Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2009 (d4d184e100*) started at 2026-04-10T08:43:31.480 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.24s ################################################################################ # 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 v4.5.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.23.0 [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 v1.3.0+1 [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 v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+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 v1.68.1+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 6.26s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5225.8 ms ✓ BGEN 6748.8 ms ✓ 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`. 26210.0 ms ✓ 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 67.96s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_bdtLsp/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.7.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [38e38edf] GLM v1.9.3 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.7.2 [2913bbd2] StatsBase v0.34.10 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v1.68.1+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 = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.9s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.5s Test Summary: | Pass Total Time _choose! | 7 7 10.7s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.7s Test Summary: | Pass Total Time project_k! | 2 2 1.0s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.4s 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 = -1587.6401003425829, backtracks = 0, tol = 1.810161612384997 Iteration 2: loglikelihood = -1433.3401320082853, backtracks = 0, tol = 0.1280891656757196 Iteration 3: loglikelihood = -1424.0153214296981, backtracks = 0, tol = 0.026127072032094245 Iteration 4: loglikelihood = -1423.9427060638586, backtracks = 0, tol = 0.002581958584716572 Iteration 5: loglikelihood = -1423.941536543787, backtracks = 0, tol = 0.00038145607054615666 Iteration 6: loglikelihood = -1423.9415122606167, backtracks = 0, tol = 4.388255529144207e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05364394187927246 Final loglikelihood: -1423.9415122606167 SNP PVE: 0.8997918725410036 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1252 -0.182397 2 │ 1870 -0.253278 3 │ 2164 -0.497623 4 │ 5049 -1.21538 5 │ 5362 -1.36817 6 │ 5853 1.02981 7 │ 8039 -0.126252 8 │ 8424 -2.08417 9 │ 8890 0.148979 10 │ 9462 0.51787 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.0203729Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 25.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse 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 3.9s **** 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 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 = -1458.1121013994145, backtracks = 0, tol = 0.27185141744494906 Iteration 2: loglikelihood = -1378.0313253435938, backtracks = 0, tol = 0.06185531023372436 Iteration 3: loglikelihood = -1347.6038698517843, backtracks = 0, tol = 0.076120192160638 Iteration 4: loglikelihood = -1327.5986860556573, backtracks = 0, tol = 0.07897617335995576 Iteration 5: loglikelihood = -1314.2930157267772, backtracks = 0, tol = 0.03382523368044559 Iteration 6: loglikelihood = -1306.645063059188, backtracks = 1, tol = 0.0489486772417985 Iteration 7: loglikelihood = -1304.0387288537609, backtracks = 1, tol = 0.04758913475669497 Iteration 8: loglikelihood = -1303.44957825229, backtracks = 1, tol = 0.04827726513165995 Iteration 9: loglikelihood = -1302.426017131385, backtracks = 0, tol = 0.047712536004868196 Iteration 10: loglikelihood = -1302.0265115024747, backtracks = 1, tol = 0.0046765414298511635 Iteration 11: loglikelihood = -1301.8182658111184, backtracks = 2, tol = 0.003794314272678978 Iteration 12: loglikelihood = -1301.6391815778009, backtracks = 2, tol = 0.004736587329365532 Iteration 13: loglikelihood = -1301.5705242813956, backtracks = 3, tol = 0.0022608597032164656 Iteration 14: loglikelihood = -1301.5164990638068, backtracks = 3, tol = 0.0020474680888949363 Iteration 15: loglikelihood = -1301.4744278532778, backtracks = 3, tol = 0.0018264635526384272 Iteration 16: loglikelihood = -1301.4418412823702, backtracks = 3, tol = 0.001618859306664613 Iteration 17: loglikelihood = -1301.41667772478, backtracks = 3, tol = 0.0014297367834380044 Iteration 18: loglikelihood = -1301.3972818557559, backtracks = 3, tol = 0.0012599987250817963 Iteration 19: loglikelihood = -1301.3823496560626, backtracks = 3, tol = 0.0011088642949375546 Iteration 20: loglikelihood = -1301.3708637692325, backtracks = 3, tol = 0.0009749038700038577 Iteration 21: loglikelihood = -1301.3620346354362, backtracks = 3, tol = 0.0008564980764471925 Iteration 22: loglikelihood = -1301.3552513619045, backtracks = 3, tol = 0.000752036889684584 Iteration 23: loglikelihood = -1301.3500422202258, backtracks = 3, tol = 0.0006600025931772814 Iteration 24: loglikelihood = -1301.3460434448964, backtracks = 3, tol = 0.0005790008054848458 Iteration 25: loglikelihood = -1301.3429748158808, backtracks = 3, tol = 0.0005077681271663372 Iteration 26: loglikelihood = -1301.3406206504535, backtracks = 3, tol = 0.00044516925047483313 Iteration 27: loglikelihood = -1301.3388150543392, backtracks = 3, tol = 0.0003901894275736732 Iteration 28: loglikelihood = -1301.337430503426, backtracks = 3, tol = 0.00034192507399285143 Iteration 29: loglikelihood = -1301.3363690186172, backtracks = 3, tol = 0.0002995738507990662 Iteration 30: loglikelihood = -1301.3355553538324, backtracks = 3, tol = 0.0002624248895958615 Iteration 31: loglikelihood = -1301.3349317436673, backtracks = 3, tol = 0.00022984948983422644 Iteration 32: loglikelihood = -1301.3344538572192, backtracks = 3, tol = 0.00020129244571122912 Iteration 33: loglikelihood = -1301.3340876835919, backtracks = 3, tol = 0.0001762640673068167 Iteration 34: loglikelihood = -1301.3338071361468, backtracks = 3, tol = 0.00015433290888483865 Iteration 35: loglikelihood = -1301.333592210706, backtracks = 3, tol = 0.0001351191877514086 Iteration 36: loglikelihood = -1301.3334275703578, backtracks = 3, tol = 0.000118288860251835 Iteration 37: loglikelihood = -1301.3333014585414, backtracks = 3, tol = 0.0001035483123331517 Iteration 38: loglikelihood = -1301.3332048645973, backtracks = 3, tol = 9.063961772658578e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1524.3585382199628, backtracks = 0, tol = 0.2750287111484145 Iteration 2: loglikelihood = -1480.1618490980597, backtracks = 0, tol = 0.16809891029436155 Iteration 3: loglikelihood = -1474.8386287398034, backtracks = 0, tol = 0.10926671881446472 Iteration 4: loglikelihood = -1462.663302627735, backtracks = 0, tol = 0.09793882029994962 Iteration 5: loglikelihood = -1461.5136089391926, backtracks = 0, tol = 0.06669032179967356 Iteration 6: loglikelihood = -1461.3915911735355, backtracks = 1, tol = 0.004196175981867008 Iteration 7: loglikelihood = -1461.347502005992, backtracks = 1, tol = 0.0032781678570327523 Iteration 8: loglikelihood = -1461.3382644379385, backtracks = 2, tol = 0.0013341404138227254 Iteration 9: loglikelihood = -1461.3327285187627, backtracks = 2, tol = 0.0010987144496663152 Iteration 10: loglikelihood = -1461.3294640568834, backtracks = 2, tol = 0.0008780751822526865 Iteration 11: loglikelihood = -1461.3275635805944, backtracks = 2, tol = 0.0006867090811733746 Iteration 12: loglikelihood = -1461.32646703395, backtracks = 2, tol = 0.0005294785270219723 Iteration 13: loglikelihood = -1461.3258380187922, backtracks = 2, tol = 0.0004046615814114909 Iteration 14: loglikelihood = -1461.3254785280653, backtracks = 2, tol = 0.0003076090051408723 Iteration 15: loglikelihood = -1461.3252735577041, backtracks = 2, tol = 0.00023306496214522146 Iteration 16: loglikelihood = -1461.3251568680062, backtracks = 2, tol = 0.00017622505325925545 Iteration 17: loglikelihood = -1461.3250905034108, backtracks = 2, tol = 0.00013307502938022346 Iteration 18: loglikelihood = -1461.325052785728, backtracks = 2, tol = 0.00010040673363960864 Iteration 19: loglikelihood = -1461.3250313592828, backtracks = 2, tol = 7.571657842875527e-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 = -1731.4006191840692, backtracks = 0, tol = 0.8345998323100648 Iteration 2: loglikelihood = -1445.4634543266898, backtracks = 0, tol = 0.1217948345473112 Iteration 3: loglikelihood = -1408.201217395213, backtracks = 0, tol = 0.039975426572408754 Iteration 4: loglikelihood = -1401.9065430286387, backtracks = 0, tol = 0.030290881741597712 Iteration 5: loglikelihood = -1401.4966828727481, backtracks = 1, tol = 0.0019329563989861536 Iteration 6: loglikelihood = -1401.3896103859106, backtracks = 1, tol = 0.0010056156523021481 Iteration 7: loglikelihood = -1401.3616925195565, backtracks = 1, tol = 0.0005158069900518253 Iteration 8: loglikelihood = -1401.3544526831138, backtracks = 1, tol = 0.0002604336402483885 Iteration 9: loglikelihood = -1401.3525893929339, backtracks = 1, tol = 0.00012969295155928194 Iteration 10: loglikelihood = -1401.3521135223245, backtracks = 1, tol = 6.399199331085546e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1560.5289672234264, backtracks = 0, tol = 0.32431050055015403 Iteration 2: loglikelihood = -1430.5417704843348, backtracks = 0, tol = 0.08216529645493591 Iteration 3: loglikelihood = -1405.60835448479, backtracks = 0, tol = 0.04026299809053701 Iteration 4: loglikelihood = -1402.2421022988203, backtracks = 0, tol = 0.03378391710793642 Iteration 5: loglikelihood = -1401.3646986564527, backtracks = 0, tol = 0.005666653000503164 Iteration 6: loglikelihood = -1401.3521909125486, backtracks = 0, tol = 0.0006586046034406545 Iteration 7: loglikelihood = -1401.351957882931, backtracks = 0, tol = 0.00012050423698236037 Iteration 8: loglikelihood = -1401.3519529850719, backtracks = 0, tol = 1.5647918073035113e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 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 = -1501.2960022702723, backtracks = 0, tol = 0.17600573526791752 Iteration 2: loglikelihood = -1477.7401714847967, backtracks = 0, tol = 0.10191397337222413 Iteration 3: loglikelihood = -1432.9583701685021, backtracks = 0, tol = 0.09313889002791985 Iteration 4: loglikelihood = -1424.0711178070337, backtracks = 0, tol = 0.08745247732460958 Iteration 5: loglikelihood = -1396.4481584194014, backtracks = 0, tol = 0.08384251746437639 Iteration 6: loglikelihood = -1381.259384437195, backtracks = 0, tol = 0.07898749465759851 Iteration 7: loglikelihood = -1370.0568958549702, backtracks = 0, tol = 0.05607001978228822 Iteration 8: loglikelihood = -1364.4065946231071, backtracks = 0, tol = 0.031112721256576964 Iteration 9: loglikelihood = -1361.5048402452771, backtracks = 0, tol = 0.029849313455127258 Iteration 10: loglikelihood = -1359.7458240713465, backtracks = 0, tol = 0.0161826412147127 Iteration 11: loglikelihood = -1350.4939906645554, backtracks = 0, tol = 0.07749027225901274 Iteration 12: loglikelihood = -1345.3119154972712, backtracks = 0, tol = 0.03696424312834929 Iteration 13: loglikelihood = -1344.2594810960013, backtracks = 0, tol = 0.016562962452626718 Iteration 14: loglikelihood = -1343.812829054855, backtracks = 0, tol = 0.012653544590085546 Iteration 15: loglikelihood = -1343.6261162997184, backtracks = 0, tol = 0.007533567329046523 Iteration 16: loglikelihood = -1343.5607385347712, backtracks = 1, tol = 0.0024444891085981754 Iteration 17: loglikelihood = -1343.5219101764683, backtracks = 2, tol = 0.0023145973658356164 Iteration 18: loglikelihood = -1343.4979722580865, backtracks = 2, tol = 0.0016493037991125478 Iteration 19: loglikelihood = -1343.4841073391888, backtracks = 2, tol = 0.0013503309920186298 Iteration 20: loglikelihood = -1343.4762141397234, backtracks = 2, tol = 0.0009890909466415882 Iteration 21: loglikelihood = -1343.471727640869, backtracks = 2, tol = 0.000761748850482502 Iteration 22: loglikelihood = -1343.4691853824181, backtracks = 2, tol = 0.0005679355712820416 Iteration 23: loglikelihood = -1343.467744938095, backtracks = 2, tol = 0.00043057470703487474 Iteration 24: loglikelihood = -1343.4669295749352, backtracks = 2, tol = 0.00032293696335548475 Iteration 25: loglikelihood = -1343.4664680785736, backtracks = 2, tol = 0.00024357343953696747 Iteration 26: loglikelihood = -1343.4662069755627, backtracks = 2, tol = 0.00018302698085817672 Iteration 27: loglikelihood = -1343.4660592636883, backtracks = 2, tol = 0.0001377914320444375 Iteration 28: loglikelihood = -1343.4659757154384, backtracks = 2, tol = 0.00010359716628324158 Iteration 29: loglikelihood = -1343.4659284625498, backtracks = 2, tol = 7.79376692727348e-5 1.509297 seconds (7.31 M allocations: 125.301 MiB, 2.65% gc time, 41.10% 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 = -1550.5396019944042, backtracks = 0, tol = 0.17600573526791752 Iteration 2: loglikelihood = -1520.3623179865353, backtracks = 0, tol = 0.13308967052126155 Iteration 3: loglikelihood = -1502.6200078663055, backtracks = 0, tol = 0.10016552461272901 Iteration 4: loglikelihood = -1481.506814312312, backtracks = 0, tol = 0.09179959450883365 Iteration 5: loglikelihood = -1464.711134273412, backtracks = 0, tol = 0.07408083404396701 Iteration 6: loglikelihood = -1453.8347047889936, backtracks = 0, tol = 0.0700925179816777 Iteration 7: loglikelihood = -1439.2346290623611, backtracks = 0, tol = 0.07126206236083875 Iteration 8: loglikelihood = -1426.3925850272449, backtracks = 0, tol = 0.06695820683050017 Iteration 9: loglikelihood = -1416.500865715088, backtracks = 0, tol = 0.058958047440066365 Iteration 10: loglikelihood = -1404.874872375981, backtracks = 0, tol = 0.08575164330880779 Iteration 11: loglikelihood = -1398.3046878966968, backtracks = 0, tol = 0.05921308904613448 Iteration 12: loglikelihood = -1393.5510367385775, backtracks = 0, tol = 0.0182670818898902 Iteration 13: loglikelihood = -1388.4324175695842, backtracks = 0, tol = 0.0648000858959958 Iteration 14: loglikelihood = -1384.6963698019754, backtracks = 0, tol = 0.02955046188943274 Iteration 15: loglikelihood = -1381.7479571441456, backtracks = 0, tol = 0.006759140366706011 Iteration 16: loglikelihood = -1379.3272035158757, backtracks = 0, tol = 0.002455574539499001 Iteration 17: loglikelihood = -1377.0800790510966, backtracks = 0, tol = 0.0020338559273422947 Iteration 18: loglikelihood = -1375.1295622512814, backtracks = 0, tol = 0.0008223084820347681 Iteration 19: loglikelihood = -1373.352233672734, backtracks = 0, tol = 0.0007418760970868998 Iteration 20: loglikelihood = -1371.7768985469372, backtracks = 0, tol = 0.00038428160439059214 Iteration 21: loglikelihood = -1368.8651069021537, backtracks = 1, tol = 0.00016855635518110853 Iteration 22: loglikelihood = -1366.5251261707222, backtracks = 1, tol = 0.00032106833531040177 Iteration 23: loglikelihood = -1364.580654224899, backtracks = 1, tol = 0.00037401986506525875 Iteration 24: loglikelihood = -1362.9501337173706, backtracks = 1, tol = 0.0003778893698273162 Iteration 25: loglikelihood = -1361.568752348772, backtracks = 1, tol = 0.00035829590305810053 Iteration 26: loglikelihood = -1360.3870588116229, backtracks = 1, tol = 0.0003299387715352032 Iteration 27: loglikelihood = -1359.3670530070226, backtracks = 1, tol = 0.00030011187270486994 Iteration 28: loglikelihood = -1358.4791923355613, backtracks = 1, tol = 0.000272061346491481 Iteration 29: loglikelihood = -1357.7002723677138, backtracks = 1, tol = 0.0002469862821156398 Iteration 30: loglikelihood = -1357.0119190737328, backtracks = 1, tol = 0.0002251116072834985 Iteration 31: loglikelihood = -1356.3994902789218, backtracks = 1, tol = 0.0002062347869918197 Iteration 32: loglikelihood = -1355.8512529866375, backtracks = 1, tol = 0.00018999379533846111 Iteration 33: loglikelihood = -1355.3577526544982, backtracks = 1, tol = 0.0001759933695387784 Iteration 34: loglikelihood = -1354.9113221470018, backtracks = 1, tol = 0.0001638612778903724 Iteration 35: loglikelihood = -1354.4617094331902, backtracks = 1, tol = 0.00015327067065425696 Iteration 36: loglikelihood = -1354.0481668870132, backtracks = 1, tol = 0.00015107764065634574 Iteration 37: loglikelihood = -1353.6703137880884, backtracks = 1, tol = 0.0001478748364788496 Iteration 38: loglikelihood = -1353.2800122491733, backtracks = 1, tol = 0.00014285268586464693 Iteration 39: loglikelihood = -1352.9206661847093, backtracks = 1, tol = 0.00014505474679851998 Iteration 40: loglikelihood = -1352.5924646357, backtracks = 1, tol = 0.00014437363998595482 Iteration 41: loglikelihood = -1352.2928576171669, backtracks = 1, tol = 0.0001406505139218632 Iteration 42: loglikelihood = -1352.0189151793854, backtracks = 1, tol = 0.00013530076847274722 Iteration 43: loglikelihood = -1351.7677954736648, backtracks = 1, tol = 0.00012931425650593355 Iteration 44: loglikelihood = -1351.5369217500609, backtracks = 1, tol = 0.0001232932869993317 Iteration 45: loglikelihood = -1351.3240311547215, backtracks = 1, tol = 0.00011755779390227362 Iteration 46: loglikelihood = -1351.1271698762039, backtracks = 1, tol = 0.00011224897314976508 Iteration 47: loglikelihood = -1350.944664844181, backtracks = 1, tol = 0.00010740404040917085 Iteration 48: loglikelihood = -1350.775086384972, backtracks = 1, tol = 0.00010300476608030652 Iteration 49: loglikelihood = -1350.617209514425, backtracks = 1, tol = 9.900725417857678e-5 0.546792 seconds (2.31 M allocations: 42.614 MiB, 2.42% 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 = -3539.5415, backtracks = 0, tol = 0.08752813339479998 Iteration 2: loglikelihood = -3491.277, backtracks = 0, tol = 0.044973467307619176 Iteration 3: loglikelihood = -3454.7825, backtracks = 1, tol = 0.0609455987917455 Iteration 4: loglikelihood = -3445.7046, backtracks = 1, tol = 0.018196730097048266 Iteration 5: loglikelihood = -3442.739, backtracks = 1, tol = 0.010269354539824822 Iteration 6: loglikelihood = -3441.869, backtracks = 1, tol = 0.004990259810369792 Iteration 7: loglikelihood = -3430.948, backtracks = 1, tol = 0.06458288717798875 Iteration 8: loglikelihood = -3428.2156, backtracks = 0, tol = 0.011846320338386136 Iteration 9: loglikelihood = -3427.9802, backtracks = 0, tol = 0.004070391413076316 Iteration 10: loglikelihood = -3427.959, backtracks = 1, tol = 0.0005563273030120813 Iteration 11: loglikelihood = -3427.9512, backtracks = 1, tol = 0.0004548899825928616 Iteration 12: loglikelihood = -3427.9507, backtracks = 1, tol = 0.0003068260142803495 Iteration 13: loglikelihood = -3427.9514, backtracks = 3, tol = 3.9566138078134755e-5 27.608845 seconds (15.74 M allocations: 690.842 MiB, 4.30% gc time, 97.71% 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 = -3447.117, backtracks = 0, tol = 0.08752813339479998 Iteration 2: loglikelihood = -3341.563, backtracks = 0, tol = 0.04611800048226063 Iteration 3: loglikelihood = -3138.1572, backtracks = 1, tol = 0.060396755677648996 Iteration 4: loglikelihood = -3120.652, backtracks = 0, tol = 0.09384029673582614 Iteration 5: loglikelihood = -2970.5005, backtracks = 0, tol = 0.0947872192862735 Iteration 6: loglikelihood = -2871.16, backtracks = 0, tol = 0.07969890055064263 Iteration 7: loglikelihood = -2779.1753, backtracks = 0, tol = 0.08790651181784322 Iteration 8: loglikelihood = -2688.3833, backtracks = 0, tol = 0.007889470856987827 Iteration 9: loglikelihood = -2612.6924, backtracks = 0, tol = 0.09242717781431029 Iteration 10: loglikelihood = -2513.3328, backtracks = 0, tol = 0.09222732401153723 Iteration 11: loglikelihood = -2436.3298, backtracks = 0, tol = 0.08461384828243594 Iteration 12: loglikelihood = -2367.035, backtracks = 0, tol = 0.08754267876498194 Iteration 13: loglikelihood = -2313.0422, backtracks = 0, tol = 0.08702785849872444 Iteration 14: loglikelihood = -2270.6396, backtracks = 0, tol = 0.08919498678092296 Iteration 15: loglikelihood = -2240.777, backtracks = 0, tol = 0.08873246598415717 Iteration 16: loglikelihood = -2220.5266, backtracks = 0, tol = 0.09039721421530494 Iteration 17: loglikelihood = -2207.3174, backtracks = 0, tol = 0.0899907211032366 Iteration 18: loglikelihood = -2198.013, backtracks = 0, tol = 0.0911425255129368 Iteration 19: loglikelihood = -2193.7454, backtracks = 0, tol = 0.08275674793413919 Iteration 20: loglikelihood = -2189.283, backtracks = 1, tol = 0.00731364267122218 Iteration 21: loglikelihood = -2188.0625, backtracks = 1, tol = 0.002928180307107715 Iteration 22: loglikelihood = -2187.7456, backtracks = 1, tol = 0.0012942328215207282 Iteration 23: loglikelihood = -2187.6707, backtracks = 1, tol = 0.0007354494440726024 Iteration 24: loglikelihood = -2187.6562, backtracks = 1, tol = 0.00040135117820633515 Iteration 25: loglikelihood = -2187.65, backtracks = 1, tol = 0.0002129971333882718 Iteration 26: loglikelihood = -2187.6497, backtracks = 3, tol = 2.8394688085622784e-5 0.192903 seconds (1.43 M allocations: 23.746 MiB) 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 4.842840 seconds (1.15 M allocations: 137.253 MiB, 0.87% gc time, 91.28% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.2s 9.516737 seconds (4.00 M allocations: 82.503 MiB, 0.48% gc time, 0.72% compilation time) 5.414045 seconds (3.98 M allocations: 91.675 MiB, 0.43% gc time) 10.884623 seconds (20.41 M allocations: 439.534 MiB, 0.99% gc time, 18.04% compilation time: 79% of which was recompilation) 8.373668 seconds (20.18 M allocations: 434.189 MiB, 0.95% gc time) 46.475912 seconds (3.82 M allocations: 4.243 GiB, 10.01% gc time, 28.09% compilation time) 53.321085 seconds (71.97 k allocations: 183.461 MiB, 0.19% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m34.8s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 15.204 ms (78 allocations: 4.56 KiB) 5.167 μs (0 allocations: 0 bytes) 158.138 μs (4 allocations: 288 bytes) 7.055 μs (0 allocations: 0 bytes) 48.679 μs (2 allocations: 64 bytes) 38.990 μs (0 allocations: 0 bytes) 34.710 μs (0 allocations: 0 bytes) 28.159 μs (0 allocations: 0 bytes) 93.119 μs (0 allocations: 0 bytes) 39.586 ms (78 allocations: 4.56 KiB) 27.620 μs (0 allocations: 0 bytes) 195.338 μs (4 allocations: 288 bytes) 35.079 μs (0 allocations: 0 bytes) 284.337 μs (2 allocations: 64 bytes) 97.159 μs (0 allocations: 0 bytes) 170.709 μs (0 allocations: 0 bytes) 153.398 μs (0 allocations: 0 bytes) 286.027 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m37.5s **** 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 **** **** 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 0.447153 seconds (49.53 k allocations: 5.504 MiB, 64.63% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 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 **** 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 1.970541 seconds (281.11 k allocations: 168.054 MiB, 57.67% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:53 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: 0:00:18 Cross validating... 37%|███████████▋ | ETA: 0:00:16 Cross validating... 40%|████████████▊ | ETA: 0:00:14 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:11 Cross validating... 49%|███████████████▊ | ETA: 0:00:10 Cross validating... 52%|████████████████▊ | ETA: 0:00:09 Cross validating... 56%|█████████████████▊ | ETA: 0:00:08 Cross validating... 59%|██████████████████▊ | ETA: 0:00:07 Cross validating... 62%|███████████████████▊ | ETA: 0:00:06 Cross validating... 65%|████████████████████▉ | ETA: 0:00:06 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:05 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:04 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:04 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 3370.3668407229334 1 2062.8931489690285 2 1430.5877640354051 3 911.8922212178536 4 543.433165653069 5 471.5479787384961 6 384.07673319081454 7 363.745494136386 8 358.5833627236789 9 353.0284597337021 10 355.89041226825736 11 355.3999798808278 12 354.88520463627736 13 362.30043093007464 14 357.0704009222363 15 362.8504854404617 16 365.60393624246177 17 376.38763319387976 18 380.70830399198763 19 366.3487693469795 20 416.5212242861405 Best k = 9 12.385965 seconds (11.50 M allocations: 300.997 MiB, 1.09% gc time, 63.02% 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... 5%|█▌ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | 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... 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: 0:00:04 Crossvalidation Results: k MSE 0 3370.3668407229334 1 2070.467713915989 2 1449.4129744050422 3 926.584282208292 4 552.1189904096113 5 477.6621467796544 6 388.475013085985 7 368.9538441142189 8 366.5514749386501 9 360.70614505852313 10 368.8131127281387 11 369.35105704581605 12 369.533413003699 13 387.8091047453146 14 374.11620372130466 15 387.90297103823366 16 399.3668453580996 17 400.9542518288646 18 407.0873719269653 19 406.61543394880005 20 429.4777222199815 Best k = 9 4.742618 seconds (10.67 M allocations: 225.240 MiB, 0.97% gc time, 1.01% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.0s **** 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: 0:07:26 Cross validating... 10%|███ | ETA: 0:02:20 Cross validating... 14%|████▋ | ETA: 0:01:30 Cross validating... 19%|██████▏ | ETA: 0:01:04 Cross 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100%|████████████████████████████████| Time: 0:00:17 Crossvalidation Results: k MSE 0 1658.7243328857421 1 1337.7813942871094 2 1092.1507764282226 3 907.9681011962891 4 684.867727722168 5 556.1560525512696 6 459.7063555908203 7 406.74341799926754 8 369.94415847778316 9 355.7485489196777 10 360.82208865356444 11 361.71736651611326 12 365.13940374755856 13 366.6077610778808 14 377.39660797119143 15 370.3452111816406 16 394.2761665344238 17 377.4390867004395 18 379.1566119995117 19 381.4048306274414 20 397.47278567504884 Best k = 9 18.504174 seconds (12.85 M allocations: 317.979 MiB, 0.72% gc time, 85.44% 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%|█████▋ | 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100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1658.7243328857421 1 1338.9967932128907 2 1096.6281721191406 3 908.8624942626952 4 692.3230902709961 5 561.1422892456054 6 464.3708617248535 7 411.3419481506348 8 373.7492457885742 9 361.5573282470703 10 373.1550120239258 11 377.11947970581053 12 385.82135623168944 13 392.0016399536132 14 396.3252517700195 15 401.44645367431644 16 411.42901461791996 17 422.34505014038086 18 424.9532855834961 19 435.25303952026366 20 432.5908332519531 Best k = 9 2.800886 seconds (10.94 M allocations: 201.102 MiB, 1.82% gc time, 1.59% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 22.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:01 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: 0:00:14 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 51%|████████████████▎ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:04 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 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: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 464.0388740721193 1 387.70867675571617 2 352.9314150410686 3 305.8243342249258 4 274.48860309352654 5 265.0099197594236 6 268.99930379260815 7 272.2082250610722 8 272.77029444863444 9 275.89791436760385 10 273.56720847335816 11 281.3458616609935 12 287.13215650563455 13 294.7510962698206 14 287.9762332148304 15 296.9303998390118 16 283.3940274879656 17 321.7303655587746 18 323.5943772658282 19 286.51575530611905 20 306.52177179407596 Best k = 5 8.617475 seconds (17.42 M allocations: 409.175 MiB, 1.58% gc time, 31.02% 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: 0:00:04 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... 19%|██████▏ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross 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78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 464.0388740721193 1 388.0492371345624 2 356.0308402785268 3 306.35281705062476 4 276.66179526288994 5 267.4592157804336 6 275.7266062249614 7 284.1742875475848 8 285.80273350815776 9 298.8352406969997 10 294.5788669275506 11 313.1168517226745 12 314.1687754205666 13 319.9875070506065 14 318.98726309455384 15 298.68176814463914 16 327.4468472195159 17 319.4809394911337 18 340.00131783378185 19 338.76396432266347 20 359.1921290844997 Best k = 5 5.734272 seconds (17.32 M allocations: 357.393 MiB, 1.10% gc time, 1.02% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:51 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: 0:00:12 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... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 35%|███████████▏ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 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... 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... 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 0 463.10450729892455 1 425.62283377494293 2 390.02077980169463 3 378.39147709272993 4 346.90748279424787 5 336.5721151383543 6 322.92595025223284 7 316.4994222971469 8 320.35288523201575 9 322.90783388277976 10 332.30993551992367 11 331.72343919870184 12 321.58844974997 13 343.3873710357053 14 345.8965985059087 15 340.970667947873 16 344.4702597857712 17 339.4044612718815 18 335.09924956701076 19 343.0726119192449 20 378.0430280671884 Best k = 7 7.882673 seconds (16.67 M allocations: 394.519 MiB, 12.66% gc time, 34.99% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 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: 0:00:03 Cross validating... 30%|█████████▋ | ETA: 0:00:03 Cross validating... 33%|██████████▋ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | 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: 0:00:01 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 0 463.10450729892455 1 425.6577095404573 2 391.88271290659054 3 380.9383743067126 4 354.918509118241 5 340.29815475562145 6 327.39564413114744 7 323.6441094114532 8 334.00434944760843 9 341.6284416520571 10 350.1233946334687 11 347.52928372676695 12 352.04383395827557 13 363.2790115976785 14 358.4575682175802 15 386.16746290802996 16 394.2911215559842 17 399.25973194426405 18 402.46025542263067 19 392.19695023062445 20 408.70827145171125 Best k = 7 4.241424 seconds (17.23 M allocations: 353.582 MiB, 1.37% gc time, 1.01% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:12 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 Cross validating... 35%|███████████▏ | ETA: 0:00:07 Cross validating... 38%|████████████▎ | ETA: 0:00:06 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: 0:00:05 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... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 647.0554221919004 1 541.1503132294353 2 473.8422756834414 3 395.5540368916136 4 343.68107356585074 5 342.69135267276 6 342.6750745790331 7 350.66675307977175 8 352.2279914786791 9 356.17790779480055 10 358.09373795168534 11 359.1646232814236 12 360.1219340170569 13 358.1083307185747 14 365.4110053933224 15 387.929322499387 16 354.5591078310605 17 366.29988980270554 18 358.05058600152796 19 365.36418312314146 20 378.9533150819851 Best k = 6 8.325126 seconds (16.44 M allocations: 395.834 MiB, 1.01% gc time, 31.95% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 8%|██▌ | ETA: 0:00:05 Cross validating... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 22%|███████▏ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:05 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:04 Cross validating... 41%|█████████████▎ | ETA: 0:00:04 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | 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... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 647.0554221919004 1 526.7036923625221 2 467.8754853804053 3 396.3793945215402 4 346.4374608609468 5 352.4460901621442 6 352.4804925178905 7 358.12685778896133 8 372.3667311536144 9 369.44911253533314 10 391.1072714195657 11 373.0336142110761 12 382.9473407801199 13 388.28380063547525 14 397.5889358150567 15 390.14040688154137 16 393.3075110788222 17 394.4765421306892 18 403.4522879661163 19 419.6961937821313 20 417.83133791871603 Best k = 4 6.013944 seconds (15.88 M allocations: 330.957 MiB, 0.99% gc time, 0.96% 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: 0:01:30 Cross validating... 5%|█▌ | ETA: 0:01:20 Cross validating... 6%|██ | ETA: 0:01:14 Cross validating... 10%|███ | ETA: 0:00:49 Cross validating... 11%|███▌ | ETA: 0:00:50 Cross validating... 13%|████▏ | ETA: 0:00:50 Cross validating... 14%|████▋ | ETA: 0:00:50 Cross validating... 16%|█████▏ | ETA: 0:00:50 Cross validating... 17%|█████▋ | ETA: 0:00:45 Cross validating... 19%|██████▏ | ETA: 0:00:42 Cross validating... 21%|██████▋ | ETA: 0:00:43 Cross validating... 22%|███████▏ | ETA: 0:00:40 Cross validating... 24%|███████▋ | ETA: 0:00:40 Cross validating... 25%|████████▏ | ETA: 0:00:40 Cross validating... 27%|████████▋ | ETA: 0:00:40 Cross validating... 29%|█████████▏ | ETA: 0:00:40 Cross validating... 30%|█████████▋ | ETA: 0:00:40 Cross validating... 32%|██████████▏ | ETA: 0:00:38 Cross validating... 33%|██████████▋ | ETA: 0:00:37 Cross validating... 37%|███████████▋ | ETA: 0:00:34 Cross validating... 38%|████████████▎ | ETA: 0:00:32 Cross validating... 41%|█████████████▎ | ETA: 0:00:29 Cross validating... 44%|██████████████▎ | ETA: 0:00:26 Cross validating... 46%|██████████████▊ | ETA: 0:00:26 Cross validating... 48%|███████████████▎ | ETA: 0:00:26 Cross validating... 49%|███████████████▊ | ETA: 0:00:25 Cross validating... 52%|████████████████▊ | ETA: 0:00:23 Cross validating... 54%|█████████████████▎ | ETA: 0:00:21 Cross validating... 56%|█████████████████▊ | ETA: 0:00:21 Cross validating... 57%|██████████████████▎ | ETA: 0:00:20 Cross validating... 59%|██████████████████▊ | ETA: 0:00:20 Cross validating... 60%|███████████████████▎ | ETA: 0:00:19 Cross validating... 62%|███████████████████▊ | ETA: 0:00:19 Cross validating... 63%|████████████████████▍ | ETA: 0:00:18 Cross validating... 65%|████████████████████▉ | ETA: 0:00:17 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:17 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:15 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:13 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:12 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:11 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:10 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:09 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:08 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:08 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:07 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:06 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:04 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:46 Crossvalidation Results: k MSE 0 346.84496527285273 1 291.2563039582059 2 267.0828586607752 3 236.41715072489217 4 215.32557305951104 5 214.61370444200443 6 216.29282739520983 7 216.70790203962952 8 217.2378557924572 9 220.59154805135782 10 219.9741712831526 11 220.72858012082517 12 222.50813846702613 13 223.88199894869837 14 224.4779775335445 15 224.93505874682302 16 226.40735485910196 17 227.5402936075271 18 227.95547953812644 19 227.06253709627805 20 227.92764182786794 Best k = 5 47.405676 seconds (149.91 M allocations: 3.786 GiB, 1.25% gc time, 4.79% 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... 5%|█▌ | ETA: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:08 Cross validating... 8%|██▌ | ETA: 0:00:08 Cross validating... 10%|███ | ETA: 0:00:08 Cross validating... 11%|███▌ | ETA: 0:00:08 Cross validating... 13%|████▏ | ETA: 0:00:08 Cross validating... 14%|████▋ | ETA: 0:00:08 Cross validating... 16%|█████▏ | ETA: 0:00:08 Cross validating... 17%|█████▋ | ETA: 0:00:09 Cross validating... 19%|██████▏ | ETA: 0:00:09 Cross validating... 21%|██████▋ | 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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: 0:00:13 Crossvalidation Results: k MSE 0 346.84496527285273 1 290.102330925155 2 266.7398810946315 3 237.0993266537376 4 216.09331133798793 5 216.69581598332087 6 220.7776883498522 7 223.81784251865395 8 225.36204454851577 9 234.41625616584952 10 237.25537802430205 11 235.28531883409823 12 239.44937157945662 13 245.2103536425665 14 243.3370089240242 15 251.0918157723865 16 256.54446682077497 17 261.02591052984917 18 254.06441886619848 19 261.6226003424815 20 273.43919780183467 Best k = 4 13.536783 seconds (42.23 M allocations: 887.561 MiB, 1.55% gc time, 0.45% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 1m01.4s **** 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: 0:01:10 Cross validating... 6%|██ | ETA: 0:00:35 Cross validating... 10%|███ | ETA: 0:00:24 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:15 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 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Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 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 6.428428 seconds (17.01 M allocations: 338.030 MiB, 1.37% gc time, 45.37% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 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... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross 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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 3.899406 seconds (16.17 M allocations: 286.710 MiB, 1.39% gc time, 1.48% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.8s **** 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: 0:01:18 Cross validating... 4%|█▎ | ETA: 0:00:43 Cross validating... 6%|█▉ | ETA: 0:00:31 Cross validating... 7%|██▎ 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ETA: 0:00:03 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:03 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:03 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:02 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:02 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:01 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: 0:00:16 Crossvalidation Results: k MSE 1 2616.233689791 2 1679.3603794998432 3 1368.1019676210428 4 1193.2226333655358 5 1100.844067180844 6 999.6716872481103 7 889.5279003388268 8 850.2946884280889 9 843.4539734618376 10 832.8318047872743 11 832.0285117761587 12 833.1567100975313 13 845.5216354473864 14 851.1062066463414 15 849.9022648773337 16 852.1231272168154 17 862.4879339911437 18 858.9646996002288 19 873.4908506268002 20 876.0911500104778 Best k = 11 17.089070 seconds (318.34 k allocations: 197.996 MiB, 0.37% gc time, 9.34% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 22.0s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m54.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:17 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: 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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: 0:00:05 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: 0:00:02 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: 0:00:13 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:19 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 23%|███████▍ | ETA: 0:00:17 Cross validating... 24%|███████▋ | ETA: 0:00:17 Cross validating... 25%|████████ | ETA: 0:00:16 Cross validating... 26%|████████▍ | ETA: 0:00:16 Cross validating... 27%|████████▋ | ETA: 0:00:16 Cross validating... 28%|█████████ | ETA: 0:00:16 Cross 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validating... 48%|███████████████▍ | ETA: 0:00:12 Cross validating... 49%|███████████████▋ | ETA: 0:00:12 Cross validating... 50%|████████████████ | ETA: 0:00:12 Cross validating... 51%|████████████████▍ | ETA: 0:00:11 Cross validating... 52%|████████████████▋ | ETA: 0:00:11 Cross validating... 53%|█████████████████ | ETA: 0:00:11 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: 0:00:10 Cross validating... 58%|██████████████████▌ | ETA: 0:00:10 Cross validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:10 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 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: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:16 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:19 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:19 Cross validating... 19%|██████▏ | ETA: 0:00:20 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 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validating... 59%|██████████████████▉ | ETA: 0:00:10 Cross validating... 60%|███████████████████▎ | ETA: 0:00:10 Cross validating... 61%|███████████████████▌ | ETA: 0:00:10 Cross validating... 62%|███████████████████▉ | ETA: 0:00:09 Cross validating... 63%|████████████████████▏ | ETA: 0:00:09 Cross validating... 64%|████████████████████▌ | ETA: 0:00:09 Cross validating... 65%|████████████████████▊ | ETA: 0:00:08 Cross validating... 66%|█████████████████████▏ | ETA: 0:00:08 Cross validating... 67%|█████████████████████▌ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▊ | ETA: 0:00:08 Cross validating... 69%|██████████████████████▏ | ETA: 0:00:07 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 71%|██████████████████████▊ | ETA: 0:00:07 Cross validating... 72%|███████████████████████ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:06 Cross validating... 74%|███████████████████████▋ | ETA: 0:00:06 Cross validating... 75%|████████████████████████ | ETA: 0:00:06 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:06 Cross validating... 77%|████████████████████████▋ | ETA: 0:00:06 Cross validating... 78%|█████████████████████████ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▎ | ETA: 0:00:05 Cross validating... 80%|█████████████████████████▋ | ETA: 0:00:05 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:05 Cross validating... 82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:25 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 1m31.3s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [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:324 [13] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [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:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.9s RNG of the outermost testset: Xoshiro(0x42b0d74292ecc724, 0xa6f5da74a2f18d6b, 0x662abc35bd26d030, 0x04e78abcaf4ae5eb, 0x58bcded5f88fc9c2) 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 1181.3s 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:3160 [3] test @ /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] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1301.49s: package tests unexpectedly errored