Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2168 (2569364ac4*) started at 2026-05-10T23:39:42.401 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.73s ################################################################################ # 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 v1.9.3+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.33+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 6.11s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.2 s ✓ BGEN 7.9 s ✓ VCFTools WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 25.5 s ✓ MendelIHT 3 dependencies successfully precompiled in 41 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 67.67s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_vCh7wH/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 15.8s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.4s Test Summary: | Pass Total Time _choose! | 7 7 9.4s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.2s Test Summary: | Pass Total Time project_k! | 2 2 0.9s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.0s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1644.8054998779603, backtracks = 0, tol = 2.130054872525972 Iteration 2: loglikelihood = -1447.3141594275553, backtracks = 0, tol = 0.1534262711743646 Iteration 3: loglikelihood = -1431.916431121088, backtracks = 0, tol = 0.047737456207395355 Iteration 4: loglikelihood = -1431.6022996359166, backtracks = 0, tol = 0.004260386292089309 Iteration 5: loglikelihood = -1431.598561023501, backtracks = 0, tol = 0.0004110872177259216 Iteration 6: loglikelihood = -1431.5984933823834, backtracks = 0, tol = 7.978507067800255e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.04725813865661621 Final loglikelihood: -1431.5984933823834 SNP PVE: 0.9399071501198332 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1051 -2.29335 2 │ 3102 -0.421267 3 │ 3289 0.261782 4 │ 5213 0.37323 5 │ 6048 -0.634377 6 │ 7022 2.15035 7 │ 7341 0.773547 8 │ 8215 -1.27194 9 │ 8355 -1.47318 10 │ 8702 0.118519 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0176456Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 20.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -2251.8802111034793, backtracks = 0, tol = 0.3755680609605568 Iteration 2: loglikelihood = -1654.937391864141, backtracks = 0, tol = 0.05641487022807758 Iteration 3: loglikelihood = -1500.3944841319794, backtracks = 0, tol = 0.0556899199794715 Iteration 4: loglikelihood = -1438.1633443759767, backtracks = 0, tol = 0.10596710007272539 Iteration 5: loglikelihood = -1413.3768929068722, backtracks = 0, tol = 0.07147686562937376 Iteration 6: loglikelihood = -1390.287976907129, backtracks = 0, tol = 0.03474676699167867 Iteration 7: loglikelihood = -1376.3450527494806, backtracks = 1, tol = 0.06629708996782234 Iteration 8: loglikelihood = -1370.839669858802, backtracks = 0, tol = 0.025265613483270284 Iteration 9: loglikelihood = -1368.756912615204, backtracks = 0, tol = 0.015271275676257913 Iteration 10: loglikelihood = -1361.6458843135765, backtracks = 0, tol = 0.043683940351848846 Iteration 11: loglikelihood = -1359.3686603071285, backtracks = 0, tol = 0.014636586748175785 Iteration 12: loglikelihood = -1358.4090869381694, backtracks = 0, tol = 0.01177009083840244 Iteration 13: loglikelihood = -1357.8654629246412, backtracks = 0, tol = 0.006444435356808347 Iteration 14: loglikelihood = -1357.5418973321327, backtracks = 0, tol = 0.007183123767628458 Iteration 15: loglikelihood = -1355.065664524597, backtracks = 0, tol = 0.048808525770849556 Iteration 16: loglikelihood = -1354.4884425248054, backtracks = 1, tol = 0.005424534614322409 Iteration 17: loglikelihood = -1354.1737937022788, backtracks = 1, tol = 0.004393339478773623 Iteration 18: loglikelihood = -1354.048428499271, backtracks = 1, tol = 0.0034613381604846217 Iteration 19: loglikelihood = -1353.9871816021137, backtracks = 1, tol = 0.0015690709602730372 Iteration 20: loglikelihood = -1353.9466812547391, backtracks = 1, tol = 0.0023474376495814134 Iteration 21: loglikelihood = -1353.92347939437, backtracks = 1, tol = 0.0009525958922870257 Iteration 22: loglikelihood = -1353.9061592187675, backtracks = 1, tol = 0.0016351207341198507 Iteration 23: loglikelihood = -1353.8968765631066, backtracks = 1, tol = 0.0005858084294684549 Iteration 24: loglikelihood = -1353.8887170046419, backtracks = 1, tol = 0.001198851508827739 Iteration 25: loglikelihood = -1353.885186025027, backtracks = 1, tol = 0.0003445774835900777 Iteration 26: loglikelihood = -1353.8826732316713, backtracks = 2, tol = 0.0004899706842017173 Iteration 27: loglikelihood = -1353.8803958750268, backtracks = 2, tol = 0.00042386004487961535 Iteration 28: loglikelihood = -1353.879058398987, backtracks = 2, tol = 0.0003860539256448294 Iteration 29: loglikelihood = -1353.8781785499166, backtracks = 2, tol = 0.00024394973229705031 Iteration 30: loglikelihood = -1353.8775971439516, backtracks = 2, tol = 0.00025457505834846256 Iteration 31: loglikelihood = -1353.877212952949, backtracks = 2, tol = 0.00016135566642556446 Iteration 32: loglikelihood = -1353.8769591043847, backtracks = 2, tol = 0.00016829826329985717 Iteration 33: loglikelihood = -1353.8767912909957, backtracks = 2, tol = 0.0001066641245500251 Iteration 34: loglikelihood = -1353.876680372805, backtracks = 2, tol = 0.00011127655043636795 Iteration 35: loglikelihood = -1353.8766070340307, backtracks = 2, tol = 7.051738092384534e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1629.0491051244862, backtracks = 0, tol = 0.38042718019658256 Iteration 2: loglikelihood = -1530.1408164118996, backtracks = 0, tol = 0.21679430309250586 Iteration 3: loglikelihood = -1499.7491672257586, backtracks = 0, tol = 0.14314381204234244 Iteration 4: loglikelihood = -1497.7522437993543, backtracks = 0, tol = 0.09569011012674539 Iteration 5: loglikelihood = -1492.0420363476537, backtracks = 0, tol = 0.08982698565532904 Iteration 6: loglikelihood = -1491.4435558126681, backtracks = 0, tol = 0.07961466167202659 Iteration 7: loglikelihood = -1490.6598439576026, backtracks = 0, tol = 0.01694985700973784 Iteration 8: loglikelihood = -1490.6308113202183, backtracks = 1, tol = 0.0020878705182475824 Iteration 9: loglikelihood = -1490.6211910412503, backtracks = 1, tol = 0.0012846378685362977 Iteration 10: loglikelihood = -1489.585314893178, backtracks = 1, tol = 0.05691640799225734 Iteration 11: loglikelihood = -1489.4410678177378, backtracks = 0, tol = 0.007747569036879893 Iteration 12: loglikelihood = -1489.4299217703958, backtracks = 0, tol = 0.003449539066319821 Iteration 13: loglikelihood = -1489.4282406344157, backtracks = 1, tol = 0.0005309632602250689 Iteration 14: loglikelihood = -1489.4273783327992, backtracks = 1, tol = 0.00042249699001524043 Iteration 15: loglikelihood = -1489.427060555091, backtracks = 1, tol = 0.00041025154990386093 Iteration 16: loglikelihood = -1489.4269757803359, backtracks = 1, tol = 0.00017447394749112058 Iteration 17: loglikelihood = -1489.4269626164291, backtracks = 2, tol = 5.391048886190718e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1986.792912378941, backtracks = 0, tol = 0.7326318847927661 Iteration 2: loglikelihood = -1507.1209444119072, backtracks = 0, tol = 0.1585367544346729 Iteration 3: loglikelihood = -1406.8380190543974, backtracks = 0, tol = 0.06471019545737942 Iteration 4: loglikelihood = -1396.2231682762297, backtracks = 0, tol = 0.03023290748734835 Iteration 5: loglikelihood = -1396.0166425055188, backtracks = 0, tol = 0.02515706466877335 Iteration 6: loglikelihood = -1395.915179249816, backtracks = 1, tol = 0.001049425699840767 Iteration 7: loglikelihood = -1395.8872992699776, backtracks = 1, tol = 0.0005896533587022889 Iteration 8: loglikelihood = -1395.8796846102975, backtracks = 1, tol = 0.0003137101288690551 Iteration 9: loglikelihood = -1395.8776486048585, backtracks = 1, tol = 0.0001567716509928027 Iteration 10: loglikelihood = -1395.8771169247434, backtracks = 1, tol = 7.458510703156885e-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 = -1726.1139638920854, backtracks = 0, tol = 0.5912121373746618 Iteration 2: loglikelihood = -1451.8328648613308, backtracks = 0, tol = 0.1212416751172526 Iteration 3: loglikelihood = -1399.6168837232026, backtracks = 0, tol = 0.049017199349886124 Iteration 4: loglikelihood = -1396.4633442634315, backtracks = 0, tol = 0.03416262507244159 Iteration 5: loglikelihood = -1396.0314911846217, backtracks = 0, tol = 0.02874767073436108 Iteration 6: loglikelihood = -1395.938652381848, backtracks = 1, tol = 0.0012076900008850425 Iteration 7: loglikelihood = -1395.9144513112358, backtracks = 1, tol = 0.0006021124990901485 Iteration 8: loglikelihood = -1395.9081430289202, backtracks = 1, tol = 0.00029567238686100506 Iteration 9: loglikelihood = -1395.9065020183139, backtracks = 1, tol = 0.00015105574988783307 Iteration 10: loglikelihood = -1395.9060766336625, backtracks = 1, tol = 7.946694088286018e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 = -1438.5357528627967, backtracks = 0, tol = 0.2065381334623478 Iteration 2: loglikelihood = -1398.2669547942437, backtracks = 0, tol = 0.10410388440474654 Iteration 3: loglikelihood = -1374.088177267722, backtracks = 0, tol = 0.06974071168912117 Iteration 4: loglikelihood = -1367.0319160025113, backtracks = 0, tol = 0.10996435964495352 Iteration 5: loglikelihood = -1362.6884811393334, backtracks = 0, tol = 0.0811124315094769 Iteration 6: loglikelihood = -1342.02158987027, backtracks = 0, tol = 0.07806778447983023 Iteration 7: loglikelihood = -1334.5463026447414, backtracks = 0, tol = 0.05240048138770215 Iteration 8: loglikelihood = -1325.6299623526893, backtracks = 0, tol = 0.042616330385746706 Iteration 9: loglikelihood = -1323.2804024094135, backtracks = 0, tol = 0.023595630340747686 Iteration 10: loglikelihood = -1322.7704745606034, backtracks = 0, tol = 0.01349903842007263 Iteration 11: loglikelihood = -1322.5785419114309, backtracks = 0, tol = 0.006588153368356801 Iteration 12: loglikelihood = -1322.5021444330764, backtracks = 0, tol = 0.005542477648937676 Iteration 13: loglikelihood = -1322.4704419394307, backtracks = 0, tol = 0.002814557739026414 Iteration 14: loglikelihood = -1322.4574329882412, backtracks = 0, tol = 0.0022714830201765825 Iteration 15: loglikelihood = -1322.4262843117524, backtracks = 0, tol = 0.06540820463213576 Iteration 16: loglikelihood = -1322.1799686332777, backtracks = 0, tol = 0.005520241312770935 Iteration 17: loglikelihood = -1322.147451992054, backtracks = 0, tol = 0.003350904334915656 Iteration 18: loglikelihood = -1322.137446132751, backtracks = 0, tol = 0.0014261840812186477 Iteration 19: loglikelihood = -1322.133231423005, backtracks = 0, tol = 0.0014796657447934329 Iteration 20: loglikelihood = -1322.1314122249319, backtracks = 0, tol = 0.0006097701393309409 Iteration 21: loglikelihood = -1322.1306261062464, backtracks = 0, tol = 0.0006395628553632905 Iteration 22: loglikelihood = -1322.1302858348722, backtracks = 0, tol = 0.0002645702794907779 Iteration 23: loglikelihood = -1322.1301385385777, backtracks = 0, tol = 0.0002761815409909347 Iteration 24: loglikelihood = -1322.130074768707, backtracks = 0, tol = 0.00011481033314796559 Iteration 25: loglikelihood = -1322.1300471506092, backtracks = 0, tol = 0.00011932667417953043 Iteration 26: loglikelihood = -1322.1300351951409, backtracks = 0, tol = 4.9808903994083e-5 0.935566 seconds (2.43 M allocations: 48.092 MiB, 61.77% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1498.407806092199, backtracks = 0, tol = 0.2065381334623478 Iteration 2: loglikelihood = -1476.944024206407, backtracks = 0, tol = 0.14339626682364043 Iteration 3: loglikelihood = -1450.8720596747796, backtracks = 0, tol = 0.10376351892375503 Iteration 4: loglikelihood = -1432.255843344154, backtracks = 0, tol = 0.10043765597729619 Iteration 5: loglikelihood = -1420.3896665164473, backtracks = 0, tol = 0.08207764716971597 Iteration 6: loglikelihood = -1404.4823020743383, backtracks = 0, tol = 0.07811908076665258 Iteration 7: loglikelihood = -1399.2128308088577, backtracks = 0, tol = 0.06414489758530505 Iteration 8: loglikelihood = -1388.327633229562, backtracks = 0, tol = 0.05139506251007792 Iteration 9: loglikelihood = -1376.1767724024776, backtracks = 0, tol = 0.04853084638769125 Iteration 10: loglikelihood = -1369.2083649674798, backtracks = 0, tol = 0.07351866097692687 Iteration 11: loglikelihood = -1365.9230011287984, backtracks = 0, tol = 0.07412194610008868 Iteration 12: loglikelihood = -1361.1026202325133, backtracks = 0, tol = 0.07265712447222444 Iteration 13: loglikelihood = -1357.8316144107794, backtracks = 0, tol = 0.007071276797411161 Iteration 14: loglikelihood = -1355.5933653020686, backtracks = 0, tol = 0.07409708964610459 Iteration 15: loglikelihood = -1353.0676107767197, backtracks = 0, tol = 0.006080294291881677 Iteration 16: loglikelihood = -1350.7439026917343, backtracks = 0, tol = 0.07190935741890285 Iteration 17: loglikelihood = -1348.7487059591135, backtracks = 0, tol = 0.00522581846455459 Iteration 18: loglikelihood = -1347.054558533879, backtracks = 0, tol = 0.0010160661243006504 Iteration 19: loglikelihood = -1344.4008340542157, backtracks = 1, tol = 0.00014118240039788396 Iteration 20: loglikelihood = -1343.7524080629646, backtracks = 0, tol = 0.06997350471735662 Iteration 21: loglikelihood = -1342.129291825586, backtracks = 0, tol = 0.06998497929437643 Iteration 22: loglikelihood = -1341.0077015861657, backtracks = 0, tol = 0.004534393879610381 Iteration 23: loglikelihood = -1340.0514644186887, backtracks = 0, tol = 0.0007429233133898565 Iteration 24: loglikelihood = -1339.8979848891843, backtracks = 0, tol = 0.07171384324951961 Iteration 25: loglikelihood = -1338.508890890099, backtracks = 0, tol = 0.07169819240789609 Iteration 26: loglikelihood = -1337.6830298243171, backtracks = 0, tol = 0.004545932119511225 Iteration 27: loglikelihood = -1336.9909382916453, backtracks = 0, tol = 0.0007763768317012539 Iteration 28: loglikelihood = -1335.8194652395744, backtracks = 1, tol = 0.00014083875695142307 Iteration 29: loglikelihood = -1334.8079812417047, backtracks = 1, tol = 0.00016542301459239206 Iteration 30: loglikelihood = -1333.917655252656, backtracks = 1, tol = 0.00015432518969147655 Iteration 31: loglikelihood = -1333.2204882921487, backtracks = 1, tol = 0.0001504015068315229 Iteration 32: loglikelihood = -1332.5531508657316, backtracks = 1, tol = 0.00013899428442380504 Iteration 33: loglikelihood = -1332.0904132617309, backtracks = 1, tol = 0.00012616864698493542 Iteration 34: loglikelihood = -1331.7827587803897, backtracks = 1, tol = 0.0001070667598692533 Iteration 35: loglikelihood = -1331.643986700447, backtracks = 1, tol = 9.555108002332883e-5 0.354723 seconds (1.42 M allocations: 26.113 MiB, 6.85% 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 = -3588.4, backtracks = 0, tol = 0.07919183989922042 Iteration 2: loglikelihood = -3567.0857, backtracks = 0, tol = 0.031823088505143995 Iteration 3: loglikelihood = -3541.7246, backtracks = 1, tol = 0.05725342431295005 Iteration 4: loglikelihood = -3536.04, backtracks = 1, tol = 0.012968319299962772 Iteration 5: loglikelihood = -3534.1335, backtracks = 1, tol = 0.007467318024052452 Iteration 6: loglikelihood = -3520.036, backtracks = 1, tol = 0.06178315006836528 Iteration 7: loglikelihood = -3517.1836, backtracks = 1, tol = 0.009849670077699456 Iteration 8: loglikelihood = -3516.258, backtracks = 1, tol = 0.005161198799304567 Iteration 9: loglikelihood = -3515.9705, backtracks = 1, tol = 0.002933708016292507 Iteration 10: loglikelihood = -3515.8918, backtracks = 1, tol = 0.0017674024500114042 Iteration 11: loglikelihood = -3515.8752, backtracks = 1, tol = 0.0009494310302718518 Iteration 12: loglikelihood = -3515.868, backtracks = 1, tol = 0.00048729701070837573 Iteration 13: loglikelihood = -3515.8667, backtracks = 1, tol = 0.00024559758860449713 Iteration 14: loglikelihood = -3515.8674, backtracks = 3, tol = 3.075652950981978e-5 23.613336 seconds (16.54 M allocations: 702.418 MiB, 1.48% gc time, 97.57% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3505.4607, backtracks = 0, tol = 0.07919183989922042 Iteration 2: loglikelihood = -3422.9556, backtracks = 0, tol = 0.03243379523445447 Iteration 3: loglikelihood = -3178.4307, backtracks = 1, tol = 0.056899329397064734 Iteration 4: loglikelihood = -3134.6824, backtracks = 0, tol = 0.09351353474367156 Iteration 5: loglikelihood = -2968.6663, backtracks = 0, tol = 0.08562023309578702 Iteration 6: loglikelihood = -2828.3628, backtracks = 0, tol = 0.08405381251825028 Iteration 7: loglikelihood = -2717.9163, backtracks = 0, tol = 0.012272547349566778 Iteration 8: loglikelihood = -2628.0322, backtracks = 0, tol = 0.09149106292593386 Iteration 9: loglikelihood = -2494.987, backtracks = 0, tol = 0.09150543101811591 Iteration 10: loglikelihood = -2401.737, backtracks = 0, tol = 0.014409393204398609 Iteration 11: loglikelihood = -2331.8428, backtracks = 0, tol = 0.08380898326057133 Iteration 12: loglikelihood = -2268.5486, backtracks = 0, tol = 0.08972693495790898 Iteration 13: loglikelihood = -2225.6792, backtracks = 0, tol = 0.010789933639031666 Iteration 14: loglikelihood = -2197.2744, backtracks = 0, tol = 0.002382840189267311 Iteration 15: loglikelihood = -2182.0112, backtracks = 0, tol = 0.08689630463723394 Iteration 16: loglikelihood = -2170.92, backtracks = 0, tol = 0.090535462364399 Iteration 17: loglikelihood = -2161.0835, backtracks = 0, tol = 0.09508999602580641 Iteration 18: loglikelihood = -2156.7463, backtracks = 0, tol = 0.08283000430853385 Iteration 19: loglikelihood = -2154.8083, backtracks = 0, tol = 0.011429913863868147 Iteration 20: loglikelihood = -2153.966, backtracks = 0, tol = 0.0026427544561657954 Iteration 21: loglikelihood = -2153.5437, backtracks = 0, tol = 0.0006975889252190047 Iteration 22: loglikelihood = -2153.3345, backtracks = 0, tol = 0.00019936254312944977 Iteration 23: loglikelihood = -2153.1836, backtracks = 1, tol = 5.8874014242792376e-5 1.055390 seconds (1.08 M allocations: 17.854 MiB, 86.01% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 28.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 4.304719 seconds (1.14 M allocations: 136.650 MiB, 1.15% gc time, 89.78% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 4.8s 9.902615 seconds (4.00 M allocations: 82.493 MiB, 0.78% gc time, 0.58% compilation time) 5.079533 seconds (3.98 M allocations: 91.674 MiB, 0.11% gc time) 9.624409 seconds (20.41 M allocations: 439.370 MiB, 1.01% gc time, 15.52% compilation time: 78% of which was recompilation) 8.135975 seconds (20.18 M allocations: 434.186 MiB, 0.89% gc time) 39.059961 seconds (3.77 M allocations: 4.239 GiB, 12.30% gc time, 28.95% compilation time) 54.495943 seconds (70.38 k allocations: 183.438 MiB, 0.18% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m24.7s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 14.806 ms (78 allocations: 4.56 KiB) 4.337 μs (0 allocations: 0 bytes) 138.189 μs (4 allocations: 288 bytes) 6.642 μs (0 allocations: 0 bytes) 44.970 μs (2 allocations: 64 bytes) 29.069 μs (0 allocations: 0 bytes) 24.970 μs (0 allocations: 0 bytes) 28.020 μs (0 allocations: 0 bytes) 99.899 μs (0 allocations: 0 bytes) 38.653 ms (78 allocations: 4.56 KiB) 18.300 μs (0 allocations: 0 bytes) 167.539 μs (4 allocations: 288 bytes) 40.999 μs (0 allocations: 0 bytes) 196.148 μs (2 allocations: 64 bytes) 84.619 μs (0 allocations: 0 bytes) 125.329 μs (0 allocations: 0 bytes) 144.609 μs (0 allocations: 0 bytes) 238.268 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m18.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.396391 seconds (49.38 k allocations: 5.492 MiB, 62.02% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 10.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 1.664612 seconds (282.22 k allocations: 168.333 MiB, 56.45% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:09 Cross validating... 13%|████▏ | ETA: 0:00:46 Cross validating... 16%|█████▏ | ETA: 0:00:36 Cross validating... 19%|██████▏ | ETA: 0:00:29 Cross validating... 22%|███████▏ | ETA: 0:00:25 Cross validating... 25%|████████▏ | ETA: 0:00:21 Cross validating... 29%|█████████▏ | ETA: 0:00:18 Cross validating... 32%|██████████▏ | ETA: 0:00:16 Cross validating... 35%|███████████▏ | ETA: 0:00:14 Cross validating... 38%|████████████▎ | ETA: 0:00:13 Cross 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validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:10 Crossvalidation Results: k MSE 0 5711.232458964979 1 3733.1039522339315 2 2100.6543582390805 3 1366.9676363400345 4 845.1107864140229 5 621.1284861479297 6 482.5855549993606 7 414.00709345698544 8 372.76003249255973 9 350.77339422661123 10 353.2376341141818 11 354.4468866089915 12 360.94287449558954 13 359.08654433370316 14 370.2486372867553 15 365.9062779817866 16 389.38694569635805 17 389.12202374269725 18 365.4592100423939 19 381.7768787799771 20 378.6697845253655 Best k = 9 10.412258 seconds (11.50 M allocations: 301.269 MiB, 1.50% gc time, 61.01% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 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: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 5711.232458964979 1 3735.321226102841 2 2104.6550383585222 3 1383.1666696869604 4 858.2995376250219 5 628.3830159323288 6 492.55254971858017 7 420.25171637215533 8 377.3371550410975 9 356.528202972858 10 362.2249319744653 11 367.72276980739963 12 383.1815787433127 13 377.7733256455929 14 387.05217341114553 15 398.82120424610684 16 400.9199890596477 17 401.43168642125863 18 400.25497407971494 19 404.4261893698915 20 406.8409251579633 Best k = 9 4.241872 seconds (10.21 M allocations: 214.215 MiB, 1.05% gc time, 1.03% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 15.5s **** 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: 0:05:51 Cross validating... 8%|██▌ | ETA: 0:02:15 Cross validating... 13%|████▏ | ETA: 0:01:21 Cross validating... 17%|█████▋ | ETA: 0:00:56 Cross validating... 24%|███████▋ | ETA: 0:00:38 Cross validating... 29%|█████████▏ | ETA: 0:00:30 Cross validating... 33%|██████████▋ | ETA: 0:00:25 Cross validating... 40%|████████████▊ | ETA: 0:00:19 Cross validating... 46%|██████████████▊ | ETA: 0:00:15 Cross validating... 52%|████████████████▊ | ETA: 0:00:11 Cross validating... 56%|█████████████████▊ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:08 Cross validating... 65%|████████████████████▉ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:13 Crossvalidation Results: k MSE 0 1591.726319580078 1 1265.0481750488282 2 1000.1330535888671 3 864.3568313598632 4 627.8375228881837 5 553.7609481811523 6 451.0696965026856 7 401.7955397033692 8 353.13026580810543 9 338.9257627868652 10 342.8549513244629 11 343.8488818359375 12 344.47744674682616 13 346.37738357543947 14 344.6139891052246 15 348.8608093261719 16 344.7989833068848 17 364.72237884521485 18 358.91323760986324 19 348.95743896484373 20 393.5367613220215 Best k = 9 15.104712 seconds (12.76 M allocations: 316.957 MiB, 0.52% gc time, 83.94% 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... 11%|███▌ | ETA: 0:00:02 Cross validating... 17%|█████▋ | 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... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1591.726319580078 1 1265.0629022216797 2 1001.3359887695312 3 864.3568313598632 4 635.712177734375 5 565.7895809936524 6 455.46171417236326 7 414.23105606079105 8 364.43774002075196 9 350.46241073608394 10 359.1028126525879 11 368.2578355407715 12 364.43172775268556 13 373.0412698364258 14 374.60809143066405 15 386.1124755859375 16 379.4318428039551 17 387.6221298217773 18 384.7084735107422 19 393.8637648010254 20 390.49359451293947 Best k = 9 2.533208 seconds (10.62 M allocations: 194.603 MiB, 2.02% gc time, 1.60% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 19.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:56 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 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... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 464.52415639322624 1 402.56290580356085 2 324.3703224319446 3 296.2098209353915 4 258.05517475914655 5 235.0659521231496 6 230.1332678507661 7 235.1788352863003 8 231.56497221845223 9 240.03048839199016 10 236.32693215942317 11 239.9487186964333 12 260.7651909203259 13 242.30771166624342 14 241.68800598899753 15 257.09943874769436 16 234.79635732470985 17 258.33845211479144 18 245.28829575311352 19 253.84707086188223 20 281.6070525395022 Best k = 6 7.663754 seconds (17.33 M allocations: 403.609 MiB, 1.26% gc time, 31.30% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 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: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 464.52415639322624 1 402.91010629462295 2 325.12223097894906 3 298.0340343984392 4 260.3417183393634 5 236.57006919395752 6 232.82303007940436 7 240.85046046404756 8 241.45946516762007 9 246.26491960101202 10 270.99614676574464 11 251.48749994410386 12 280.35104461056864 13 279.481910046792 14 274.6940170729733 15 277.0511512739149 16 276.4954698645637 17 276.7189508066641 18 286.8439284416794 19 310.10703365001604 20 300.91080463047774 Best k = 6 5.781137 seconds (17.77 M allocations: 367.953 MiB, 1.29% gc time, 0.99% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 13.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:48 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 10%|███ | ETA: 0:00:17 Cross validating... 13%|████▏ | ETA: 0:00:14 Cross validating... 16%|█████▏ | ETA: 0:00:11 Cross validating... 19%|██████▏ | ETA: 0:00:10 Cross validating... 22%|███████▏ | ETA: 0:00:09 Cross validating... 25%|████████▏ | ETA: 0:00:08 Cross validating... 29%|█████████▏ | ETA: 0:00:07 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: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 462.55826266947435 1 438.76167588290343 2 408.5557861347286 3 373.8649664550828 4 364.92969022751197 5 341.34768744661363 6 336.1710936208858 7 336.74379390418596 8 339.00304225824357 9 347.6886629566662 10 355.42637088545393 11 343.527752923305 12 360.9314469509917 13 350.926760540894 14 346.21993913589426 15 351.5117050357444 16 376.3896070324847 17 353.9130761266706 18 361.1485828196787 19 404.3490033397549 20 361.7282033079674 Best k = 6 7.914303 seconds (16.74 M allocations: 392.477 MiB, 13.70% gc time, 33.93% 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: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 462.55826266947435 1 439.95351508792487 2 410.7170717405663 3 377.80434342531635 4 369.2914633911246 5 346.6745640462581 6 342.61036655751775 7 353.50646437215255 8 359.43403777602623 9 362.71442995812083 10 378.15042473014637 11 380.16603235508876 12 396.62234324195356 13 402.4949844056173 14 399.0058536111525 15 420.30388180644593 16 433.67615677361323 17 438.05519016068774 18 452.04791226907406 19 444.96645971459395 20 453.1132347273789 Best k = 6 4.424264 seconds (17.08 M allocations: 350.145 MiB, 2.30% gc time, 1.00% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 11%|███▌ | ETA: 0:00:20 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:09 Cross validating... 32%|██████████▏ | ETA: 0:00:08 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86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1167.1820258472185 1 892.6425897147806 2 609.5132368241386 3 517.5488913318482 4 437.20734801773466 5 404.0320858090461 6 384.60524525702004 7 386.40586041702545 8 384.40906127926064 9 397.2214550975433 10 390.37870221862175 11 393.97028383058927 12 405.4301713241346 13 414.92390994735393 14 430.2269290069147 15 425.0708079882402 16 418.22097607781916 17 437.0271487794629 18 442.2796060343541 19 443.53491992498203 20 411.0187903753423 Best k = 8 7.960712 seconds (15.46 M allocations: 357.148 MiB, 0.81% gc time, 32.89% 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: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | 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98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1167.1820258472185 1 837.0029140254205 2 600.5191077491111 3 506.48259955201354 4 434.26055858321496 5 397.4856583107503 6 379.284427666252 7 379.3745163193393 8 386.3706084213998 9 388.6116905654845 10 399.6204202647702 11 392.2605397221664 12 410.9357327137727 13 425.3781586988235 14 435.81654037344373 15 432.1496413978958 16 440.32239892610596 17 445.50698997901395 18 460.09590657698027 19 469.70060850571093 20 459.30302131852886 Best k = 6 5.501535 seconds (14.15 M allocations: 283.710 MiB, 1.26% gc time, 1.10% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:31 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 11%|███▌ | ETA: 0:00:27 Cross validating... 13%|████▏ | ETA: 0:00:24 Cross validating... 14%|████▋ | ETA: 0:00:27 Cross validating... 16%|█████▏ | ETA: 0:00:24 Cross validating... 17%|█████▋ | ETA: 0:00:26 Cross validating... 19%|██████▏ | ETA: 0:00:28 Cross validating... 21%|██████▋ | ETA: 0:00:29 Cross validating... 22%|███████▏ | ETA: 0:00:30 Cross validating... 24%|███████▋ | ETA: 0:00:30 Cross validating... 25%|████████▏ | ETA: 0:00:31 Cross validating... 27%|████████▋ | ETA: 0:00:31 Cross validating... 29%|█████████▏ | ETA: 0:00:31 Cross validating... 30%|█████████▋ | ETA: 0:00:32 Cross validating... 32%|██████████▏ | ETA: 0:00:32 Cross validating... 33%|██████████▋ | ETA: 0:00:31 Cross validating... 37%|███████████▋ | ETA: 0:00:27 Cross validating... 40%|████████████▊ | ETA: 0:00:26 Cross 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ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:41 Crossvalidation Results: k MSE 0 467.85080780634075 1 354.29605145872586 2 267.7620692541051 3 235.9986596164786 4 209.1298406373034 5 203.5947989438785 6 195.78386551037033 7 197.64467075511806 8 198.5961684769083 9 201.40235605950693 10 200.9836204076755 11 202.59790540540885 12 203.86811775002758 13 203.0389170348668 14 206.1319818854346 15 207.91446891657785 16 207.68907649162875 17 209.76055288431525 18 209.99958014632875 19 210.62933846548484 20 213.19710379349814 Best k = 6 42.326322 seconds (133.23 M allocations: 3.421 GiB, 1.16% gc time, 5.31% 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 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validating... 73%|███████████████████████▍ | ETA: 0:00:03 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:03 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 467.85080780634075 1 351.36723921608285 2 266.9508900938929 3 241.79005637069764 4 211.31411790567594 5 206.36915563660713 6 199.06584473063418 7 202.87666200090024 8 205.07878975868883 9 212.0590077565785 10 213.14678077511167 11 216.17508487857674 12 225.11784705319184 13 220.21439472016183 14 229.99572010043852 15 232.36154805993334 16 231.85842644498655 17 240.92303461102966 18 238.48232556994742 19 240.26540931384915 20 235.5216922886529 Best k = 6 12.765043 seconds (41.71 M allocations: 873.287 MiB, 1.21% gc time, 0.49% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 55.5s **** 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: 0:00:49 Cross validating... 6%|██ | ETA: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:06 Cross validating... 33%|██████████▋ | ETA: 0:00:05 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 54%|█████████████████▎ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 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 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 5.353194 seconds (17.00 M allocations: 337.695 MiB, 2.03% gc time, 38.28% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | 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 3.084914 seconds (16.17 M allocations: 286.696 MiB, 1.67% gc time, 1.69% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 8.8s **** 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... 2%|▋ | ETA: 0:01:11 Cross validating... 3%|█ | ETA: 0:00:50 Cross validating... 4%|█▎ | ETA: 0:00:40 Cross validating... 5%|█▋ | ETA: 0:00:34 Cross validating... 6%|█▉ | ETA: 0:00:30 Cross 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0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 1 2152.1517118683364 2 1766.4202743185515 3 1517.385871050961 4 1384.2289643628533 5 1206.8295889189812 6 1032.365635453374 7 993.589438320098 8 951.7903014784055 9 954.4384773627154 10 956.8305584733503 11 955.8480372826617 12 957.1910420977719 13 965.1118851335406 14 974.569343172477 15 974.4118598242984 16 994.4337233589022 17 1007.5643837406855 18 1004.5025581549733 19 1014.2269109559369 20 1006.7828682642989 Best k = 8 15.835889 seconds (308.97 k allocations: 199.013 MiB, 0.54% gc time, 9.36% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 20.4s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m58.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:10 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:13 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:15 Cross validating... 13%|████▏ | ETA: 0:00:15 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:16 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100%|████████████████████████████████| Time: 0:00:23 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ 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Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:12 Cross validating... 8%|██▌ | ETA: 0:00:12 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:16 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:18 Cross validating... 20%|██████▍ | ETA: 0:00:18 Cross validating... 21%|██████▊ | ETA: 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2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m25.5s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] 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(0x375b72895dd46b2f, 0x45e832e0d71a80db, 0xba5ef16a6a9e38f5, 0x43a975e1ae353ce3, 0x8690fb6bbbafb4be) 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 1058.3s 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 1168.26s: package tests unexpectedly errored