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1.5.0-DEV-f014071421.log
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Julia Version 1.5.0-DEV.232
Commit f014071421 (2020-02-03 21:36 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 SortingAlgorithms ─────────── v0.3.1
Installed Arpack_jll ────────────────── v3.5.0+2
Installed WeakRefStrings ────────────── v0.6.2
Installed FillArrays ────────────────── v0.8.4
Installed TableTraits ───────────────── v1.0.0
Installed StatsFuns ─────────────────── v0.9.3
Installed QuadGK ────────────────────── v2.3.1
Installed JWAS ──────────────────────── v0.7.4
Installed ProgressMeter ─────────────── v1.2.0
Installed Missings ──────────────────── v0.4.3
Installed Reexport ──────────────────── v0.2.0
Installed Rmath ─────────────────────── v0.6.0
Installed FilePathsBase ─────────────── v0.7.0
Installed SpecialFunctions ──────────── v0.9.0
Installed CategoricalArrays ─────────── v0.7.7
Installed OpenBLAS_jll ──────────────── v0.3.7+5
Installed DataValueInterfaces ───────── v1.0.0
Installed InvertedIndices ───────────── v1.0.0
Installed JSON ──────────────────────── v0.21.0
Installed Distributions ─────────────── v0.22.4
Installed StatsBase ─────────────────── v0.32.0
Installed PDMats ────────────────────── v0.9.11
Installed Arpack ────────────────────── v0.4.0
Installed DataAPI ───────────────────── v1.1.0
Installed BinaryProvider ────────────── v0.5.8
Installed DataFrames ────────────────── v0.20.0
Installed DataStructures ────────────── v0.17.9
Installed Parsers ───────────────────── v0.3.11
Installed PooledArrays ──────────────── v0.5.3
Installed OpenSpecFun_jll ───────────── v0.5.3+1
Installed Tables ────────────────────── v0.2.11
Installed Compat ────────────────────── v3.2.0
Installed OrderedCollections ────────── v1.1.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed CSV ───────────────────────── v0.5.23
#=#=# ######################################################################## 100.0%
#=#=# # 2.7%###### 9.2%############## 19.6%####################### 32.5%################################ 45.5%########################################## 59.6%####################################################### 77.6%######################################################################## 100.0%
#=#=# ############################################# 63.8%######################################################################## 100.0%
Updating `~/.julia/environments/v1.5/Project.toml`
[c9a035f4] + JWAS v0.7.4
Updating `~/.julia/environments/v1.5/Manifest.toml`
[7d9fca2a] + Arpack v0.4.0
[68821587] + Arpack_jll v3.5.0+2
[b99e7846] + BinaryProvider v0.5.8
[336ed68f] + CSV v0.5.23
[324d7699] + CategoricalArrays v0.7.7
[34da2185] + Compat v3.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.20.0
[864edb3b] + DataStructures v0.17.9
[e2d170a0] + DataValueInterfaces v1.0.0
[31c24e10] + Distributions v0.22.4
[48062228] + FilePathsBase v0.7.0
[1a297f60] + FillArrays v0.8.4
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[c9a035f4] + JWAS v0.7.4
[e1d29d7a] + Missings v0.4.3
[4536629a] + OpenBLAS_jll v0.3.7+5
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.11
[69de0a69] + Parsers v0.3.11
[2dfb63ee] + PooledArrays v0.5.3
[92933f4c] + ProgressMeter v1.2.0
[1fd47b50] + QuadGK v2.3.1
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.6.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.9.3
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[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
Building Rmath → `~/.julia/packages/Rmath/BoBag/deps/build.log`
Testing JWAS
Status `/tmp/jl_BCOnyh/Manifest.toml`
[7d9fca2a] Arpack v0.4.0
[68821587] Arpack_jll v3.5.0+2
[b99e7846] BinaryProvider v0.5.8
[336ed68f] CSV v0.5.23
[324d7699] CategoricalArrays v0.7.7
[34da2185] Compat v3.2.0
[9a962f9c] DataAPI v1.1.0
[a93c6f00] DataFrames v0.20.0
[864edb3b] DataStructures v0.17.9
[e2d170a0] DataValueInterfaces v1.0.0
[31c24e10] Distributions v0.22.4
[48062228] FilePathsBase v0.7.0
[1a297f60] FillArrays v0.8.4
[41ab1584] InvertedIndices v1.0.0
[82899510] IteratorInterfaceExtensions v1.0.0
[682c06a0] JSON v0.21.0
[c9a035f4] JWAS v0.7.4
[e1d29d7a] Missings v0.4.3
[4536629a] OpenBLAS_jll v0.3.7+5
[efe28fd5] OpenSpecFun_jll v0.5.3+1
[bac558e1] OrderedCollections v1.1.0
[90014a1f] PDMats v0.9.11
[69de0a69] Parsers v0.3.11
[2dfb63ee] PooledArrays v0.5.3
[92933f4c] ProgressMeter v1.2.0
[1fd47b50] QuadGK v2.3.1
[189a3867] Reexport v0.2.0
[79098fc4] Rmath v0.6.0
[a2af1166] SortingAlgorithms v0.3.1
[276daf66] SpecialFunctions v0.9.0
[2913bbd2] StatsBase v0.32.0
[4c63d2b9] StatsFuns v0.9.3
[3783bdb8] TableTraits v1.0.0
[bd369af6] Tables v0.2.11
[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 BayesC 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.
The prior for marker effects variance is calculated from the genetic variance and π.
The mean of the prior for the marker effects variance is: 0.492462
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 BayesC
complete genomic data
(i.e., non-single-step analysis)
chain_length 100
burnin 0
estimatePi true
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
genetic variances (genomic): 1.000
marker effect variances: 0.492
π 0.0
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 BayesC... 1%|▎ | ETA: 0:05:13[Krunning MCMC for BayesC... 2%|▌ | ETA: 0:03:48[Krunning MCMC for BayesC... 10%|██▌ | ETA: 0:01:22[Krunning MCMC for BayesC... 20%|█████ | ETA: 0:00:39[K
Posterior means at iteration: 50
Residual variance: 2.087779
Posterior means at iteration: 100
Residual variance: 1.649025
running MCMC for BayesC...100%|█████████████████████████| Time: 0:00:09[K
The version of Julia and Platform in use:
Julia Version 1.5.0-DEV.232
Commit f014071421 (2020-02-03 21:36 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_BCOnyh
The analysis has finished. Results are saved in the returned variable and text files. MCMC samples are saved in text files.
Compute the model frequency for each marker (the probability the marker is included in the model).
5×2 DataFrame
│ Row │ marker_ID │ modelfrequency │
│ │ Abstract… │ Float64 │
├─────┼───────────┼────────────────┤
│ 1 │ m1 │ 0.7 │
│ 2 │ m2 │ 0.5 │
│ 3 │ m3 │ 0.6 │
│ 4 │ m4 │ 0.2 │
│ 5 │ m5 │ 0.4 │
Compute the posterior probability of association of the genomic window that explains more than 0.001 of the total genetic variance.
3×10 DataFrame. Omitted printing of 3 columns
│ Row │ window │ chr │ wStart │ wEnd │ start_SNP │ end_SNP │ numSNP │
│ │ Int64 │ String │ Int64 │ Int64 │ Int64 │ Int64 │ Int64 │
├─────┼────────┼────────┼─────────┼─────────┼───────────┼─────────┼────────┤
│ 1 │ 1 │ 1 │ 0 │ 1000000 │ 16977 │ 434311 │ 2 │
│ 2 │ 2 │ 1 │ 1000000 │ 2000000 │ 1025513 │ 1025513 │ 1 │
│ 3 │ 3 │ 2 │ 0 │ 1000000 │ 70350 │ 101135 │ 2 │
Test multi-trait BayesC 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{LibGit2.GitHash}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/LibGit2/src/oid.jl:220
...
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{Float32,Int64}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/SparseArrays/src/higherorderfns.jl:159
[4] map(::typeof(+), ::SparseArrays.SparseMatrixCSC{Any,Int64}, ::SparseArrays.SparseMatrixCSC{Float32,Int64}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/SparseArrays/src/higherorderfns.jl:1153
[5] +(::SparseArrays.SparseMatrixCSC{Any,Int64}, ::SparseArrays.SparseMatrixCSC{Float32,Int64}) at /workspace/srcdir/usr/share/julia/stdlib/v1.5/SparseArrays/src/sparsematrix.jl:1648
[6] addVinv(::JWAS.MME) at /home/pkgeval/.julia/packages/JWAS/eHpWF/src/1.JWAS/src/buildMME/random_effects.jl:205
[7] getMME(::JWAS.MME, ::DataFrame) at /home/pkgeval/.julia/packages/JWAS/eHpWF/src/1.JWAS/src/buildMME/build_MME.jl:264
[8] init_mixed_model_equations(::JWAS.MME, ::DataFrame, ::Bool) at /home/pkgeval/.julia/packages/JWAS/eHpWF/src/1.JWAS/src/JWAS.jl:565
[9] runMCMC(::JWAS.MME, ::DataFrame; heterogeneous_residuals::Bool, chain_length::Int64, starting_value::Bool, burnin::Int64, output_samples_frequency::Int64, output_samples_file::String, 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) at /home/pkgeval/.julia/packages/JWAS/eHpWF/src/1.JWAS/src/JWAS.jl:234
[10] top-level scope at /home/pkgeval/.julia/packages/JWAS/eHpWF/test/test_BayesianAlphabet.jl:100
[11] include(::String) at ./client.jl:439
[12] top-level scope at /home/pkgeval/.julia/packages/JWAS/eHpWF/test/runtests.jl:3
[13] include(::String) at ./client.jl:439
[14] top-level scope at none:6
in expression starting at /home/pkgeval/.julia/packages/JWAS/eHpWF/test/test_BayesianAlphabet.jl:17
in expression starting at /home/pkgeval/.julia/packages/JWAS/eHpWF/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:1503
[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