Package evaluation to test MendelIHT on Julia 1.14.0-DEV.1786 (45ee44a91e*) started at 2026-02-22T23:00:01.649 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.26s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [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 v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [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 v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.94s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4480.5 ms ✓ BGEN 6400.1 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`. 25125.6 ms ✓ MendelIHT 3 dependencies successfully precompiled in 39 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 61.06s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_w9nKAf/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [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 v2.7.1 [2913bbd2] StatsBase v0.34.10 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v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ Core ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 16.5s Test Summary: | Pass Total Time deviance | 1 1 0.5s Test Summary: | Pass Total Time update_μ! | 4 4 1.6s Test Summary: | Pass Total Time _choose! | 7 7 10.1s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.6s Test Summary: | Pass Total Time project_k! | 2 2 1.1s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.3s Test Summary: | Pass Total Time maf_weights | 6 6 2.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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 = -1630.490843756262, backtracks = 0, tol = 1.7170650019736118 Iteration 2: loglikelihood = -1455.577794437526, backtracks = 0, tol = 0.16095232390523284 Iteration 3: loglikelihood = -1447.2377909267589, backtracks = 0, tol = 0.039875378391557054 Iteration 4: loglikelihood = -1447.1822429257218, backtracks = 0, tol = 0.002239455794164173 Iteration 5: loglikelihood = -1447.1816272895608, backtracks = 0, tol = 0.00028852093248834545 Iteration 6: loglikelihood = -1447.1816185774544, backtracks = 0, tol = 2.530151545911495e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.05636119842529297 Final loglikelihood: -1447.1816185774544 SNP PVE: 0.926847627855868 Iterations: 6 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 847 1.49201 2 │ 1376 -0.642641 3 │ 2605 1.96359 4 │ 4050 -0.122534 5 │ 4571 -2.00777 6 │ 4786 0.403572 7 │ 7774 0.469294 8 │ 8263 0.891413 9 │ 9036 -1.12228 10 │ 9344 0.739317 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 0.0869188Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 25.2s **** 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 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 3.7s **** 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 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 = -2805.627296739336, backtracks = 0, tol = 0.4490705556243959 Iteration 2: loglikelihood = -1713.7774343122278, backtracks = 0, tol = 0.0702754296700149 Iteration 3: loglikelihood = -1457.325916595913, backtracks = 0, tol = 0.05512632675898345 Iteration 4: loglikelihood = -1414.849530093747, backtracks = 0, tol = 0.0479971907798887 Iteration 5: loglikelihood = -1362.5444509440965, backtracks = 0, tol = 0.06936600832336316 Iteration 6: loglikelihood = -1353.3666447067349, backtracks = 0, tol = 0.03173290046990626 Iteration 7: loglikelihood = -1347.4679233409113, backtracks = 0, tol = 0.024389462531930948 Iteration 8: loglikelihood = -1344.0498329621378, backtracks = 0, tol = 0.016670489965318062 Iteration 9: loglikelihood = -1341.6053361763209, backtracks = 0, tol = 0.06359803104998403 Iteration 10: loglikelihood = -1339.3283921011173, backtracks = 0, tol = 0.009711267942772371 Iteration 11: loglikelihood = -1338.284553691088, backtracks = 0, tol = 0.011778355149324831 Iteration 12: loglikelihood = -1337.7283979323952, backtracks = 0, tol = 0.005896456794286636 Iteration 13: loglikelihood = -1337.3253836994008, backtracks = 0, tol = 0.009119598244981207 Iteration 14: loglikelihood = -1337.0289420654544, backtracks = 0, tol = 0.003725959081949414 Iteration 15: loglikelihood = -1336.7833047126046, backtracks = 0, tol = 0.008455319048848343 Iteration 16: loglikelihood = -1336.5881159031194, backtracks = 0, tol = 0.002733530943224473 Iteration 17: loglikelihood = -1336.4599718778263, backtracks = 1, tol = 0.003950152425643687 Iteration 18: loglikelihood = -1336.3338323516164, backtracks = 0, tol = 0.005463105816216903 Iteration 19: loglikelihood = -1336.2251427159867, backtracks = 0, tol = 0.002341979173006316 Iteration 20: loglikelihood = -1336.1317504942613, backtracks = 0, tol = 0.0046102658965918655 Iteration 21: loglikelihood = -1336.0490399449704, backtracks = 0, tol = 0.0021442423290256364 Iteration 22: loglikelihood = -1335.9761862573814, backtracks = 0, tol = 0.0039772147114809815 Iteration 23: loglikelihood = -1335.9105130597359, backtracks = 0, tol = 0.00198312228177384 Iteration 24: loglikelihood = -1335.851672040661, backtracks = 0, tol = 0.003490025246695618 Iteration 25: loglikelihood = -1335.7979621990514, backtracks = 0, tol = 0.0018490006505642504 Iteration 26: loglikelihood = -1335.749229939033, backtracks = 0, tol = 0.003104385456903633 Iteration 27: loglikelihood = -1335.704323782039, backtracks = 0, tol = 0.0017353804068038505 Iteration 28: loglikelihood = -1335.6631783047667, backtracks = 0, tol = 0.0027920266155037686 Iteration 29: loglikelihood = -1335.6249771741964, backtracks = 0, tol = 0.0016377273245849204 Iteration 30: loglikelihood = -1335.5896979437357, backtracks = 0, tol = 0.0025341646614513904 Iteration 31: loglikelihood = -1335.5567409352793, backtracks = 0, tol = 0.0015527658117681143 Iteration 32: loglikelihood = -1335.5261056031138, backtracks = 0, tol = 0.002317864222298457 Iteration 33: loglikelihood = -1335.497338697919, backtracks = 0, tol = 0.0014780683975665688 Iteration 34: loglikelihood = -1335.4704509984695, backtracks = 0, tol = 0.002133946452539878 Iteration 35: loglikelihood = -1335.4450917803226, backtracks = 0, tol = 0.0014117965488447458 Iteration 36: loglikelihood = -1335.4212775486073, backtracks = 0, tol = 0.001975727838116681 Iteration 37: loglikelihood = -1335.3987314722685, backtracks = 0, tol = 0.0013525316668494712 Iteration 38: loglikelihood = -1335.3774727123673, backtracks = 0, tol = 0.001838231940611382 Iteration 39: loglikelihood = -1335.3572790063488, backtracks = 0, tol = 0.001299161295275661 Iteration 40: loglikelihood = -1335.3381704538067, backtracks = 0, tol = 0.0017176804922822769 Iteration 41: loglikelihood = -1335.3199659372654, backtracks = 0, tol = 0.0012508004913453139 Iteration 42: loglikelihood = -1335.3026855307153, backtracks = 0, tol = 0.00161115535569001 Iteration 43: loglikelihood = -1335.286179706482, backtracks = 0, tol = 0.001206736263595334 Iteration 44: loglikelihood = -1335.2704679801861, backtracks = 0, tol = 0.0015163682544210779 Iteration 45: loglikelihood = -1335.255425466285, backtracks = 0, tol = 0.001166387536858008 Iteration 46: loglikelihood = -1335.2410708409673, backtracks = 0, tol = 0.0014315003729054704 Iteration 47: loglikelihood = -1335.2272987141455, backtracks = 0, tol = 0.0011292758054016092 Iteration 48: loglikelihood = -1335.2141267898376, backtracks = 0, tol = 0.0013550883783192324 Iteration 49: loglikelihood = -1335.201465297424, backtracks = 0, tol = 0.0010950032889559072 Iteration 50: loglikelihood = -1335.1893309234183, backtracks = 0, tol = 0.0012859419710958457 Iteration 51: loglikelihood = -1335.1776465542114, backtracks = 0, tol = 0.0010632364478596295 Iteration 52: loglikelihood = -1335.166427864477, backtracks = 0, tol = 0.0012230832756037339 Iteration 53: loglikelihood = -1335.1556081030355, backtracks = 0, tol = 0.0010336933859293061 Iteration 54: loglikelihood = -1335.1452019673038, backtracks = 0, tol = 0.0011657016315428093 Iteration 55: loglikelihood = -1335.135151269746, backtracks = 0, tol = 0.0010061341133650425 Iteration 56: loglikelihood = -1335.1254697805555, backtracks = 0, tol = 0.0011131194220363127 Iteration 57: loglikelihood = -1335.1161064501316, backtracks = 0, tol = 0.0009803529405938906 Iteration 58: loglikelihood = -1335.1070741787391, backtracks = 0, tol = 0.0010647659282539848 Iteration 59: loglikelihood = -1335.0983279133166, backtracks = 0, tol = 0.0009561724784397783 Iteration 60: loglikelihood = -1335.089879743796, backtracks = 0, tol = 0.0010201571005963332 Iteration 61: loglikelihood = -1335.0816896914039, backtracks = 0, tol = 0.0009334388622564123 Iteration 62: loglikelihood = -1335.0737690946896, backtracks = 0, tol = 0.0009788797455181032 Iteration 63: loglikelihood = -1335.0660822976124, backtracks = 0, tol = 0.0009120179180372104 Iteration 64: loglikelihood = -1335.0586399439335, backtracks = 0, tol = 0.0009405790457464656 Iteration 65: loglikelihood = -1335.0514100830883, backtracks = 0, tol = 0.0008917920602700467 Iteration 66: loglikelihood = -1335.044402717395, backtracks = 0, tol = 0.000904948623746344 Iteration 67: loglikelihood = -1335.037589091061, backtracks = 0, tol = 0.0008726577632028626 Iteration 68: loglikelihood = -1335.030978614641, backtracks = 0, tol = 0.0008717225647936846 Iteration 69: loglikelihood = -1335.024545301707, backtracks = 0, tol = 0.0008545234851433628 Iteration 70: loglikelihood = -1335.0182980169698, backtracks = 0, tol = 0.0008406689638960755 Iteration 71: loglikelihood = -1335.01221318672, backtracks = 0, tol = 0.000837307953455973 Iteration 72: loglikelihood = -1335.0062991720133, backtracks = 0, tol = 0.000811584667917228 Iteration 73: loglikelihood = -1335.0005345111358, backtracks = 0, tol = 0.0008209387388402421 Iteration 74: loglikelihood = -1334.9949271001306, backtracks = 0, tol = 0.0007842909627021274 Iteration 75: loglikelihood = -1334.9894573342315, backtracks = 0, tol = 0.0008053510632039289 Iteration 76: loglikelihood = -1334.9841326798062, backtracks = 0, tol = 0.0007586300130350002 Iteration 77: loglikelihood = -1334.9789351716406, backtracks = 0, tol = 0.0007904867974065094 Iteration 78: loglikelihood = -1334.9738718786411, backtracks = 0, tol = 0.0007344619065984215 Iteration 79: loglikelihood = -1334.9689262889326, backtracks = 0, tol = 0.0007762936142711696 Iteration 80: loglikelihood = -1334.9641051033677, backtracks = 0, tol = 0.0007116621857735781 Iteration 81: loglikelihood = -1334.9593931031156, backtracks = 0, tol = 0.0007627242693184383 Iteration 82: loglikelihood = -1334.9547966478153, backtracks = 0, tol = 0.0006901197759411893 Iteration 83: loglikelihood = -1334.9503016731258, backtracks = 0, tol = 0.000749735987139786 Iteration 84: loglikelihood = -1334.9459142219498, backtracks = 0, tol = 0.000669735237963425 Iteration 85: loglikelihood = -1334.9416212641754, backtracks = 0, tol = 0.000737289935609964 Iteration 86: loglikelihood = -1334.9374285483093, backtracks = 0, tol = 0.0006504192872109205 Iteration 87: loglikelihood = -1334.9333239736736, backtracks = 0, tol = 0.0007253507734909499 Iteration 88: loglikelihood = -1334.9293130148037, backtracks = 0, tol = 0.0006320915329090225 Iteration 89: loglikelihood = -1334.9253844087627, backtracks = 0, tol = 0.000713886259661498 Iteration 90: loglikelihood = -1334.9215433747868, backtracks = 0, tol = 0.0006146794005158988 Iteration 91: loglikelihood = -1334.9177794072377, backtracks = 0, tol = 0.0007028669143094209 Iteration 92: loglikelihood = -1334.9140974871416, backtracks = 0, tol = 0.0005981172068823996 Iteration 93: loglikelihood = -1334.9104877952625, backtracks = 0, tol = 0.0006922657241387859 Iteration 94: loglikelihood = -1334.906955090085, backtracks = 0, tol = 0.0005823453635204449 Iteration 95: loglikelihood = -1334.9034901761559, backtracks = 0, tol = 0.0006820578850046813 Iteration 96: loglikelihood = -1334.9000976037994, backtracks = 0, tol = 0.0005673096877611747 Iteration 97: loglikelihood = -1334.8967687458248, backtracks = 0, tol = 0.000672220576503174 Iteration 98: loglikelihood = -1334.8935079576067, backtracks = 0, tol = 0.0005529608051445746 Iteration 99: loglikelihood = -1334.8903071308691, backtracks = 0, tol = 0.0006627327639382811 Iteration 100: loglikelihood = -1334.8871704381738, backtracks = 0, tol = 0.0005392536292567613 Iteration 101: loglikelihood = -1334.884090246183, backtracks = 0, tol = 0.0006535750238344538 Iteration 102: loglikelihood = -1334.8810705558342, backtracks = 0, tol = 0.0005261469075649621 Iteration 103: loglikelihood = -1334.878104169401, backtracks = 0, tol = 0.0006447293897629065 Iteration 104: loglikelihood = -1334.8751949265204, backtracks = 0, tol = 0.000513602823688224 Iteration 105: loglikelihood = -1334.87233602983, backtracks = 0, tol = 0.0006361792157517768 Iteration 106: loglikelihood = -1334.8695311671931, backtracks = 0, tol = 0.0005015866480954403 Iteration 107: loglikelihood = -1334.8667739099683, backtracks = 0, tol = 0.0006279090549630978 Iteration 108: loglikelihood = -1334.864067803043, backtracks = 0, tol = 0.0004900664304948738 Iteration 109: loglikelihood = -1334.8614067579877, backtracks = 0, tol = 0.0006199045516683339 Iteration 110: loglikelihood = -1334.8587941848755, backtracks = 0, tol = 0.00047901272822631184 Iteration 111: loglikelihood = -1334.8562243097463, backtracks = 0, tol = 0.0006121523448319347 Iteration 112: loglikelihood = -1334.8537004154164, backtracks = 0, tol = 0.00046839836584069153 Iteration 113: loglikelihood = -1334.8512170191336, backtracks = 0, tol = 0.0006046399818692465 Iteration 114: loglikelihood = -1334.8487772834544, backtracks = 0, tol = 0.0004581982217685699 Iteration 115: loglikelihood = -1334.8463759957513, backtracks = 0, tol = 0.0005973558413278999 Iteration 116: loglikelihood = -1334.8440162048273, backtracks = 0, tol = 0.00044838903858913253 Iteration 117: loglikelihood = -1334.841692949009, backtracks = 0, tol = 0.0005902890634307247 Iteration 118: loglikelihood = -1334.8394091694126, backtracks = 0, tol = 0.00043894925390854095 Iteration 119: loglikelihood = -1334.8371601378938, backtracks = 0, tol = 0.0005834294875550531 Iteration 120: loglikelihood = -1334.8349486935076, backtracks = 0, tol = 0.0004298588492874579 Iteration 121: loglikelihood = -1334.8327703257348, backtracks = 0, tol = 0.0005767675958404829 Iteration 122: loglikelihood = -1334.8306277768277, backtracks = 0, tol = 0.00042109921501119345 Iteration 123: loglikelihood = -1334.8285167393872, backtracks = 0, tol = 0.0005702944622388078 Iteration 124: loglikelihood = -1334.826439863759, backtracks = 0, tol = 0.0004126530287989236 Iteration 125: loglikelihood = -1334.824393032363, backtracks = 0, tol = 0.0005640017063887118 Iteration 126: loglikelihood = -1334.8223788082355, backtracks = 0, tol = 0.0004045041468077065 Iteration 127: loglikelihood = -1334.8203932514375, backtracks = 0, tol = 0.0005578814517929522 Iteration 128: loglikelihood = -1334.8184388419756, backtracks = 0, tol = 0.00039663750550148207 Iteration 129: loglikelihood = -1334.8165118063728, backtracks = 0, tol = 0.0005519262878289763 Iteration 130: loglikelihood = -1334.8146145456128, backtracks = 0, tol = 0.0003890390331438266 Iteration 131: loglikelihood = -1334.81274344241, backtracks = 0, tol = 0.0005461292351857192 Iteration 132: loglikelihood = -1334.810900822466, backtracks = 0, tol = 0.00038169556983421533 Iteration 133: loglikelihood = -1334.8090832152348, backtracks = 0, tol = 0.0005404837143718898 Iteration 134: loglikelihood = -1334.8072928746644, backtracks = 0, tol = 0.00037459479513916925 Iteration 135: loglikelihood = -1334.8055264681896, backtracks = 0, tol = 0.0005349835169746151 Iteration 136: loglikelihood = -1334.8037861813357, backtracks = 0, tol = 0.00036772516249334393 Iteration 137: loglikelihood = -1334.8020688114664, backtracks = 0, tol = 0.0005296227793933337 Iteration 138: loglikelihood = -1334.8003764787682, backtracks = 0, tol = 0.00036107583964320114 Iteration 139: loglikelihood = -1334.7987061030808, backtracks = 0, tol = 0.0005243959587988846 Iteration 140: loglikelihood = -1334.7970597421736, backtracks = 0, tol = 0.0003546366544935598 Iteration 141: loglikelihood = -1334.795434431467, backtracks = 0, tol = 0.0005192978111015782 Iteration 142: loglikelihood = -1334.7938321690638, backtracks = 0, tol = 0.00034839804579680106 Iteration 143: loglikelihood = -1334.7922500995571, backtracks = 0, tol = 0.0005143233707321143 Iteration 144: loglikelihood = -1334.7906901639724, backtracks = 0, tol = 0.00034235101818502967 Iteration 145: loglikelihood = -1334.7891496101236, backtracks = 0, tol = 0.000509467932062495 Iteration 146: loglikelihood = -1334.7876303244207, backtracks = 0, tol = 0.00033648710110742035 Iteration 147: loglikelihood = -1334.786129652358, backtracks = 0, tol = 0.000504727032310445 Iteration 148: loglikelihood = -1334.7846494280277, backtracks = 0, tol = 0.0003307983112841094 Iteration 149: loglikelihood = -1334.7831870894884, backtracks = 0, tol = 0.0005000964357942981 Iteration 150: loglikelihood = -1334.781744420672, backtracks = 0, tol = 0.0003252771183283661 Iteration 151: loglikelihood = -1334.780318947402, backtracks = 0, tol = 0.000495572119410984 Iteration 152: loglikelihood = -1334.7789124055262, backtracks = 0, tol = 0.0003199164132320563 Iteration 153: loglikelihood = -1334.7775224041557, backtracks = 0, tol = 0.0004911502592258968 Iteration 154: loglikelihood = -1334.7761506330012, backtracks = 0, tol = 0.00031470947943993403 Iteration 155: loglikelihood = -1334.7747947802761, backtracks = 0, tol = 0.0004868272180791204 Iteration 156: loglikelihood = -1334.7734564913999, backtracks = 0, tol = 0.0003096499662673063 Iteration 157: loglikelihood = -1334.7721335298036, backtracks = 0, tol = 0.0004825995341174756 Iteration 158: loglikelihood = -1334.7708274983474, backtracks = 0, tol = 0.00030473186444411967 Iteration 159: loglikelihood = -1334.7695362320171, backtracks = 0, tol = 0.0004784639101680918 Iteration 160: loglikelihood = -1334.76826129278, backtracks = 0, tol = 0.0002999494835896607 Iteration 161: loglikelihood = -1334.767000583753, backtracks = 0, tol = 0.00047441720388869996 Iteration 162: loglikelihood = -1334.7657556275788, backtracks = 0, tol = 0.0002952974314425555 Iteration 163: loglikelihood = -1334.7645243923093, backtracks = 0, tol = 0.00047045641862242975 Iteration 164: loglikelihood = -1334.763308362738, backtracks = 0, tol = 0.0002907705946880337 Iteration 165: loglikelihood = -1334.7621055688373, backtracks = 0, tol = 0.0004665786949011935 Iteration 166: loglikelihood = -1334.7609174589763, backtracks = 0, tol = 0.000286364121242623 Iteration 167: loglikelihood = -1334.759742122215, backtracks = 0, tol = 0.0004627813025457241 Iteration 168: loglikelihood = -1334.758580971851, backtracks = 0, tol = 0.00028207340386820964 Iteration 169: loglikelihood = -1334.7574321533693, backtracks = 0, tol = 0.0004590616333086272 Iteration 170: loglikelihood = -1334.7562970462636, backtracks = 0, tol = 0.00027789406500002754 Iteration 171: loglikelihood = -1334.7551738499526, backtracks = 0, tol = 0.00045541719402341914 Iteration 172: loglikelihood = -1334.754063911343, backtracks = 0, tol = 0.00027382194268644403 Iteration 173: loglikelihood = -1334.7529654814182, backtracks = 0, tol = 0.0004518456002136621 Iteration 174: loglikelihood = -1334.7518798756776, backtracks = 0, tol = 0.0002698530775453606 Iteration 175: loglikelihood = -1334.7508053944362, backtracks = 0, tol = 0.0004483445701291842 Iteration 176: loglikelihood = -1334.7497433228752, backtracks = 0, tol = 0.00026598370065446236 Iteration 177: loglikelihood = -1334.7486920085682, backtracks = 0, tol = 0.0004449119191740829 Iteration 178: loglikelihood = -1334.7476527074225, backtracks = 0, tol = 0.0002622102222960425 Iteration 179: loglikelihood = -1334.7466238122868, backtracks = 0, tol = 0.00044154555470124663 Iteration 180: loglikelihood = -1334.745606550812, backtracks = 0, tol = 0.00025852922148913673 Iteration 181: loglikelihood = -1334.7445993592346, backtracks = 0, tol = 0.00043824347113683424 Iteration 182: loglikelihood = -1334.7436034379143, backtracks = 0, tol = 0.0002549374362447126 Iteration 183: loglikelihood = -1334.7426172647024, backtracks = 0, tol = 0.0004350037454203732 Iteration 184: loglikelihood = -1334.7416420135908, backtracks = 0, tol = 0.00025143175448557806 Iteration 185: loglikelihood = -1334.7406762023816, backtracks = 0, tol = 0.0004318245327288188 Iteration 186: loglikelihood = -1334.7397209795454, backtracks = 0, tol = 0.0002480092055804075 Iteration 187: loglikelihood = -1334.7387749012569, backtracks = 0, tol = 0.0004287040624664419 Iteration 188: loglikelihood = -1334.7378390913234, backtracks = 0, tol = 0.0002446669524433676 Iteration 189: loglikelihood = -1334.7369121427748, backtracks = 0, tol = 0.00042564063450542365 Iteration 190: loglikelihood = -1334.7359951555525, backtracks = 0, tol = 0.00024140228415479764 Iteration 191: loglikelihood = -1334.735086758121, backtracks = 0, tol = 0.0004226326156516046 Iteration 192: loglikelihood = -1334.7341880273154, backtracks = 0, tol = 0.00023821260906558043 Iteration 193: loglikelihood = -1334.7332976256903, backtracks = 0, tol = 0.0004196784363241377 Iteration 194: loglikelihood = -1334.7324166077005, backtracks = 0, tol = 0.00023509544834599566 Iteration 195: loglikelihood = -1334.7315436687118, backtracks = 0, tol = 0.00041677658743499577 Iteration 196: loglikelihood = -1334.7306798415036, backtracks = 0, tol = 0.00023204842994877515 Iteration 197: loglikelihood = -1334.7298238530211, backtracks = 0, tol = 0.0004139256174506886 Iteration 198: loglikelihood = -1334.7289767150528, backtracks = 0, tol = 0.00022906928295358253 Iteration 199: loglikelihood = -1334.7281371849529, backtracks = 0, tol = 0.000411124129626043 Did not converge after 200 iterations! IHT run time was 1.8709790706634521 seconds Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 4.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1607.6298428694847, backtracks = 0, tol = 0.45592101404687013 Iteration 2: loglikelihood = -1522.5095103077902, backtracks = 0, tol = 0.16742619095335187 Iteration 3: loglikelihood = -1506.5118735731144, backtracks = 0, tol = 0.08964129684606421 Iteration 4: loglikelihood = -1497.8469068784163, backtracks = 0, tol = 0.09429346134976146 Iteration 5: loglikelihood = -1496.0871282024125, backtracks = 0, tol = 0.08337640867850228 Iteration 6: loglikelihood = -1495.9893159010508, backtracks = 0, tol = 0.006757905363932831 Iteration 7: loglikelihood = -1495.9861567083865, backtracks = 1, tol = 0.000585312394004332 Iteration 8: loglikelihood = -1495.9850143694612, backtracks = 1, tol = 0.0005667224959316137 Iteration 9: loglikelihood = -1495.9846569461488, backtracks = 1, tol = 0.0003812253177956861 Iteration 10: loglikelihood = -1495.9845616841417, backtracks = 1, tol = 0.00019769653686981426 Iteration 11: loglikelihood = -1495.9845372427703, backtracks = 1, tol = 9.978919833736753e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1922.8217745988554, backtracks = 0, tol = 0.7598985657898368 Iteration 2: loglikelihood = -1493.4845455612256, backtracks = 0, tol = 0.12715333255848188 Iteration 3: loglikelihood = -1403.034480808998, backtracks = 0, tol = 0.06542638910149276 Iteration 4: loglikelihood = -1385.7056557210315, backtracks = 0, tol = 0.03478188201517997 Iteration 5: loglikelihood = -1384.2037017167615, backtracks = 0, tol = 0.027147654352972683 Iteration 6: loglikelihood = -1384.0653659809047, backtracks = 0, tol = 0.002443233478229687 Iteration 7: loglikelihood = -1384.062725779437, backtracks = 0, tol = 0.00032507355276696956 Iteration 8: loglikelihood = -1384.0626591034904, backtracks = 0, tol = 5.134945587460873e-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 = -1523.3698394094276, backtracks = 0, tol = 0.35637454107867794 Iteration 2: loglikelihood = -1393.3330361781784, backtracks = 0, tol = 0.07433597612910357 Iteration 3: loglikelihood = -1384.2384143533409, backtracks = 0, tol = 0.038152921214716896 Iteration 4: loglikelihood = -1384.0661559854593, backtracks = 0, tol = 0.0026953569008084017 Iteration 5: loglikelihood = -1384.0630249455073, backtracks = 0, tol = 0.00035999565622384696 Iteration 6: loglikelihood = -1384.0629527871376, backtracks = 0, tol = 7.206555408205595e-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 10.5s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1517.8161418298675, backtracks = 0, tol = 0.15494312969985327 Iteration 2: loglikelihood = -1449.1743940324052, backtracks = 0, tol = 0.06809761292409544 Iteration 3: loglikelihood = -1399.2876661427888, backtracks = 0, tol = 0.18138735603228442 Iteration 4: loglikelihood = -1383.5546650748695, backtracks = 0, tol = 0.11313340011815365 Iteration 5: loglikelihood = -1369.6212504400683, backtracks = 0, tol = 0.06641083450838065 Iteration 6: loglikelihood = -1355.6044594748462, backtracks = 0, tol = 0.06474513519938471 Iteration 7: loglikelihood = -1343.6769896179023, backtracks = 0, tol = 0.05908300770742607 Iteration 8: loglikelihood = -1342.4173386408697, backtracks = 0, tol = 0.015521274099446382 Iteration 9: loglikelihood = -1342.1429199786048, backtracks = 0, tol = 0.006563874504596806 Iteration 10: loglikelihood = -1342.0678484340292, backtracks = 0, tol = 0.0052265503117012915 Iteration 11: loglikelihood = -1340.9941852431593, backtracks = 0, tol = 0.06595187324249302 Iteration 12: loglikelihood = -1340.718218345262, backtracks = 0, tol = 0.007284552271977248 Iteration 13: loglikelihood = -1340.6718505310548, backtracks = 0, tol = 0.003345713583319911 Iteration 14: loglikelihood = -1340.6578314599196, backtracks = 0, tol = 0.0018813587872704145 Iteration 15: loglikelihood = -1340.6531287186876, backtracks = 0, tol = 0.001321498422242213 Iteration 16: loglikelihood = -1340.651203450449, backtracks = 0, tol = 0.0006381836159951482 Iteration 17: loglikelihood = -1340.650401460059, backtracks = 0, tol = 0.0005783879235230487 Iteration 18: loglikelihood = -1340.6500479144015, backtracks = 0, tol = 0.0002459803581546911 Iteration 19: loglikelihood = -1340.6498936354262, backtracks = 0, tol = 0.0002588901219467055 Iteration 20: loglikelihood = -1340.6498244900793, backtracks = 0, tol = 0.00010289938314263529 Iteration 21: loglikelihood = -1340.6497938656375, backtracks = 0, tol = 0.000117159848012383 Iteration 22: loglikelihood = -1340.6497800289633, backtracks = 0, tol = 4.4756397931783834e-5 0.864480 seconds (1.98 M allocations: 40.980 MiB, 62.38% 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 = -1546.819117415414, backtracks = 0, tol = 0.15494312969985327 Iteration 2: loglikelihood = -1500.8394985882014, backtracks = 0, tol = 0.10372934532721151 Iteration 3: loglikelihood = -1460.928817674368, backtracks = 0, tol = 0.13525943756217493 Iteration 4: loglikelihood = -1441.080009122834, backtracks = 0, tol = 0.08178913910518455 Iteration 5: loglikelihood = -1427.9163486215925, backtracks = 0, tol = 0.056306445521355844 Iteration 6: loglikelihood = -1414.2223167340799, backtracks = 0, tol = 0.07266540866735084 Iteration 7: loglikelihood = -1405.3371672007268, backtracks = 0, tol = 0.06805597662902055 Iteration 8: loglikelihood = -1398.3438022965008, backtracks = 0, tol = 0.017064676659209795 Iteration 9: loglikelihood = -1388.442518111631, backtracks = 1, tol = 0.0022220546642600808 Iteration 10: loglikelihood = -1381.3859417554472, backtracks = 1, tol = 0.0016227098375454136 Iteration 11: loglikelihood = -1379.2093621746485, backtracks = 0, tol = 0.073670822911716 Iteration 12: loglikelihood = -1374.3520390322244, backtracks = 0, tol = 0.07211318383433973 Iteration 13: loglikelihood = -1370.835391087519, backtracks = 0, tol = 0.07629651435476704 Iteration 14: loglikelihood = -1368.648381910786, backtracks = 0, tol = 0.00933143920710262 Iteration 15: loglikelihood = -1366.6983589472948, backtracks = 0, tol = 0.0035823046559559867 Iteration 16: loglikelihood = -1363.912860748056, backtracks = 1, tol = 0.0007072202815663304 Iteration 17: loglikelihood = -1361.9310003902308, backtracks = 1, tol = 0.00048354788230984153 Iteration 18: loglikelihood = -1359.988318788563, backtracks = 1, tol = 0.00026856028898949774 Iteration 19: loglikelihood = -1358.9194841228111, backtracks = 0, tol = 0.07505946469680984 Iteration 20: loglikelihood = -1357.788551196667, backtracks = 0, tol = 0.005147783405040768 Iteration 21: loglikelihood = -1356.8849214287454, backtracks = 0, tol = 0.0015091535156745175 Iteration 22: loglikelihood = -1356.0422630196006, backtracks = 0, tol = 0.0006966869362889863 Iteration 23: loglikelihood = -1355.409525908366, backtracks = 0, tol = 0.07200755646846932 Iteration 24: loglikelihood = -1354.7187048756962, backtracks = 0, tol = 0.004944179259409951 Iteration 25: loglikelihood = -1354.0615711916553, backtracks = 0, tol = 0.0012130536565193525 Iteration 26: loglikelihood = -1353.464113739511, backtracks = 0, tol = 0.07265681039853603 Iteration 27: loglikelihood = -1352.7851659843147, backtracks = 0, tol = 0.004684668690174584 Iteration 28: loglikelihood = -1352.257555929231, backtracks = 0, tol = 0.0014478641502384743 Iteration 29: loglikelihood = -1351.7544278249804, backtracks = 0, tol = 0.0007105536390574179 Iteration 30: loglikelihood = -1351.2979077420237, backtracks = 0, tol = 0.0004693203057954523 Iteration 31: loglikelihood = -1350.8651566611095, backtracks = 0, tol = 0.0001896483203216435 Iteration 32: loglikelihood = -1350.6927544315793, backtracks = 0, tol = 0.07951164952809754 Iteration 33: loglikelihood = -1350.2323801841214, backtracks = 0, tol = 0.008461463956311645 Iteration 34: loglikelihood = -1349.8711783693134, backtracks = 0, tol = 0.0012442805507375445 Iteration 35: loglikelihood = -1349.4642765241447, backtracks = 1, tol = 0.0002663407223326984 Iteration 36: loglikelihood = -1349.1539259136455, backtracks = 0, tol = 0.0736442465201358 Iteration 37: loglikelihood = -1348.742918055163, backtracks = 0, tol = 0.004529342858201746 Iteration 38: loglikelihood = -1348.456021443246, backtracks = 0, tol = 0.0014620131158489878 Iteration 39: loglikelihood = -1348.1774094269356, backtracks = 0, tol = 0.0007350037478108851 Iteration 40: loglikelihood = -1347.9250334759572, backtracks = 0, tol = 0.0004733413569138545 Iteration 41: loglikelihood = -1347.6815955705074, backtracks = 0, tol = 0.00017141292335581926 Iteration 42: loglikelihood = -1347.2177151666358, backtracks = 1, tol = 0.000113899076812204 Iteration 43: loglikelihood = -1347.1601440593386, backtracks = 0, tol = 0.07033053557142331 Iteration 44: loglikelihood = -1346.9539854871994, backtracks = 0, tol = 0.004364017068874841 Iteration 45: loglikelihood = -1346.7616221693336, backtracks = 0, tol = 0.001250319551440983 Iteration 46: loglikelihood = -1346.5917466545181, backtracks = 0, tol = 0.0007105492617131851 Iteration 47: loglikelihood = -1346.4240285835442, backtracks = 0, tol = 0.00025677217109049236 Iteration 48: loglikelihood = -1346.2976252928954, backtracks = 1, tol = 5.994465487121302e-5 0.523957 seconds (1.89 M allocations: 34.347 MiB, 5.32% 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 = -3630.8728, backtracks = 0, tol = 0.08155097562609076 Iteration 2: loglikelihood = -3585.9177, backtracks = 0, tol = 0.04296904218223809 Iteration 3: loglikelihood = -3552.5916, backtracks = 1, tol = 0.062053736109640635 Iteration 4: loglikelihood = -3546.3784, backtracks = 1, tol = 0.00807023177498629 Iteration 5: loglikelihood = -3543.9463, backtracks = 1, tol = 0.007338916069852676 Iteration 6: loglikelihood = -3543.196, backtracks = 1, tol = 0.00577000629665953 Iteration 7: loglikelihood = -3542.9858, backtracks = 1, tol = 0.003024398276477207 Iteration 8: loglikelihood = -3542.938, backtracks = 1, tol = 0.001638959234776994 Iteration 9: loglikelihood = -3542.928, backtracks = 1, tol = 0.0008131499357973696 Iteration 10: loglikelihood = -3542.925, backtracks = 1, tol = 0.0004193949481087655 Iteration 11: loglikelihood = -3542.9243, backtracks = 2, tol = 0.0001035977565507366 Iteration 12: loglikelihood = -3542.9238, backtracks = 2, tol = 7.816178955316733e-5 25.218092 seconds (15.25 M allocations: 674.210 MiB, 4.45% gc time, 94.83% 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 = -3521.6467, backtracks = 0, tol = 0.08155097562609076 Iteration 2: loglikelihood = -3403.3506, backtracks = 0, tol = 0.0441039436539226 Iteration 3: loglikelihood = -3178.7415, backtracks = 1, tol = 0.05968079970832176 Iteration 4: loglikelihood = -3097.2004, backtracks = 0, tol = 0.08660534127966818 Iteration 5: loglikelihood = -2960.9348, backtracks = 0, tol = 0.08206848759001009 Iteration 6: loglikelihood = -2866.591, backtracks = 0, tol = 0.08672472702233568 Iteration 7: loglikelihood = -2738.4116, backtracks = 0, tol = 0.0811699557535214 Iteration 8: loglikelihood = -2646.5728, backtracks = 0, tol = 0.08802769016260537 Iteration 9: loglikelihood = -2527.7659, backtracks = 0, tol = 0.08878089047307014 Iteration 10: loglikelihood = -2434.207, backtracks = 0, tol = 0.0880293958164867 Iteration 11: loglikelihood = -2356.6426, backtracks = 0, tol = 0.008753258853128656 Iteration 12: loglikelihood = -2297.8582, backtracks = 0, tol = 0.09257053437900663 Iteration 13: loglikelihood = -2252.6753, backtracks = 0, tol = 0.01494689410237886 Iteration 14: loglikelihood = -2222.067, backtracks = 0, tol = 0.0013732496874972798 Iteration 15: loglikelihood = -2202.0066, backtracks = 0, tol = 0.08143740444074911 Iteration 16: loglikelihood = -2189.5264, backtracks = 0, tol = 0.010164580613676743 Iteration 17: loglikelihood = -2182.5735, backtracks = 0, tol = 0.0022648873873745688 Iteration 18: loglikelihood = -2178.7136, backtracks = 0, tol = 0.0006626877589213608 Iteration 19: loglikelihood = -2176.6335, backtracks = 0, tol = 0.00029108000422208415 Iteration 20: loglikelihood = -2175.541, backtracks = 0, tol = 0.000209946036092945 Iteration 21: loglikelihood = -2174.975, backtracks = 0, tol = 0.00014574180707023292 Iteration 22: loglikelihood = -2174.69, backtracks = 0, tol = 0.00010464117171451787 Iteration 23: loglikelihood = -2174.541, backtracks = 0, tol = 7.415703095243548e-5 0.160935 seconds (1.06 M allocations: 17.488 MiB) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 29.4s **** 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 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 4.848302 seconds (1.17 M allocations: 138.688 MiB, 0.71% gc time, 91.10% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.3s 9.586540 seconds (4.00 M allocations: 82.481 MiB, 0.75% gc time, 0.64% compilation time) 5.389113 seconds (3.98 M allocations: 91.676 MiB, 0.19% gc time) 10.571328 seconds (20.40 M allocations: 439.345 MiB, 1.06% gc time, 17.34% compilation time: 79% of which was recompilation) 8.391712 seconds (20.18 M allocations: 434.192 MiB, 1.04% gc time) 41.873550 seconds (3.72 M allocations: 4.237 GiB, 11.08% gc time, 28.94% compilation time) 52.397600 seconds (71.97 k allocations: 183.461 MiB) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m27.3s Test Summary: | Pass Total Time update_support! | 10 10 0.7s 14.802 ms (78 allocations: 4.56 KiB) 5.093 μs (0 allocations: 0 bytes) 144.689 μs (4 allocations: 288 bytes) 6.553 μs (0 allocations: 0 bytes) 46.199 μs (2 allocations: 64 bytes) 39.760 μs (0 allocations: 0 bytes) 33.710 μs (0 allocations: 0 bytes) 29.180 μs (0 allocations: 0 bytes) 91.039 μs (0 allocations: 0 bytes) 39.069 ms (78 allocations: 4.56 KiB) 26.350 μs (0 allocations: 0 bytes) 172.579 μs (4 allocations: 288 bytes) 33.400 μs (0 allocations: 0 bytes) 232.097 μs (2 allocations: 64 bytes) 90.369 μs (0 allocations: 0 bytes) 152.609 μs (0 allocations: 0 bytes) 139.229 μs (0 allocations: 0 bytes) 264.047 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 3m35.0s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.414069 seconds (49.11 k allocations: 5.471 MiB, 61.03% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 12.1s **** 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 Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.077906 seconds (313.07 k allocations: 170.025 MiB, 61.38% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:03:39 Cross validating... 19%|██████▏ | ETA: 0:00:34 Cross validating... 22%|███████▏ | ETA: 0:00:29 Cross validating... 25%|████████▏ | ETA: 0:00:24 Cross validating... 29%|█████████▏ | ETA: 0:00:21 Cross validating... 32%|██████████▏ | ETA: 0:00:19 Cross validating... 35%|███████████▏ | ETA: 0:00:16 Cross validating... 38%|████████████▎ | ETA: 0:00:15 Cross validating... 41%|█████████████▎ | ETA: 0:00:13 Cross validating... 44%|██████████████▎ | ETA: 0:00:11 Cross validating... 48%|███████████████▎ | ETA: 0:00:10 Cross validating... 51%|████████████████▎ | ETA: 0:00:09 Cross validating... 54%|█████████████████▎ | ETA: 0:00:08 Cross validating... 57%|██████████████████▎ | ETA: 0:00:07 Cross validating... 60%|███████████████████▎ | ETA: 0:00:07 Cross validating... 63%|████████████████████▍ | ETA: 0:00:06 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:05 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:05 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:04 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:03 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:03 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:02 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 4834.28753324329 1 3594.4167676759116 2 2233.9950204934926 3 1490.3704655293145 4 1100.1002734402623 5 824.8088598144134 6 620.5362855985139 7 488.3861646979392 8 414.5839064163021 9 359.12271256144027 10 364.1809496123076 11 365.4390534642551 12 366.9451996011403 13 370.90008097647626 14 384.9910382561961 15 372.301098554929 16 385.470442175662 17 373.6869630017323 18 390.47358213700625 19 379.6637752038383 20 416.6546486055214 Best k = 9 11.965444 seconds (11.42 M allocations: 300.706 MiB, 1.14% gc time, 61.44% 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... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 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... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 4834.28753324329 1 3596.996738450809 2 2250.0215666773156 3 1504.9909647287118 4 1110.3727191401686 5 838.9893233051648 6 632.0211408365299 7 506.60283851253246 8 433.6862042736652 9 375.9131538382579 10 388.97615855030244 11 394.7995210495119 12 399.5096465063199 13 403.98927420145895 14 409.30926810945465 15 411.6783255835576 16 416.5029742311002 17 428.00751234166125 18 424.53062903821916 19 441.40772221998526 20 436.7941421036597 Best k = 9 4.568028 seconds (10.07 M allocations: 211.686 MiB, 0.82% gc time, 1.10% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 17.4s **** 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: 0:07:09 Cross validating... 8%|██▌ | ETA: 0:02:45 Cross validating... 13%|████▏ | ETA: 0:01:38 Cross validating... 17%|█████▋ | ETA: 0:01:09 Cross validating... 22%|███████▏ | ETA: 0:00:51 Cross validating... 25%|████████▏ | ETA: 0:00:43 Cross validating... 30%|█████████▋ | ETA: 0:00:34 Cross validating... 35%|███████████▏ | ETA: 0:00:28 Cross validating... 38%|████████████▎ | ETA: 0:00:25 Cross validating... 43%|█████████████▊ | ETA: 0:00:20 Cross validating... 48%|███████████████▎ | ETA: 0:00:17 Cross validating... 52%|████████████████▊ | ETA: 0:00:14 Cross validating... 57%|██████████████████▎ | ETA: 0:00:12 Cross validating... 62%|███████████████████▊ | ETA: 0:00:10 Cross validating... 65%|████████████████████▉ | ETA: 0:00:08 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:07 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:16 Crossvalidation Results: k MSE 0 1619.8444727783203 1 1330.2915653076172 2 986.4448230590821 3 748.0254447021484 4 625.2764931030274 5 483.52685049438475 6 407.102462097168 7 380.65507498168944 8 345.0074142761231 9 330.98948550415037 10 334.94593530273437 11 338.79118872070313 12 339.48930413818357 13 351.9771564331055 14 345.3253996887207 15 348.3927620239258 16 364.4520648498535 17 351.8351992797852 18 351.50638635253904 19 354.87900650024415 20 390.04747567749024 Best k = 9 17.862453 seconds (12.82 M allocations: 316.565 MiB, 0.74% gc time, 84.74% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 27%|████████▋ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:01 Cross validating... 51%|████████████████▎ | ETA: 0:00:01 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 60%|███████████████████▎ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1619.8444727783203 1 1330.8872982177734 2 987.1967517089844 3 748.0244620361328 4 625.2799264526367 5 483.5232962646484 6 413.08781552124026 7 387.2576622619629 8 352.41199420166015 9 338.2066294555664 10 351.48674456787114 11 354.70878732299803 12 365.9227757568359 13 371.29474664306645 14 380.42386752319334 15 386.63233242797855 16 392.9072543334961 17 405.4678742370605 18 402.184094329834 19 412.46062490844724 20 413.1416592407227 Best k = 9 2.753454 seconds (11.24 M allocations: 206.383 MiB, 2.51% gc time, 1.41% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 22.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:08 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: 0:00:04 Cross validating... 54%|█████████████████▎ | ETA: 0:00:04 Cross validating... 57%|██████████████████▎ | ETA: 0:00:04 Cross validating... 60%|███████████████████▎ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 462.80486992397323 1 397.3338465960637 2 361.2575016556924 3 337.11826882604583 4 300.7273107320906 5 284.74673708176175 6 277.1623035816848 7 261.8568128236327 8 257.61489497161483 9 255.13361778623172 10 251.9284172725028 11 256.68813134844754 12 254.51241137078466 13 276.2962983768448 14 267.84488413087644 15 278.1340233576054 16 270.49692106509696 17 268.8826024557326 18 298.7632641833246 19 292.78282270368834 20 307.66215839571805 Best k = 10 8.016716 seconds (17.17 M allocations: 405.599 MiB, 1.26% gc time, 30.59% 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... 11%|███▌ | ETA: 0:00:05 Cross validating... 14%|████▋ | ETA: 0:00:05 Cross validating... 17%|█████▋ | ETA: 0:00:05 Cross validating... 21%|██████▋ | ETA: 0:00:05 Cross validating... 24%|███████▋ | ETA: 0:00:04 Cross validating... 27%|████████▋ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 37%|███████████▋ | ETA: 0:00:04 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 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Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 462.80486992397323 1 398.56653822299336 2 363.00077381853407 3 339.6736232616594 4 304.9792830048596 5 288.53517170808567 6 282.56234394706627 7 267.2228111979533 8 267.47184402189106 9 252.76287171127834 10 262.6348188481736 11 271.6835409115849 12 286.4941682821287 13 289.5630251821501 14 292.6450995502131 15 292.6922652745203 16 301.64909160318894 17 303.7623524401171 18 340.4312344073604 19 333.88366981526787 20 332.9607644842644 Best k = 9 5.804538 seconds (17.43 M allocations: 361.110 MiB, 1.72% gc time, 0.94% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:47 Cross validating... 8%|██▌ | ETA: 0:00:20 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:12 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:09 Cross validating... 24%|███████▋ | ETA: 0:00:08 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:06 Cross validating... 38%|████████████▎ | ETA: 0:00:05 Cross validating... 41%|█████████████▎ | ETA: 0:00:05 Cross validating... 44%|██████████████▎ | ETA: 0:00:04 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... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:06 Crossvalidation Results: k MSE 0 465.848032177213 1 429.77808728888556 2 411.22152342333163 3 382.4766247374367 4 368.39030132940684 5 357.9677660002684 6 337.47102955314534 7 331.8222204897164 8 331.08322086713724 9 327.8892072408906 10 326.1634339323936 11 329.7246965328043 12 330.2434929376134 13 335.24860896024984 14 337.0827072059525 15 348.031024111155 16 350.1050899546169 17 387.8655473384926 18 355.84840141341954 19 383.4752521182367 20 373.48959630442863 Best k = 10 7.840492 seconds (16.76 M allocations: 395.690 MiB, 13.65% gc time, 32.36% 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... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:01 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 465.848032177213 1 430.7363849722863 2 412.87888118536296 3 384.3299751714665 4 371.68396312120467 5 362.7624690528436 6 342.9583157929508 7 345.2758726257883 8 341.63087272019663 9 342.6402076463012 10 342.6675211029732 11 356.03429104848396 12 351.79065076373746 13 373.3155857839853 14 372.30128046500045 15 389.8082660980819 16 404.8615243938706 17 431.5926090103901 18 424.07168230468136 19 423.7925730208202 20 446.53669712613606 Best k = 8 4.299153 seconds (17.05 M allocations: 348.979 MiB, 1.38% gc time, 0.92% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 13.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:58 Cross validating... 6%|██ | ETA: 0:00:30 Cross validating... 10%|███ | ETA: 0:00:21 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 14%|████▋ | ETA: 0:00:15 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross validating... 21%|██████▋ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross 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ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1089.6353426799267 1 812.2252146745354 2 589.0398084265103 3 538.6954600780687 4 478.5329143857047 5 429.68418747129135 6 412.0159054134557 7 403.79037132937503 8 387.9894181956985 9 397.7814303039322 10 406.0910233503258 11 413.17922896892514 12 403.4373226778748 13 397.66214109426323 14 397.1967969092819 15 404.22154173498427 16 405.11644421391634 17 426.4983604800725 18 409.46743376115086 19 399.3279517832762 20 404.8039452557015 Best k = 8 7.945963 seconds (15.52 M allocations: 366.513 MiB, 0.89% gc time, 31.07% 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: 0:00:04 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 37%|███████████▋ | ETA: 0:00:03 Cross validating... 40%|████████████▊ | ETA: 0:00:03 Cross validating... 43%|█████████████▊ | ETA: 0:00:03 Cross validating... 46%|██████████████▊ | ETA: 0:00:03 Cross validating... 49%|███████████████▊ | ETA: 0:00:03 Cross validating... 52%|████████████████▊ | ETA: 0:00:03 Cross validating... 56%|█████████████████▊ | ETA: 0:00:02 Cross validating... 59%|██████████████████▊ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1089.6353426799267 1 781.2061859597916 2 577.7820992457575 3 533.0062227424796 4 467.70258726015777 5 425.63335655557694 6 401.91046019620535 7 389.78469354398976 8 377.6760829897664 9 386.4248535297567 10 393.2853185384481 11 397.9909815119776 12 394.210458706738 13 400.89720323564234 14 417.58905587809755 15 429.4243852188266 16 429.07961318940147 17 430.75139817084727 18 440.6736667588191 19 447.77196622404404 20 441.8178561360123 Best k = 8 5.494428 seconds (14.01 M allocations: 279.570 MiB, 0.94% gc time, 1.04% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 13.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:26 Cross validating... 6%|██ | ETA: 0:00:57 Cross validating... 10%|███ | ETA: 0:00:47 Cross validating... 13%|████▏ | ETA: 0:00:42 Cross validating... 14%|████▋ | ETA: 0:00:43 Cross validating... 16%|█████▏ | ETA: 0:00:39 Cross validating... 17%|█████▋ | ETA: 0:00:39 Cross validating... 19%|██████▏ | 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0:00:07 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:06 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:05 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:05 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:04 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:03 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:03 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:02 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:42 Crossvalidation Results: k MSE 0 419.5546853932958 1 320.1711547494033 2 262.4228349874717 3 251.44776577526102 4 231.56037844585597 5 226.96602907924876 6 226.57924843962599 7 219.36876247284795 8 218.523268200359 9 219.50869326514743 10 219.20588664696604 11 218.38756318401437 12 220.7425667432255 13 220.59602684612034 14 223.2176219484157 15 223.84260208567156 16 225.71299180212833 17 221.4344719246931 18 225.41633751994277 19 225.35418642219645 20 223.15898435134866 Best k = 11 43.417945 seconds (136.32 M allocations: 3.518 GiB, 1.35% gc time, 4.97% 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: 0:00:06 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 11%|███▌ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:06 Cross validating... 21%|██████▋ | ETA: 0:00:06 Cross 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Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 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 0 419.5546853932958 1 319.39379058349834 2 262.8486038022495 3 252.09427885781062 4 232.2707311322347 5 228.31783543135623 6 229.58100083511977 7 223.3711663083162 8 224.30146882452217 9 225.59420933151955 10 226.7607242420732 11 232.38578610791973 12 231.47987440925098 13 239.85743005870415 14 243.73139355890711 15 242.13850124975895 16 249.3651667908538 17 255.2606807238207 18 264.7100483306958 19 258.4503680760451 20 260.8444686232956 Best k = 7 13.149809 seconds (38.99 M allocations: 801.828 MiB, 1.40% gc time, 0.45% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 57.0s **** 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: 0:01:06 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:02 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 709.7238911132813 1 600.8470166015625 2 478.37098138427734 3 399.75837347412113 4 316.3170971069336 5 274.59901690673826 6 232.61785809326173 7 221.00282696533208 8 205.62119918823245 9 198.3431817626953 10 200.94596459960937 11 201.86666357421876 12 202.35683154296873 13 208.02664166259768 14 206.9071481628418 15 209.87240182495117 16 216.0480528869629 17 212.0296098022461 18 217.49209603881837 19 225.60646734619144 20 213.36869631958012 Best k = 9 6.364570 seconds (17.00 M allocations: 337.853 MiB, 2.01% gc time, 42.51% 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: 0:00:02 Cross validating... 33%|██████████▋ | ETA: 0:00:02 Cross validating... 38%|████████████▎ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 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100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 709.7238911132813 1 580.5206424560547 2 462.45179821777344 3 375.725685546875 4 311.8335130615235 5 265.69685809326177 6 235.52074707031255 7 221.8731430358887 8 209.48005477905275 9 202.0256286010742 10 206.40357376098632 11 209.8904744873047 12 212.83695938110353 13 217.36745034790042 14 219.17275009155276 15 218.94907879638671 16 225.10276358032226 17 228.24513723754882 18 225.50167910766604 19 235.0626920776367 20 227.98946899414062 Best k = 9 3.457964 seconds (16.17 M allocations: 286.698 MiB, 1.54% gc time, 1.64% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** 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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: 0:00:18 Crossvalidation Results: k MSE 1 2966.1644636911824 2 2364.9232643072396 3 2101.469111482149 4 1838.1481405776647 5 1566.7376011135154 6 1335.7457063668774 7 1280.1871503118814 8 1257.5952268329747 9 1273.2294675313212 10 1281.032851993602 11 1290.0902381488027 12 1297.606767318378 13 1312.6654594591205 14 1332.0990766126445 15 1324.4655579523178 16 1344.8566945651078 17 1377.3846603333368 18 1357.8909041054626 19 1357.120079141987 20 1370.851319529594 Best k = 8 18.926598 seconds (334.99 k allocations: 235.201 MiB, 0.39% gc time, 10.61% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 23.9s Test Summary: | Pass Total Time wrapper univariate | 20 20 1m49.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross 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97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross 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2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:11 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 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 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Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m28.4s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [8] macro expansion @ ./timing.jl:739 [inlined] [9] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [inlined] [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl: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:489 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [18] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time read BGEN and VCF | 1 1 3.1s RNG of the outermost testset: Xoshiro(0x375082bb54560de1, 0xecbee68acf8475c4, 0xbd39d0db0bb6cfe2, 0xf27ad2c07f1d3245, 0x510a0de67741de7a) 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 1142.47s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl: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 1242.19s: package tests unexpectedly errored