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1.5.0-DEV-7206b56e94.log
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Julia Version 1.5.0-DEV.485
Commit 7206b56e94 (2020-03-18 17:25 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed Rmath_jll ──────────────────── v0.2.2+0
Installed SortingAlgorithms ──────────── v0.3.1
Installed PDMats ─────────────────────── v0.9.12
Installed DataValueInterfaces ────────── v1.0.0
Installed CategoricalArrays ──────────── v0.7.7
Installed DataFrames ─────────────────── v0.20.2
Installed Distributions ──────────────── v0.22.6
Installed JWAS ───────────────────────── v0.8.2
Installed WeakRefStrings ─────────────── v0.6.2
Installed Arpack_jll ─────────────────── v3.5.0+2
Installed QuadGK ─────────────────────── v2.3.1
Installed StatsFuns ──────────────────── v0.9.4
Installed JSON ───────────────────────── v0.21.0
Installed DataStructures ─────────────── v0.17.10
Installed OpenBLAS_jll ───────────────── v0.3.7+7
Installed StatsBase ──────────────────── v0.32.2
Installed CompilerSupportLibraries_jll ─ v0.3.0+0
Installed Reexport ───────────────────── v0.2.0
Installed ProgressMeter ──────────────── v1.2.0
Installed PooledArrays ───────────────── v0.5.3
Installed InvertedIndices ────────────── v1.0.0
Installed OpenSpecFun_jll ────────────── v0.5.3+3
Installed DataAPI ────────────────────── v1.1.0
Installed Parsers ────────────────────── v0.3.12
Installed Rmath ──────────────────────── v0.6.1
Installed SpecialFunctions ───────────── v0.10.0
Installed Missings ───────────────────── v0.4.3
Installed IteratorInterfaceExtensions ── v1.0.0
Installed Compat ─────────────────────── v3.8.0
Installed OrderedCollections ─────────── v1.1.0
Installed Arpack ─────────────────────── v0.4.0
Installed Tables ─────────────────────── v1.0.3
Installed FilePathsBase ──────────────── v0.7.0
Installed FillArrays ─────────────────── v0.8.5
Installed TableTraits ────────────────── v1.0.0
Installed CSV ────────────────────────── v0.5.26
#=#=# ######################################################################## 100.0%
#=#=# ######################################################################## 100.0%
#=#=# # 2.1%##### 8.3%############ 17.6%#################### 28.4%############################# 41.4%######################################### 58.0%######################################################### 79.6%######################################################################## 100.0%
#=#=# 0.4%#### 6.3%########## 14.1%################## 25.9%############################ 39.3%######################################### 57.9%########################################################## 80.9%######################################################################## 100.0%
#=#=# ############################## 42.2%######################################################################## 100.0%
Updating `~/.julia/environments/v1.5/Project.toml`
c9a035f4 + JWAS v0.8.2
Updating `~/.julia/environments/v1.5/Manifest.toml`
7d9fca2a + Arpack v0.4.0
68821587 + Arpack_jll v3.5.0+2
336ed68f + CSV v0.5.26
324d7699 + CategoricalArrays v0.7.7
34da2185 + Compat v3.8.0
e66e0078 + CompilerSupportLibraries_jll v0.3.0+0
9a962f9c + DataAPI v1.1.0
a93c6f00 + DataFrames v0.20.2
864edb3b + DataStructures v0.17.10
e2d170a0 + DataValueInterfaces v1.0.0
31c24e10 + Distributions v0.22.6
48062228 + FilePathsBase v0.7.0
1a297f60 + FillArrays v0.8.5
41ab1584 + InvertedIndices v1.0.0
82899510 + IteratorInterfaceExtensions v1.0.0
682c06a0 + JSON v0.21.0
c9a035f4 + JWAS v0.8.2
e1d29d7a + Missings v0.4.3
4536629a + OpenBLAS_jll v0.3.7+7
efe28fd5 + OpenSpecFun_jll v0.5.3+3
bac558e1 + OrderedCollections v1.1.0
90014a1f + PDMats v0.9.12
69de0a69 + Parsers v0.3.12
2dfb63ee + PooledArrays v0.5.3
92933f4c + ProgressMeter v1.2.0
1fd47b50 + QuadGK v2.3.1
189a3867 + Reexport v0.2.0
79098fc4 + Rmath v0.6.1
f50d1b31 + Rmath_jll v0.2.2+0
a2af1166 + SortingAlgorithms v0.3.1
276daf66 + SpecialFunctions v0.10.0
2913bbd2 + StatsBase v0.32.2
4c63d2b9 + StatsFuns v0.9.4
3783bdb8 + TableTraits v1.0.0
bd369af6 + Tables v1.0.3
ea10d353 + WeakRefStrings v0.6.2
2a0f44e3 + Base64
ade2ca70 + Dates
8bb1440f + DelimitedFiles
8ba89e20 + Distributed
9fa8497b + Future
b77e0a4c + InteractiveUtils
76f85450 + LibGit2
8f399da3 + Libdl
37e2e46d + LinearAlgebra
56ddb016 + Logging
d6f4376e + Markdown
a63ad114 + Mmap
44cfe95a + Pkg
de0858da + Printf
3fa0cd96 + REPL
9a3f8284 + Random
ea8e919c + SHA
9e88b42a + Serialization
1a1011a3 + SharedArrays
6462fe0b + Sockets
2f01184e + SparseArrays
10745b16 + Statistics
4607b0f0 + SuiteSparse
8dfed614 + Test
cf7118a7 + UUIDs
4ec0a83e + Unicode
Testing JWAS
Status `/tmp/jl_VbBn6U/Project.toml`
336ed68f CSV v0.5.26
a93c6f00 DataFrames v0.20.2
31c24e10 Distributions v0.22.6
c9a035f4 JWAS v0.8.2
92933f4c ProgressMeter v1.2.0
2913bbd2 StatsBase v0.32.2
8bb1440f DelimitedFiles
b77e0a4c InteractiveUtils
37e2e46d LinearAlgebra
de0858da Printf
9a3f8284 Random
2f01184e SparseArrays
8dfed614 Test
Status `/tmp/jl_VbBn6U/Manifest.toml`
7d9fca2a Arpack v0.4.0
68821587 Arpack_jll v3.5.0+2
336ed68f CSV v0.5.26
324d7699 CategoricalArrays v0.7.7
34da2185 Compat v3.8.0
e66e0078 CompilerSupportLibraries_jll v0.3.0+0
9a962f9c DataAPI v1.1.0
a93c6f00 DataFrames v0.20.2
864edb3b DataStructures v0.17.10
e2d170a0 DataValueInterfaces v1.0.0
31c24e10 Distributions v0.22.6
48062228 FilePathsBase v0.7.0
1a297f60 FillArrays v0.8.5
41ab1584 InvertedIndices v1.0.0
82899510 IteratorInterfaceExtensions v1.0.0
682c06a0 JSON v0.21.0
c9a035f4 JWAS v0.8.2
e1d29d7a Missings v0.4.3
4536629a OpenBLAS_jll v0.3.7+7
efe28fd5 OpenSpecFun_jll v0.5.3+3
bac558e1 OrderedCollections v1.1.0
90014a1f PDMats v0.9.12
69de0a69 Parsers v0.3.12
2dfb63ee PooledArrays v0.5.3
92933f4c ProgressMeter v1.2.0
1fd47b50 QuadGK v2.3.1
189a3867 Reexport v0.2.0
79098fc4 Rmath v0.6.1
f50d1b31 Rmath_jll v0.2.2+0
a2af1166 SortingAlgorithms v0.3.1
276daf66 SpecialFunctions v0.10.0
2913bbd2 StatsBase v0.32.2
4c63d2b9 StatsFuns v0.9.4
3783bdb8 TableTraits v1.0.0
bd369af6 Tables v1.0.3
ea10d353 WeakRefStrings v0.6.2
2a0f44e3 Base64
ade2ca70 Dates
8bb1440f DelimitedFiles
8ba89e20 Distributed
9fa8497b Future
b77e0a4c InteractiveUtils
76f85450 LibGit2
8f399da3 Libdl
37e2e46d LinearAlgebra
56ddb016 Logging
d6f4376e Markdown
a63ad114 Mmap
44cfe95a Pkg
de0858da Printf
3fa0cd96 REPL
9a3f8284 Random
ea8e919c SHA
9e88b42a Serialization
1a1011a3 SharedArrays
6462fe0b Sockets
2f01184e SparseArrays
10745b16 Statistics
4607b0f0 SuiteSparse
8dfed614 Test
cf7118a7 UUIDs
4ec0a83e Unicode
The delimiter in pedigree.txt is ','.
calculating inbreeding... 8%|██▏ | ETA: 0:00:03[Kcalculating inbreeding... 100%|█████████████████████████| Time: 0:00:00[K
Pedigree informatin:
#individuals: 12
#sires: 4
#dams: 5
#founders: 3
Test single-trait GBLUP analysis using complete genomic data
The delimiter in genotypes.txt is ','.
The header (marker IDs) is provided in genotypes.txt.
5 markers on 7 individuals were added.
Checking phenotypes...
Individual IDs (strings) are provided in the first column of the phenotypic data.
Phenotypes for all traits included in the model for individual a7 in the row 5 are missing. This record is deleted.
The number of observations with both genotypes and phenotypes used in the analysis is 4.
The number of observations with both phenotype and pedigree information used in the analysis is 4.
Missing values are found in independent variables: dam.
A Linear Mixed Model was build using model equations:
y1 = intercept + x1*x3 + x2 + x3 + ID + dam
Model Information:
Term C/F F/R nLevels
intercept factor fixed 1
x1*x3 interaction fixed 2
x2 factor random 2
x3 factor fixed 2
ID factor random 12
dam factor random 12
MCMC Information:
methods GBLUP
complete genomic data
(i.e., non-single-step analysis)
chain_length 100
burnin 0
estimateScale false
starting_value false
printout_frequency 50
output_samples_frequency 10
constraint false
missing_phenotypes true
update_priors_frequency 0
seed 314
Hyper-parameters Information:
random effect variances (y1:ID,y1:dam): [1.0 0.5; 0.5 1.0]
random effect variances (y1:x2): [1.0]
residual variances: 1.000
Degree of freedom for hyper-parameters:
residual variances: 4.000
random effect variances: 5.000
polygenic effect variances: 6.000
marker effect variances: 4.000
The file MCMC_samples_residual_variance.txt is created to save MCMC samples for residual_variance.
The file MCMC_samples_polygenic_effects_variance.txt is created to save MCMC samples for polygenic_effects_variance.
The file MCMC_samples_marker_effects_y1.txt is created to save MCMC samples for marker_effects_y1.
The file MCMC_samples_marker_effects_variances.txt is created to save MCMC samples for marker_effects_variances.
The file MCMC_samples_pi.txt is created to save MCMC samples for pi.
The file MCMC_samples_y1.x2.txt is created to save MCMC samples for y1:x2.
The file MCMC_samples_y1.ID_y1.dam_variances.txt is created to save MCMC samples for y1:ID_y1:dam_variances.
The file MCMC_samples_y1.x2_variances.txt is created to save MCMC samples for y1:x2_variances.
The file MCMC_samples_EBV_y1.txt is created to save MCMC samples for EBV_y1.
The file MCMC_samples_genetic_variance.txt is created to save MCMC samples for genetic_variance.
The file MCMC_samples_heritability.txt is created to save MCMC samples for heritability.
running MCMC for GBLUP... 1%|▎ | ETA: 0:04:30[Krunning MCMC for GBLUP... 2%|▌ | ETA: 0:02:32[Krunning MCMC for GBLUP... 10%|██▋ | ETA: 0:00:53[K
Posterior means at iteration: 50
Residual variance: 1.475534
running MCMC for GBLUP... 50%|█████████████ | ETA: 0:00:06[K
Posterior means at iteration: 100
Residual variance: 1.175473
running MCMC for GBLUP...100%|██████████████████████████| Time: 0:00:06[K
The version of Julia and Platform in use:
Julia Version 1.5.0-DEV.485
Commit 7206b56e94 (2020-03-18 17:25 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-9.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
JULIA_PKGEVAL = true
JULIA_LOAD_PATH = @:/tmp/jl_VbBn6U
The analysis has finished. Results are saved in the returned variable and text files. MCMC samples are saved in text files.
Test multi-trait GBLUP analysis using complete genomic data
dam is not found in model equation 2.
dam is not found in model equation 3.
x2 is not found in model equation 1.
The delimiter in genotypes.txt is ','.
The header (marker IDs) is provided in genotypes.txt.
5 markers on 7 individuals were added.
Checking phenotypes...
Individual IDs (strings) are provided in the first column of the phenotypic data.
Phenotypes for all traits included in the model for individual a7 in the row 5 are missing. This record is deleted.
The number of observations with both genotypes and phenotypes used in the analysis is 4.
The number of observations with both phenotype and pedigree information used in the analysis is 4.
Missing values are found in independent variables: dam.
ERROR: LoadError: LoadError: MethodError: no method matching zero(::Type{Any})
Closest candidates are:
zero(::Type{Union{Missing, T}}) where T at missing.jl:105
zero(!Matched::Type{Missing}) at missing.jl:103
zero(!Matched::Type{Pkg.Resolve.FieldValue}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Resolve/fieldvalues.jl:38
...
Stacktrace:
[1] zero(::Type{Any}) at ./missing.jl:105
[2] _zeros_eltypes at /workspace/srcdir/usr/share/julia/stdlib/v1.5/SparseArrays/src/higherorderfns.jl:204 [inlined]
[3] _noshapecheck_map(::typeof(+), ::SparseArrays.SparseMatrixCSC{Any,Int64}, ::SparseArrays.SparseMatrixCSC{Float64,Int64}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/SparseArrays/src/higherorderfns.jl:159
[4] map(::typeof(+), ::SparseArrays.SparseMatrixCSC{Any,Int64}, ::SparseArrays.SparseMatrixCSC{Float64,Int64}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/SparseArrays/src/higherorderfns.jl:1153
[5] +(::SparseArrays.SparseMatrixCSC{Any,Int64}, ::SparseArrays.SparseMatrixCSC{Float64,Int64}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/SparseArrays/src/sparsematrix.jl:1679
[6] addVinv(::JWAS.MME) at /home/pkgeval/.julia/packages/JWAS/X2ZiX/src/1.JWAS/src/buildMME/random_effects.jl:205
[7] getMME(::JWAS.MME, ::DataFrame) at /home/pkgeval/.julia/packages/JWAS/X2ZiX/src/1.JWAS/src/buildMME/build_MME.jl:261
[8] init_mixed_model_equations(::JWAS.MME, ::DataFrame, ::Bool) at /home/pkgeval/.julia/packages/JWAS/X2ZiX/src/1.JWAS/src/JWAS.jl:578
[9] runMCMC(::JWAS.MME, ::DataFrame; heterogeneous_residuals::Bool, chain_length::Int64, starting_value::Bool, burnin::Int64, output_samples_frequency::Int64, update_priors_frequency::Int64, methods::String, estimate_variance::Bool, Pi::Float64, estimatePi::Bool, estimateScale::Bool, single_step_analysis::Bool, pedigree::Bool, categorical_trait::Bool, missing_phenotypes::Bool, constraint::Bool, causal_structure::Bool, outputEBV::Bool, output_heritability::Bool, seed::Int64, printout_model_info::Bool, printout_frequency::Int64, big_memory::Bool, double_precision::Bool, output_samples_file::String, output_samples_for_all_parameters::Bool) at /home/pkgeval/.julia/packages/JWAS/X2ZiX/src/1.JWAS/src/JWAS.jl:249
[10] top-level scope at /home/pkgeval/.julia/packages/JWAS/X2ZiX/test/test_BayesianAlphabet.jl:100
[11] include(::String) at ./client.jl:441
[12] top-level scope at /home/pkgeval/.julia/packages/JWAS/X2ZiX/test/runtests.jl:3
[13] include(::String) at ./client.jl:441
[14] top-level scope at none:6
in expression starting at /home/pkgeval/.julia/packages/JWAS/X2ZiX/test/test_BayesianAlphabet.jl:17
in expression starting at /home/pkgeval/.julia/packages/JWAS/X2ZiX/test/runtests.jl:3
ERROR: Package JWAS errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:53
[2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1523
[3] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:316
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:303
[5] #test#68 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:297 [inlined]
[6] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:297 [inlined]
[7] #test#67 at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:296 [inlined]
[8] test at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:296 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:295
[10] test(::String) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:295
[11] top-level scope at none:13