-
Notifications
You must be signed in to change notification settings - Fork 5
/
1.5.0-DEV-ed177d17d6.log
355 lines (305 loc) · 18.4 KB
/
1.5.0-DEV-ed177d17d6.log
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
Julia Version 1.5.0-DEV.158
Commit ed177d17d6 (2020-01-27 16:45 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed SortingAlgorithms ─────────── v0.3.1
Installed Parsers ───────────────────── v0.3.10
Installed Compat ────────────────────── v3.2.0
Installed Arpack ────────────────────── v0.4.0
Installed QuadGK ────────────────────── v2.3.1
Installed StatsFuns ─────────────────── v0.9.3
Installed Distributions ─────────────── v0.21.12
Installed JWAS ──────────────────────── v0.7.3
Installed OpenBLAS_jll ──────────────── v0.3.7+4
Installed OpenSpecFun_jll ───────────── v0.5.3+1
Installed Arpack_jll ────────────────── v3.5.0+2
Installed BinaryProvider ────────────── v0.5.8
Installed Tables ────────────────────── v0.2.11
Installed OrderedCollections ────────── v1.1.0
Installed FilePathsBase ─────────────── v0.7.0
Installed WeakRefStrings ────────────── v0.6.2
Installed SpecialFunctions ──────────── v0.9.0
Installed StatsBase ─────────────────── v0.32.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed DataValueInterfaces ───────── v1.0.0
Installed DataStructures ────────────── v0.17.9
Installed Missings ──────────────────── v0.4.3
Installed JSON ──────────────────────── v0.21.0
Installed CategoricalArrays ─────────── v0.7.7
Installed PooledArrays ──────────────── v0.5.3
Installed TableTraits ───────────────── v1.0.0
Installed DataAPI ───────────────────── v1.1.0
Installed FillArrays ────────────────── v0.8.4
Installed DataFrames ────────────────── v0.20.0
Installed InvertedIndices ───────────── v1.0.0
Installed ProgressMeter ─────────────── v1.2.0
Installed Reexport ──────────────────── v0.2.0
Installed PDMats ────────────────────── v0.9.11
Installed Rmath ─────────────────────── v0.6.0
Installed CSV ───────────────────────── v0.5.22
Updating `~/.julia/environments/v1.5/Project.toml`
[c9a035f4] + JWAS v0.7.3
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 v0.5.22
[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 v0.21.12
[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 v0.7.3
[e1d29d7a] + Missings v0.4.3
[4536629a] + OpenBLAS_jll v0.3.7+4
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.11
[69de0a69] + Parsers v0.3.10
[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`
Updating `/tmp/jl_i788MB/Project.toml`
[no changes]
Updating `/tmp/jl_i788MB/Manifest.toml`
[no changes]
Testing JWAS
Updating `/tmp/jl_orsYGD/Project.toml`
[no changes]
Updating `/tmp/jl_orsYGD/Manifest.toml`
[no changes]
Running sandbox
Status `/tmp/jl_orsYGD/Project.toml`
[336ed68f] CSV v0.5.22
[a93c6f00] DataFrames v0.20.0
[31c24e10] Distributions v0.21.12
[c9a035f4] JWAS v0.7.3
[92933f4c] ProgressMeter v1.2.0
[2913bbd2] StatsBase v0.32.0
[8bb1440f] DelimitedFiles
[b77e0a4c] InteractiveUtils
[37e2e46d] LinearAlgebra
[de0858da] Printf
[9a3f8284] Random
[2f01184e] SparseArrays
[8dfed614] Test
The delimiter in pedigree.txt is ','.
coding pedigree... 8%|██▋ | ETA: 0:00:01[Kcoding pedigree... 100%|████████████████████████████████| Time: 0:00:00[K
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: 0:04:39[Krunning MCMC for BayesC... 2%|▌ | ETA: 0:03:10[Krunning MCMC for BayesC... 10%|██▌ | ETA: 0:01:18[Krunning MCMC for BayesC... 20%|█████ | ETA: 0:00:37[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.158
Commit ed177d17d6 (2020-01-27 16:45 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
JULIA_PKGEVAL = true
JULIA_LOAD_PATH = @:/tmp/jl_orsYGD
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.
Progress: 33%|█████████████▋ | ETA: 0:00:00[KProgress: 100%|█████████████████████████████████████████| Time: 0:00:00[K
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 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/LibGit2/src/oid.jl:220
...
Stacktrace:
[1] zero(::Type{Any}) at ./missing.jl:105
[2] _zeros_eltypes at /buildworker/worker/package_linux64/build/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 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/SparseArrays/src/higherorderfns.jl:159
[4] map(::typeof(+), ::SparseArrays.SparseMatrixCSC{Any,Int64}, ::SparseArrays.SparseMatrixCSC{Float32,Int64}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/SparseArrays/src/higherorderfns.jl:1153
[5] +(::SparseArrays.SparseMatrixCSC{Any,Int64}, ::SparseArrays.SparseMatrixCSC{Float32,Int64}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/SparseArrays/src/sparsematrix.jl:1648
[6] addVinv(::JWAS.MME) at /home/pkgeval/.julia/packages/JWAS/SvVxa/src/1.JWAS/src/buildMME/random_effects.jl:205
[7] getMME(::JWAS.MME, ::DataFrame) at /home/pkgeval/.julia/packages/JWAS/SvVxa/src/1.JWAS/src/buildMME/build_MME.jl:264
[8] init_mixed_model_equations(::JWAS.MME, ::DataFrame, ::Bool) at /home/pkgeval/.julia/packages/JWAS/SvVxa/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/SvVxa/src/1.JWAS/src/JWAS.jl:234
[10] top-level scope at /home/pkgeval/.julia/packages/JWAS/SvVxa/test/test_BayesianAlphabet.jl:100
[11] include(::String) at ./client.jl:439
[12] top-level scope at /home/pkgeval/.julia/packages/JWAS/SvVxa/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/SvVxa/test/test_BayesianAlphabet.jl:17
in expression starting at /home/pkgeval/.julia/packages/JWAS/SvVxa/test/runtests.jl:3
err = ProcessFailedException(Base.Process[Process(`/opt/julia/bin/julia -Cnative -J/opt/julia/lib/julia/sys.so -g1 --code-coverage=none --color=no --compiled-modules=yes --check-bounds=yes --inline=yes --startup-file=no --track-allocation=none --eval 'append!(empty!(Base.DEPOT_PATH), ["/home/pkgeval/.julia", "/opt/julia/local/share/julia", "/opt/julia/share/julia", "/usr/local/share/julia"])
append!(empty!(Base.DL_LOAD_PATH), String[])
cd("/home/pkgeval/.julia/packages/JWAS/SvVxa/test")
append!(empty!(ARGS), String[])
include("/home/pkgeval/.julia/packages/JWAS/SvVxa/test/runtests.jl")
'`, ProcessExited(1))])
ERROR: Package JWAS errored during testing
Stacktrace:
[1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:54
[2] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1471
[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 /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:313
[4] test(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:300
[5] #test#66 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:294 [inlined]
[6] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:294 [inlined]
[7] #test#65 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:293 [inlined]
[8] test at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:293 [inlined]
[9] test(::String; kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:292
[10] test(::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:292
[11] top-level scope at none:13