 0, tol = 1.3116120456010558 Iteration 2: loglikelihood = -1422.2999289050942, backtracks = 0, tol = 0.11643999864632314 Iteration 3: loglikelihood = -1396.2405011316498, backtracks = 0, tol = 0.06261060542824609 Iteration 4: loglikelihood = -1393.971841396019, backtracks = 0, tol = 0.042087880094358245 Iteration 5: loglikelihood = -1393.7627037553882, backtracks = 0, tol = 0.0416325566668122 Iteration 6: loglikelihood = -1391.6835809236009, backtracks = 0, tol = 0.041345866824409785 Iteration 7: loglikelihood = -1390.095666698727, backtracks = 0, tol = 0.04491913400647653 Iteration 8: loglikelihood = -1389.994486178463, backtracks = 0, tol = 0.002945710273454699 Iteration 9: loglikelihood = -1389.9938298427005, backtracks = 0, tol = 0.00023827394309946048 Iteration 10: loglikelihood = -1389.9938216215724, backtracks = 0, tol = 2.4972709343398853e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.08486700057983398 Final loglikelihood: -1389.9938216215724 SNP PVE: 0.8733099672324319 Iterations: 10 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 23 1.25368 2 │ 284 1.57575 3 │ 1371 0.115886 4 │ 2598 -0.11711 5 │ 2797 0.11686 6 │ 4405 0.115861 7 │ 4528 -0.793786 8 │ 6390 -0.887632 9 │ 8869 -0.117259 10 │ 9802 0.802182 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0248064Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 24.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 4.1s **** 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 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 = -2331.875823837147, backtracks = 0, tol = 0.4592502675947198 Iteration 2: loglikelihood = -1580.533736003169, backtracks = 0, tol = 0.07512791503546287 Iteration 3: loglikelihood = -1359.603827952107, backtracks = 0, tol = 0.07447952276198677 Iteration 4: loglikelihood = -1324.7337453668817, backtracks = 0, tol = 0.044207160005222124 Iteration 5: loglikelihood = -1305.2394517168611, backtracks = 0, tol = 0.06943998244238153 Iteration 6: loglikelihood = -1297.225800449656, backtracks = 0, tol = 0.041796172955614073 Iteration 7: loglikelihood = -1294.9253966199637, backtracks = 0, tol = 0.020846277156799282 Iteration 8: loglikelihood = -1293.5683626138177, backtracks = 0, tol = 0.015703204288631974 Iteration 9: loglikelihood = -1292.790707565023, backtracks = 0, tol = 0.01100434576449872 Iteration 10: loglikelihood = -1292.308180924187, backtracks = 0, tol = 0.00906216612684092 Iteration 11: loglikelihood = -1292.0230182037158, backtracks = 0, tol = 0.006192640008220104 Iteration 12: loglikelihood = -1291.8471623705009, backtracks = 0, tol = 0.005341355944319981 Iteration 13: loglikelihood = -1291.7436003555476, backtracks = 0, tol = 0.003550010288225775 Iteration 14: loglikelihood = -1291.6809547017883, backtracks = 0, tol = 0.003133417158026564 Iteration 15: loglikelihood = -1291.644399269928, backtracks = 0, tol = 0.0020460637390503473 Iteration 16: loglikelihood = -1291.622701780132, backtracks = 0, tol = 0.001821803132844399 Iteration 17: loglikelihood = -1291.610140827684, backtracks = 0, tol = 0.0012102217397270266 Iteration 18: loglikelihood = -1291.6027919735293, backtracks = 0, tol = 0.001051379667039154 Iteration 19: loglikelihood = -1291.598560936652, backtracks = 0, tol = 0.0007063604706959873 Iteration 20: loglikelihood = -1291.596109352715, backtracks = 0, tol = 0.0006037611942783137 Iteration 21: loglikelihood = -1291.5947027242664, backtracks = 0, tol = 0.0004087378124837519 Iteration 22: loglikelihood = -1291.5938925841308, backtracks = 0, tol = 0.00034568931723084786 Iteration 23: loglikelihood = -1291.5934287049704, backtracks = 0, tol = 0.00023526553100015324 Iteration 24: loglikelihood = -1291.5931624986904, backtracks = 0, tol = 0.0001976042053125713 Iteration 25: loglikelihood = -1291.5930102508362, backtracks = 0, tol = 0.0001349867266574838 Iteration 26: loglikelihood = -1291.592923064264, backtracks = 0, tol = 0.00011286010363738791 Iteration 27: loglikelihood = -1291.5928732340567, backtracks = 0, tol = 7.730498918049922e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.3s **** 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 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 = -1527.3493569995173, backtracks = 0, tol = 0.40620301774637557 Iteration 2: loglikelihood = -1476.4235540196387, backtracks = 0, tol = 0.09669389778798466 Iteration 3: loglikelihood = -1457.443002477916, backtracks = 0, tol = 0.06494710505182423 Iteration 4: loglikelihood = -1454.386888606021, backtracks = 0, tol = 0.08555975455590473 Iteration 5: loglikelihood = -1450.3898866999982, backtracks = 0, tol = 0.08355997389376779 Iteration 6: loglikelihood = -1450.0545809619487, backtracks = 0, tol = 0.012305163764102416 Iteration 7: loglikelihood = -1450.0292723355049, backtracks = 0, tol = 0.0030347215982255305 Iteration 8: loglikelihood = -1450.0257537125567, backtracks = 0, tol = 0.001751539741405645 Iteration 9: loglikelihood = -1450.0251720821464, backtracks = 0, tol = 0.0006135776795801114 Iteration 10: loglikelihood = -1450.025076735461, backtracks = 0, tol = 0.0003004951180309947 Iteration 11: loglikelihood = -1450.025064632419, backtracks = 1, tol = 5.737716825365614e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1808.7566275399415, backtracks = 0, tol = 0.7973307307551347 Iteration 2: loglikelihood = -1446.0422421567102, backtracks = 0, tol = 0.14591938036477384 Iteration 3: loglikelihood = -1388.231379513975, backtracks = 0, tol = 0.04860883766366175 Iteration 4: loglikelihood = -1386.921130898637, backtracks = 0, tol = 0.02720335447248797 Iteration 5: loglikelihood = -1386.1795627559384, backtracks = 0, tol = 0.026091748320521156 Iteration 6: loglikelihood = -1386.0333482665883, backtracks = 0, tol = 0.002224759562250875 Iteration 7: loglikelihood = -1386.0329414647106, backtracks = 1, tol = 6.770410270329095e-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 = -1480.0449960658057, backtracks = 0, tol = 0.2535953872153148 Iteration 2: loglikelihood = -1401.952147918402, backtracks = 0, tol = 0.08351993728395517 Iteration 3: loglikelihood = -1386.9995199459959, backtracks = 0, tol = 0.03179044205129843 Iteration 4: loglikelihood = -1386.722738550611, backtracks = 1, tol = 0.0015782074203419358 Iteration 5: loglikelihood = -1386.6507938243408, backtracks = 1, tol = 0.0008063238310511038 Iteration 6: loglikelihood = -1386.6322304048067, backtracks = 1, tol = 0.00043226537560040184 Iteration 7: loglikelihood = -1386.6274800300853, backtracks = 1, tol = 0.00022772260761236453 Iteration 8: loglikelihood = -1386.6262733478904, backtracks = 1, tol = 0.0001175626839350906 Iteration 9: loglikelihood = -1386.6259685417551, backtracks = 1, tol = 5.984122937548269e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 11.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1593.1270774955824, backtracks = 0, tol = 0.15327798469131138 Iteration 2: loglikelihood = -1537.6353237523635, backtracks = 0, tol = 0.09293493427246144 Iteration 3: loglikelihood = -1477.9661222460786, backtracks = 1, tol = 0.09502871670128774 Iteration 4: loglikelihood = -1463.3612996548218, backtracks = 0, tol = 0.1171635764259618 Iteration 5: loglikelihood = -1455.6065847036236, backtracks = 0, tol = 0.1276264319348913 Iteration 6: loglikelihood = -1431.9134127776945, backtracks = 0, tol = 0.04815189318380568 Iteration 7: loglikelihood = -1418.4932654158251, backtracks = 0, tol = 0.07851101680878642 Iteration 8: loglikelihood = -1410.4230171205131, backtracks = 0, tol = 0.06958202795289552 Iteration 9: loglikelihood = -1409.7128009179232, backtracks = 0, tol = 0.014537926350268938 Iteration 10: loglikelihood = -1409.5201707158265, backtracks = 0, tol = 0.005570378369068875 Iteration 11: loglikelihood = -1409.4447346972158, backtracks = 0, tol = 0.006239681659774437 Iteration 12: loglikelihood = -1409.4118515036048, backtracks = 0, tol = 0.002251518642182858 Iteration 13: loglikelihood = -1409.3974934489843, backtracks = 0, tol = 0.002759447445891314 Iteration 14: loglikelihood = -1409.3911512307045, backtracks = 0, tol = 0.0009792854133477925 Iteration 15: loglikelihood = -1409.3883581483606, backtracks = 0, tol = 0.0012333743088434965 Iteration 16: loglikelihood = -1409.3871192111294, backtracks = 0, tol = 0.0004293745818791696 Iteration 17: loglikelihood = -1409.3865702078508, backtracks = 0, tol = 0.0005555588577273913 Iteration 18: loglikelihood = -1409.3863262015989, backtracks = 0, tol = 0.00018856319758567424 Iteration 19: loglikelihood = -1409.386217604071, backtracks = 0, tol = 0.00025141314688931915 Iteration 20: loglikelihood = -1409.386169354766, backtracks = 0, tol = 8.29011976987095e-5 0.979375 seconds (2.05 M allocations: 42.083 MiB, 67.68% 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 = -1619.9738753698534, backtracks = 0, tol = 0.15327798469131138 Iteration 2: loglikelihood = -1578.5139608189347, backtracks = 0, tol = 0.10906839925880511 Iteration 3: loglikelihood = -1576.6031776942773, backtracks = 0, tol = 0.1775391503702242 Iteration 4: loglikelihood = -1526.3298453924983, backtracks = 0, tol = 0.12928155020339133 Iteration 5: loglikelihood = -1512.5227950922708, backtracks = 0, tol = 0.0786347860556912 Iteration 6: loglikelihood = -1488.5479547990674, backtracks = 0, tol = 0.07738329023758722 Iteration 7: loglikelihood = -1473.1128146738004, backtracks = 0, tol = 0.06583926056069926 Iteration 8: loglikelihood = -1464.3995476783505, backtracks = 0, tol = 0.026260112105629136 Iteration 9: loglikelihood = -1458.0717100092413, backtracks = 0, tol = 0.07387863964250689 Iteration 10: loglikelihood = -1452.0181138488736, backtracks = 0, tol = 0.08336724061114234 Iteration 11: loglikelihood = -1447.4812017711586, backtracks = 0, tol = 0.009393915302842485 Iteration 12: loglikelihood = -1443.5323638243722, backtracks = 0, tol = 0.004069272547718632 Iteration 13: loglikelihood = -1440.235521204837, backtracks = 0, tol = 0.001126184675338335 Iteration 14: loglikelihood = -1437.3338100925664, backtracks = 0, tol = 0.000989450954444873 Iteration 15: loglikelihood = -1434.828566857603, backtracks = 0, tol = 0.00039347133441391345 Iteration 16: loglikelihood = -1432.6205069891228, backtracks = 0, tol = 0.0003243717118463474 Iteration 17: loglikelihood = -1430.679600370789, backtracks = 0, tol = 0.0003335570100853039 Iteration 18: loglikelihood = -1428.9556309364093, backtracks = 0, tol = 0.00031171174870191985 Iteration 19: loglikelihood = -1427.421872723131, backtracks = 0, tol = 0.00030356127524379357 Iteration 20: loglikelihood = -1426.0477690786538, backtracks = 0, tol = 0.0002810542243917766 Iteration 21: loglikelihood = -1424.8135389823067, backtracks = 0, tol = 0.0002679804361676457 Iteration 22: loglikelihood = -1423.6990683967938, backtracks = 0, tol = 0.0002490741546625211 Iteration 23: loglikelihood = -1422.6900648615656, backtracks = 0, tol = 0.00023685450843659837 Iteration 24: loglikelihood = -1421.7726822451286, backtracks = 0, tol = 0.00022156969503834146 Iteration 25: loglikelihood = -1420.9365167337662, backtracks = 0, tol = 0.00021094760679819214 Iteration 26: loglikelihood = -1420.171718868873, backtracks = 0, tol = 0.00019845697315407527 Iteration 27: loglikelihood = -1419.4706009598724, backtracks = 0, tol = 0.0001892924145063068 Iteration 28: loglikelihood = -1418.8259678928628, backtracks = 0, tol = 0.00017891244996940861 Iteration 29: loglikelihood = -1418.2320465346086, backtracks = 0, tol = 0.00017098266595343492 Iteration 30: loglikelihood = -1417.6834627224837, backtracks = 0, tol = 0.00016222838971036814 Iteration 31: loglikelihood = -1417.1758136509861, backtracks = 0, tol = 0.0001553354948179069 Iteration 32: loglikelihood = -1416.7050086397785, backtracks = 0, tol = 0.00014786053415443256 Iteration 33: loglikelihood = -1416.2676418069498, backtracks = 0, tol = 0.00014183938112211317 Iteration 34: loglikelihood = -1415.8605481418335, backtracks = 0, tol = 0.00013538964457710111 Iteration 35: loglikelihood = -1415.4810585355433, backtracks = 0, tol = 0.00013010389608721396 Iteration 36: loglikelihood = -1415.1266889103206, backtracks = 0, tol = 0.00012448828154220046 Iteration 37: loglikelihood = -1414.7953227296039, backtracks = 0, tol = 0.00011982564761737975 Iteration 38: loglikelihood = -1414.484985517332, backtracks = 0, tol = 0.00011489740146895423 Iteration 39: loglikelihood = -1414.193980821772, backtracks = 0, tol = 0.00011076535548423622 Iteration 40: loglikelihood = -1413.9207213780824, backtracks = 0, tol = 0.00010640979275456798 Iteration 41: loglikelihood = -1413.6638341067844, backtracks = 0, tol = 0.00010273192540362186 Iteration 42: loglikelihood = -1413.4220299579952, backtracks = 0, tol = 9.885806816354123e-5 0.477019 seconds (1.56 M allocations: 28.110 MiB, 12.12% gc time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3712.4011, backtracks = 0, tol = 0.08605226119264395 Iteration 2: loglikelihood = -3657.9749, backtracks = 0, tol = 0.05044366391616517 Iteration 3: loglikelihood = -3631.2356, backtracks = 1, tol = 0.06389470812645001 Iteration 4: loglikelihood = -3625.45, backtracks = 1, tol = 0.012095866239333342 Iteration 5: loglikelihood = -3604.7954, backtracks = 1, tol = 0.07025815685077438 Iteration 6: loglikelihood = -3600.853, backtracks = 1, tol = 0.010889418763240757 Iteration 7: loglikelihood = -3599.4841, backtracks = 1, tol = 0.006214277560850935 Iteration 8: loglikelihood = -3599.0457, backtracks = 1, tol = 0.003938174555048993 Iteration 9: loglikelihood = -3598.9148, backtracks = 1, tol = 0.002504680829101711 Iteration 10: loglikelihood = -3598.8774, backtracks = 1, tol = 0.001393028693654588 Iteration 11: loglikelihood = -3598.8735, backtracks = 1, tol = 0.0007096043912341578 Iteration 12: loglikelihood = -3598.8728, backtracks = 1, tol = 0.00036450228241685233 Iteration 13: loglikelihood = -3598.8716, backtracks = 2, tol = 9.059689000240843e-5 28.083770 seconds (15.86 M allocations: 695.451 MiB, 3.96% gc time, 95.17% 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 = -3586.1157, backtracks = 0, tol = 0.08605226119264395 Iteration 2: loglikelihood = -3449.118, backtracks = 0, tol = 0.052351161590103876 Iteration 3: loglikelihood = -3205.5864, backtracks = 1, tol = 0.06140870089040821 Iteration 4: loglikelihood = -2951.4143, backtracks = 1, tol = 0.012093956033802958 Iteration 5: loglikelihood = -2679.847, backtracks = 1, tol = 0.06369177124202935 Iteration 6: loglikelihood = -2587.1416, backtracks = 0, tol = 0.09324184979525622 Iteration 7: loglikelihood = -2455.5693, backtracks = 0, tol = 0.11057583766813067 Iteration 8: loglikelihood = -2368.0789, backtracks = 0, tol = 0.09492294440550439 Iteration 9: loglikelihood = -2300.1665, backtracks = 0, tol = 0.09408191961636421 Iteration 10: loglikelihood = -2245.0815, backtracks = 0, tol = 0.09390161997155444 Iteration 11: loglikelihood = -2209.3726, backtracks = 0, tol = 0.10719184193860627 Iteration 12: loglikelihood = -2187.7065, backtracks = 0, tol = 0.10661516862073278 Iteration 13: loglikelihood = -2173.196, backtracks = 0, tol = 0.10545085833581701 Iteration 14: loglikelihood = -2168.017, backtracks = 0, tol = 0.1107042404364941 Iteration 15: loglikelihood = -2162.7551, backtracks = 0, tol = 0.11178978699944028 Iteration 16: loglikelihood = -2162.2134, backtracks = 0, tol = 0.11276470330571538 Iteration 17: loglikelihood = -2160.0544, backtracks = 0, tol = 0.11391080649980485 Iteration 18: loglikelihood = -2156.6665, backtracks = 1, tol = 0.025417877553926244 Iteration 19: loglikelihood = -2156.0117, backtracks = 1, tol = 0.011273980916902262 Iteration 20: loglikelihood = -2155.876, backtracks = 1, tol = 0.004824879657479134 Iteration 21: loglikelihood = -2155.845, backtracks = 1, tol = 0.0022575504541043107 Iteration 22: loglikelihood = -2155.8367, backtracks = 1, tol = 0.0011966095025835244 Iteration 23: loglikelihood = -2152.9631, backtracks = 1, tol = 0.06387883784418887 Iteration 24: loglikelihood = -2152.327, backtracks = 1, tol = 0.014859718731995555 Iteration 25: loglikelihood = -2152.1772, backtracks = 1, tol = 0.006837880975796278 Iteration 26: loglikelihood = -2152.133, backtracks = 1, tol = 0.0031807815989915 Iteration 27: loglikelihood = -2152.125, backtracks = 1, tol = 0.001478744871154188 Iteration 28: loglikelihood = -2152.1218, backtracks = 1, tol = 0.000695449064129354 Iteration 29: loglikelihood = -2152.1204, backtracks = 1, tol = 0.0004262457774189357 Iteration 30: loglikelihood = -2152.1191, backtracks = 1, tol = 0.0002586547978042914 Iteration 31: loglikelihood = -2152.1184, backtracks = 2, tol = 7.80534929699637e-5 0.283185 seconds (1.87 M allocations: 31.063 MiB, 8.09% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 32.6s **** 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 = -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 4.945217 seconds (1.15 M allocations: 137.135 MiB, 1.05% gc time, 90.86% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.4s 10.283777 seconds (4.00 M allocations: 82.502 MiB, 0.47% gc time, 0.60% compilation time) 5.486487 seconds (3.98 M allocations: 91.675 MiB, 0.49% gc time) 10.627352 seconds (20.41 M allocations: 439.466 MiB, 1.04% gc time, 18.87% compilation time: 79% of which was recompilation) 8.551585 seconds (20.18 M allocations: 434.189 MiB, 1.06% gc time) 39.968087 seconds (3.85 M allocations: 4.244 GiB, 11.86% gc time, 29.39% compilation time) 55.170332 seconds (70.38 k allocations: 183.446 MiB, 0.09% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m29.5s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.221 ms (78 allocations: 4.56 KiB) 4.346 μs (0 allocations: 0 bytes) 143.818 μs (4 allocations: 288 bytes) 6.913 μs (0 allocations: 0 bytes) 46.729 μs (2 allocations: 64 bytes) 30.700 μs (0 allocations: 0 bytes) 31.819 μs (0 allocations: 0 bytes) 28.090 μs (0 allocations: 0 bytes) 104.099 μs (0 allocations: 0 bytes) 36.847 ms (78 allocations: 4.56 KiB) 18.480 μs (0 allocations: 0 bytes) 167.179 μs (4 allocations: 288 bytes) 34.860 μs (0 allocations: 0 bytes) 239.617 μs (2 allocations: 64 bytes) 81.309 μs (0 allocations: 0 bytes) 157.148 μs (0 allocations: 0 bytes) 150.668 μs (0 allocations: 0 bytes) 216.408 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m19.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** 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 0.468808 seconds (49.46 k allocations: 5.503 MiB, 63.25% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.6s **** 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 Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.005843 seconds (282.38 k allocations: 168.302 MiB, 55.53% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:52 Cross validating... 11%|███▌ | ETA: 0:01:05 Cross validating... 14%|████▋ | ETA: 0:00:49 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:19 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 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89%|████████████████████████████▌ | ETA: 0:00:02 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: 0:00:12 Crossvalidation Results: k MSE 0 2484.04284292829 1 1656.150131505418 2 1050.0053404250323 3 845.0584737506383 4 590.5853091790625 5 336.8438086560734 6 342.1829609010821 7 345.1993930655387 8 349.6888895604281 9 351.32655207245637 10 364.1012553739093 11 354.4727948548206 12 366.2911397279138 13 372.73843200312075 14 383.9423700251268 15 381.90164803529973 16 380.6237630481511 17 374.5932505300901 18 413.82643350615194 19 408.3355591164975 20 418.36916758746406 Best k = 5 12.783858 seconds (12.00 M allocations: 308.867 MiB, 1.36% gc time, 60.63% 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... 8%|██▌ | ETA: 0:00:04 Cross validating... 11%|███▌ | ETA: 0:00:03 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... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 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Crossvalidation Results: k MSE 0 2484.04284292829 1 1658.9442553361864 2 1054.1717347874214 3 851.9728916085118 4 597.5252415891446 5 344.90762080008886 6 359.0432237673241 7 366.6671151050406 8 377.814465240478 9 381.5770740885474 10 391.84065076859787 11 389.0901052819486 12 390.9795856701683 13 405.44032539076846 14 398.7924341471734 15 414.3838515210281 16 413.5872225050182 17 416.09718740885336 18 433.1727719037169 19 429.6627537820169 20 443.40787373257535 Best k = 5 5.154864 seconds (11.00 M allocations: 231.564 MiB, 1.65% gc time, 0.93% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:09 Cross validating... 8%|██▌ | ETA: 0:02:22 Cross validating... 13%|████▏ | ETA: 0:01:25 Cross validating... 17%|█████▋ | ETA: 0:00:59 Cross validating... 22%|███████▏ | ETA: 0:00:44 Cross validating... 27%|████████▋ | ETA: 0:00:35 Cross validating... 32%|██████████▏ | ETA: 0:00:28 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 41%|█████████████▎ | ETA: 0:00:19 Cross validating... 46%|██████████████▊ | ETA: 0:00:16 Cross validating... 51%|████████████████▎ | ETA: 0:00:13 Cross validating... 56%|█████████████████▊ | ETA: 0:00:11 Cross validating... 60%|███████████████████▎ | ETA: 0:00:09 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 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... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:14 Crossvalidation Results: k MSE 0 1659.0844322509768 1 1428.224888671875 2 1093.028930053711 3 792.6621643066408 4 611.6148619995117 5 504.55983230590823 6 423.85620339965817 7 367.4773709716797 8 344.65140063476565 9 334.00643737792973 10 333.22221859741217 11 333.73595681762697 12 337.5584251403809 13 339.1146068725586 14 345.79277410888676 15 348.96388784790037 16 356.71041143798834 17 351.4726409606934 18 354.1661458129883 19 375.9519418029786 20 352.46052423095705 Best k = 10 15.917951 seconds (12.74 M allocations: 315.239 MiB, 0.75% gc time, 83.09% 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: 0:00:02 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 14%|████▋ | ETA: 0:00:02 Cross validating... 19%|██████▏ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 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... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1659.0844322509768 1 1430.301499145508 2 1095.7678103027345 3 796.1306696777344 4 613.5405668945313 5 505.79015063476567 6 424.55795071411137 7 368.7563723754883 8 346.784279296875 9 337.13433566284186 10 334.38739807128906 11 347.10343466186526 12 345.3421100463868 13 357.1301285705567 14 365.1204024047852 15 386.44651809692385 16 378.67393411254886 17 388.77095281982423 18 397.44821899414063 19 390.1346453552246 20 397.27719592285155 Best k = 10 2.768181 seconds (10.77 M allocations: 197.528 MiB, 1.72% gc time, 1.58% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.1s **** 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: 0:01:02 Cross validating... 6%|██ | ETA: 0:00:33 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:11 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:06 Cross validating... 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95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 464.55120945510043 1 384.30860951126334 2 340.5104611975582 3 326.59806361460676 4 306.4049048128322 5 279.5118499707708 6 284.9755763560258 7 288.18684572891914 8 290.1503665006651 9 294.4236392895291 10 305.6463941843608 11 298.1615295620914 12 332.4667294394617 13 315.4201626765397 14 299.60476943665356 15 321.19847858567516 16 350.8991820927906 17 345.86114007755776 18 324.2169007612697 19 347.87519188060514 20 362.9519486013569 Best k = 5 8.576191 seconds (17.83 M allocations: 420.817 MiB, 1.16% gc time, 31.75% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 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92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.55120945510043 1 384.57580815857983 2 342.4347570430999 3 329.05375610143915 4 310.30655565030276 5 282.685596810398 6 297.2296924676541 7 310.4160048550636 8 319.2816139703246 9 328.10537002695526 10 338.45215051818457 11 341.51055830145503 12 353.935231018721 13 351.88822345209564 14 357.6182965955249 15 357.6420634277409 16 376.98733049317065 17 382.8500949424797 18 377.4218230240141 19 405.27954691266035 20 410.5259314368243 Best k = 5 6.166580 seconds (17.89 M allocations: 373.317 MiB, 1.12% gc time, 0.92% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 15.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:26 Cross validating... 10%|███ | ETA: 0:00:18 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: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:08 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 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... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 463.8199706732289 1 438.9741425719558 2 396.9848473613242 3 374.6317392524776 4 365.93958009907897 5 353.73899561641093 6 330.7571468434546 7 332.4709771962015 8 335.89312801232734 9 338.92429436276643 10 344.753305162718 11 353.6603377647021 12 344.13607622299264 13 356.1089776342915 14 375.90258209401406 15 349.544598106601 16 350.2473842046494 17 358.86942757256503 18 384.72062768755893 19 348.2631559870031 20 360.2921209821667 Best k = 6 8.017390 seconds (17.05 M allocations: 400.946 MiB, 12.86% gc time, 33.34% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:04 Cross validating... 13%|████▏ | ETA: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 17%|█████▋ | ETA: 0:00:04 Cross validating... 21%|██████▋ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 463.8199706732289 1 439.6188671984405 2 400.1645326936206 3 378.86025420956787 4 370.75042956135496 5 359.88853377293793 6 337.85124166471127 7 343.6454521289489 8 353.279247790091 9 366.17227832549395 10 374.13390718325786 11 368.0770659558592 12 382.37456170425855 13 397.85499104844234 14 385.3367942036265 15 405.10254005420137 16 407.7708735062012 17 404.58356482386114 18 418.19360950180237 19 414.1631463306961 20 418.4146358609929 Best k = 6 4.566292 seconds (17.24 M allocations: 353.082 MiB, 1.33% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:13 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:10 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:07 Cross validating... 41%|█████████████▎ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:06 Cross validating... 48%|███████████████▎ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:04 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:03 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:03 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 691.8222284490116 1 550.3459985842412 2 436.92726443803826 3 404.20188094056584 4 378.95608461854044 5 373.51490220103227 6 371.8032491238498 7 367.4146130304687 8 371.6786707159601 9 376.9940823490655 10 375.6289987217093 11 368.3533639393525 12 380.27267194855546 13 382.67851502013514 14 371.0935966493222 15 375.83872501339556 16 377.6302425802281 17 380.2959815367754 18 394.51571891768015 19 395.11027256658184 20 389.19109868505086 Best k = 7 8.443530 seconds (14.97 M allocations: 355.304 MiB, 0.83% gc time, 32.02% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:05 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross 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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 0 691.8222284490116 1 549.8272262467001 2 436.07524927626423 3 405.7302432760158 4 380.6944063966446 5 367.892313000211 6 378.30718685325814 7 382.1062483686151 8 391.9952110602179 9 389.4866313623655 10 385.2946647910779 11 393.322248199929 12 400.8460111240237 13 392.5966670818276 14 402.45329272363784 15 404.55886793778467 16 418.4260766929418 17 425.7372937088728 18 424.83188629907676 19 425.2120453258959 20 430.1032928242363 Best k = 5 5.814220 seconds (13.77 M allocations: 273.256 MiB, 1.08% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:04 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 8%|██▌ | ETA: 0:00:39 Cross validating... 10%|███ | ETA: 0:00:42 Cross validating... 11%|███▌ | ETA: 0:00:44 Cross validating... 13%|████▏ | ETA: 0:00:39 Cross validating... 16%|█████▏ | ETA: 0:00:31 Cross validating... 17%|█████▋ | ETA: 0:00:28 Cross validating... 19%|██████▏ | ETA: 0:00:26 Cross validating... 21%|██████▋ | ETA: 0:00:24 Cross validating... 22%|███████▏ | ETA: 0:00:26 Cross validating... 24%|███████▋ | ETA: 0:00:27 Cross validating... 25%|████████▏ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:28 Cross validating... 29%|█████████▏ | ETA: 0:00:29 Cross validating... 30%|█████████▋ | ETA: 0:00:27 Cross validating... 32%|██████████▏ | ETA: 0:00:28 Cross validating... 33%|██████████▋ | ETA: 0:00:28 Cross validating... 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97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:43 Crossvalidation Results: k MSE 0 341.56071587664746 1 300.5262415433867 2 249.08367204407648 3 239.57465364447307 4 227.17946954046 5 224.71374290177573 6 226.01352707469243 7 224.28196248704575 8 225.13327503983663 9 227.3434149718545 10 229.29599836455787 11 231.15645600586757 12 232.2108667738487 13 233.27664400044753 14 236.22965898520584 15 236.2302646312408 16 237.95005050704043 17 239.26046630287235 18 237.1969500220581 19 240.32758739218997 20 239.67310444465085 Best k = 7 44.390779 seconds (131.71 M allocations: 3.382 GiB, 1.26% gc time, 5.18% 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: 0:00:08 Cross validating... 6%|██ | ETA: 0:00:07 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: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross validating... 22%|███████▏ | ETA: 0:00:06 Cross validating... 24%|███████▋ | ETA: 0:00:06 Cross validating... 25%|████████▏ | ETA: 0:00:06 Cross validating... 27%|████████▋ | ETA: 0:00:06 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 30%|█████████▋ | ETA: 0:00:06 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross 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validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:09 Crossvalidation Results: k MSE 0 341.56071587664746 1 301.0893083507662 2 249.56828565811497 3 241.2878416151288 4 232.92423170059595 5 229.1079596174257 6 232.6095764558465 7 235.70898144973236 8 236.9962489903719 9 243.5824501334596 10 251.68049035681082 11 252.4814540803552 12 260.35339272509384 13 266.18260411346125 14 268.78484871443885 15 273.3908304731307 16 273.4271519154842 17 285.79195190688483 18 281.9560178586872 19 281.1954342014808 20 286.58512626393286 Best k = 5 9.558571 seconds (26.30 M allocations: 529.304 MiB, 1.62% gc time, 0.63% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 54.4s **** 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: 0:01:11 Cross validating... 6%|██ | ETA: 0:00:36 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 44%|██████████████▎ | ETA: 0:00:05 Cross validating... 48%|███████████████▎ | ETA: 0:00:04 Cross validating... 51%|████████████████▎ | ETA: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:03 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 63%|████████████████████▍ | ETA: 0:00:03 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.394151 seconds (17.01 M allocations: 337.917 MiB, 1.40% gc time, 45.82% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 17%|█████▋ | ETA: 0:00:03 Cross validating... 21%|██████▋ | ETA: 0:00:03 Cross validating... 24%|███████▋ | ETA: 0:00:03 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 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... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 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: 0:00:03 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 3.380110 seconds (16.18 M allocations: 286.714 MiB, 1.58% gc time, 1.63% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:22 Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 4%|█▎ | ETA: 0:00:49 Cross validating... 5%|█▋ | ETA: 0:00:42 Cross validating... 6%|█▉ | ETA: 0:00:38 Cross validating... 7%|██▎ | ETA: 0:00:35 Cross validating... 8%|██▌ | ETA: 0:00:32 Cross validating... 9%|██▉ | ETA: 0:00:31 Cross validating... 10%|███▎ | ETA: 0:00:29 Cross validating... 11%|███▌ | ETA: 0:00:28 Cross validating... 12%|███▉ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:26 Cross validating... 14%|████▌ | ETA: 0:00:25 Cross validating... 15%|████▊ | ETA: 0:00:24 Cross validating... 16%|█████▏ | ETA: 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100%|████████████████████████████████| Time: 0:00:20 Crossvalidation Results: k MSE 1 2965.4238289581713 2 2568.544157020052 3 2390.4607646588206 4 2154.1075934440737 5 1935.2890576050336 6 1794.1361392727704 7 1700.4266592792555 8 1659.2300206021405 9 1628.572659818578 10 1593.7575903051656 11 1604.7717400741822 12 1615.670082868491 13 1623.2096424739875 14 1630.0390580455587 15 1648.0730483275483 16 1650.047874520166 17 1654.6984480753838 18 1652.0777104108317 19 1666.8963060331753 20 1666.1052264038503 Best k = 10 21.177990 seconds (343.90 k allocations: 238.941 MiB, 0.46% gc time, 7.74% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 26.3s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m53.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:12 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:12 Cross validating... 6%|█▉ | ETA: 0:00:14 Cross validating... 7%|██▎ | ETA: 0:00:14 Cross validating... 8%|██▌ | ETA: 0:00:14 Cross validating... 9%|██▉ | ETA: 0:00:16 Cross validating... 10%|███▎ | ETA: 0:00:17 Cross validating... 11%|███▌ | ETA: 0:00:18 Cross validating... 12%|███▉ | ETA: 0:00:18 Cross validating... 13%|████▏ | ETA: 0:00:19 Cross validating... 14%|████▌ | ETA: 0:00:19 Cross validating... 15%|████▊ | ETA: 0:00:19 Cross validating... 16%|█████▏ | ETA: 0:00:21 Cross validating... 17%|█████▌ | ETA: 0:00:21 Cross validating... 18%|█████▊ | ETA: 0:00:21 Cross validating... 19%|██████▏ | ETA: 0:00:21 Cross validating... 20%|██████▍ | ETA: 0:00:21 Cross validating... 21%|██████▊ | ETA: 0:00:20 Cross validating... 22%|███████ | ETA: 0:00:20 Cross validating... 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60%|███████████████████▎ | ETA: 0:00:11 Cross validating... 61%|███████████████████▌ | ETA: 0:00:10 Cross validating... 62%|███████████████████▉ | ETA: 0:00:10 Cross validating... 63%|████████████████████▏ | ETA: 0:00:10 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:09 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:09 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:08 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:07 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:07 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: 0:00:06 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: 0:00:05 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: 0:00:04 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: 0:00:03 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: 0:00:02 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: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:26 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: 0:00:14 Cross validating... 7%|██▎ | ETA: 0:00:14 Cross validating... 8%|██▌ | ETA: 0:00:14 Cross validating... 9%|██▉ | ETA: 0:00:15 Cross validating... 10%|███▎ | ETA: 0:00:16 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 14%|████▌ | ETA: 0:00:18 Cross 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Cross validating... 54%|█████████████████▎ | ETA: 0:00:11 Cross validating... 55%|█████████████████▋ | ETA: 0:00:11 Cross validating... 56%|█████████████████▉ | ETA: 0:00:11 Cross validating... 57%|██████████████████▎ | ETA: 0:00:11 Cross validating... 58%|██████████████████▌ | ETA: 0:00:11 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:10 Cross validating... 62%|███████████████████▉ | ETA: 0:00:10 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:09 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: 0:00:08 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: 0:00:07 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: 0:00:06 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: 0:00:05 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: 0:00:01 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:12 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:15 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:20 Cross validating... 20%|██████▍ | ETA: 0:00:20 Cross validating... 21%|██████▊ | ETA: 0:00:19 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 23%|███████▍ | ETA: 0:00:18 Cross validating... 24%|███████▋ | ETA: 0:00:17 Cross validating... 25%|████████ | ETA: 0:00:17 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | 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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: 0:00:25 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m32.4s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] getproperty(x::Nothing, f::Symbol) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] collect(itr::Base.Generator{UnitRange{Int64}, MendelIHT.var"#convert_bgen_gt##0#convert_bgen_gt##1"}) @ Base ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [15] top-level scope @ none:6 [16] eval(m::Module, e::Any) @ Core ./boot.jl:517 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [18] _start() @ Base ./client.jl:593 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.0s RNG of the outermost testset: Xoshiro(0x5a9e7a460ca77f16, 0x8a36b9ba305239c4, 0xbc2309af39284109, 0x7a5eb9081fdba502, 0xfe88e7199a68f49d) 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 1113.13s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1260.09s: package tests unexpectedly errored