Package evaluation to test VCFTools on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-04T19:08:38.069 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.17s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed MacroTools ────────────── v0.5.16 Installed CompositionsBase ──────── v0.1.2 Installed CommonSolve ───────────── v0.2.4 Installed FillArrays ────────────── v1.14.0 Installed DataStructures ────────── v0.19.2 Installed ConstructionBase ──────── v1.6.0 Installed CodecZlib ─────────────── v0.7.8 Installed HypergeometricFunctions ─ v0.3.28 Installed AliasTables ───────────── v1.1.3 Installed TranscodingStreams ────── v0.11.3 Installed DelimitedFiles ────────── v1.9.1 Installed VCFTools ──────────────── v0.2.10 Installed DataAPI ───────────────── v1.16.0 Installed OrderedCollections ────── v1.8.1 Installed Combinatorics ─────────── v1.0.3 Installed StatsBase ─────────────── v0.34.7 Installed SIMD ──────────────────── v3.7.2 Installed HypothesisTests ───────── v0.11.6 Installed Statistics ────────────── v1.11.1 Installed StatsAPI ──────────────── v1.7.1 Installed IrrationalConstants ───── v0.2.6 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed ProgressMeter ─────────── v1.11.0 Installed QuadGK ────────────────── v2.11.2 Installed PrecompileTools ───────── v1.3.3 Installed LogExpFunctions ───────── v0.3.29 Installed PtrArrays ─────────────── v1.3.0 Installed Roots ─────────────────── v2.2.10 Installed Rmath ─────────────────── v0.9.0 Installed SpecialFunctions ──────── v2.6.1 Installed BioGenerics ───────────── v0.1.5 Installed StatsFuns ─────────────── v1.5.2 Installed BufferedStreams ───────── v1.2.2 Installed InverseFunctions ──────── v0.1.17 Installed Reexport ──────────────── v1.2.2 Installed Distributions ─────────── v0.25.122 Installed JLLWrappers ───────────── v1.7.1 Installed Missings ──────────────── v1.2.0 Installed Preferences ───────────── v1.5.0 Installed PDMats ────────────────── v0.11.36 Installed Automa ────────────────── v1.1.0 Installed BGZFStreams ───────────── v0.3.2 Installed SortingAlgorithms ─────── v1.2.2 Installed VariantCallFormat ─────── v0.5.9 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.42 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.2 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.14.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.7 [4c63d2b9] + StatsFuns v1.5.2 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf 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 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 8.17s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4528.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 3971.3 ms ✓ MacroTools 740.9 ms ✓ Reexport 1054.2 ms ✓ Statistics 810.5 ms ✓ DataAPI 1073.8 ms ✓ ConstructionBase 2007.2 ms ✓ IrrationalConstants 856.5 ms ✓ StatsAPI 1214.3 ms ✓ OrderedCollections 869.9 ms ✓ InverseFunctions 781.8 ms ✓ CompositionsBase 1095.0 ms ✓ DocStringExtensions 1965.6 ms ✓ Combinatorics 2041.9 ms ✓ FillArrays 961.3 ms ✓ BufferedStreams 766.1 ms ✓ PtrArrays 711.4 ms ✓ CommonSolve 1224.5 ms ✓ TranscodingStreams 1202.2 ms ✓ SuiteSparse 939.0 ms ✓ DelimitedFiles 1699.8 ms ✓ ProgressMeter 1097.2 ms ✓ Preferences 1547.1 ms ✓ Statistics → SparseArraysExt 947.0 ms ✓ Missings 764.0 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3485.0 ms ✓ DataStructures 789.0 ms ✓ InverseFunctions → InverseFunctionsDatesExt 764.2 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1341.0 ms ✓ LogExpFunctions 1489.2 ms ✓ FillArrays → FillArraysSparseArraysExt 908.2 ms ✓ FillArrays → FillArraysStatisticsExt 917.9 ms ✓ AliasTables 878.9 ms ✓ BioGenerics 915.3 ms ✓ CodecZlib 1792.5 ms ✓ PDMats 1164.8 ms ✓ JLLWrappers 896.3 ms ✓ PrecompileTools 1035.0 ms ✓ SortingAlgorithms 2203.7 ms ✓ QuadGK 4602.9 ms ✓ Accessors 741.4 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 911.0 ms ✓ BGZFStreams 1349.7 ms ✓ FillArrays → FillArraysPDMatsExt 1374.1 ms ✓ Rmath_jll 1411.1 ms ✓ OpenSpecFun_jll 16421.9 ms ✓ SIMD 4358.0 ms ✓ StatsBase 2434.6 ms ✓ Accessors → LinearAlgebraExt 1415.4 ms ✓ Rmath 4880.1 ms ✓ SpecialFunctions 21307.4 ms ✓ Automa 1374.6 ms ✓ PDMats → StatsBaseExt 6709.5 ms ✓ Roots 2424.8 ms ✓ HypergeometricFunctions 18948.1 ms ✓ VariantCallFormat 2715.5 ms ✓ StatsFuns 957.0 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 8809.4 ms ✓ Distributions 4046.9 ms ✓ HypothesisTests 6348.3 ms ✓ VCFTools 59 dependencies successfully precompiled in 163 seconds. 11 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 179.05s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_OJHLqo/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.7 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_OJHLqo/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.2 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.14.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.7 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v1.0.0 [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 [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 v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [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 v8.16.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+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 v1.67.1+0 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 8.1s Test Summary: | Pass Total Time openvcf | 4 4 2.8s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.5s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.2s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:30:30 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 13.495165 seconds (10.25 M allocations: 576.995 MiB, 4.62% gc time, 96.07% compilation time: 19% of which was recompilation) 0.427574 seconds (2.40 M allocations: 143.761 MiB, 12.38% gc time, 18.69% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:30:22 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.146968 seconds (4.09 M allocations: 241.948 MiB, 2.39% gc time, 85.48% compilation time) 0.429320 seconds (2.38 M allocations: 143.474 MiB, 6.35% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 21.2s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.7s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 5.8s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:16:43 Progress: 0%|▏ | ETA: 0:16:38 Progress: 0%|▏ | ETA: 0:16:32 Progress: 0%|▏ | ETA: 0:16:28 Progress: 1%|▎ | ETA: 0:16:25 Progress: 1%|▎ | ETA: 0:16:23 Progress: 1%|▎ | ETA: 0:16:24 Progress: 1%|▍ | ETA: 0:16:20 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100%|█████████████████████████████████████████| Time: 0:01:42 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:49:07 Progress: 20%|████████▏ | ETA: 0:06:48 Progress: 40%|████████████████▋ | ETA: 0:02:30 Progress: 62%|█████████████████████████▌ | ETA: 0:01:03 Progress: 84%|██████████████████████████████████▍ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: 823 records are matched 218.024823 seconds (2.01 G allocations: 106.139 GiB, 6.41% gc time, 0.55% compilation time: 5% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:06 Progress: 0%|▏ | ETA: 0:16:52 Progress: 0%|▏ | ETA: 0:16:07 Progress: 0%|▏ | ETA: 0:15:54 Progress: 1%|▎ | ETA: 0:15:28 Progress: 1%|▎ | ETA: 0:15:41 Progress: 1%|▎ | ETA: 0:15:47 Progress: 1%|▍ | ETA: 0:15:51 Progress: 1%|▍ | ETA: 0:15:51 Progress: 1%|▌ | ETA: 0:15:52 Progress: 1%|▌ | ETA: 0:15:53 Progress: 1%|▌ | ETA: 0:15:54 Progress: 1%|▋ | ETA: 0:15:56 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21%|████████▌ | ETA: 0:06:29 Progress: 42%|█████████████████▍ | ETA: 0:02:20 Progress: 64%|██████████████████████████▍ | ETA: 0:00:58 Progress: 87%|███████████████████████████████████▉ | ETA: 0:00:15 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 488 records are matched 219.061871 seconds (2.01 G allocations: 106.121 GiB, 6.40% gc time, 0.35% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:16:51 Progress: 0%|▏ | ETA: 0:16:49 Progress: 0%|▏ | ETA: 0:16:49 Progress: 0%|▏ | ETA: 0:16:48 Progress: 0%|▎ | ETA: 0:16:47 Progress: 1%|▎ | ETA: 0:16:43 Progress: 1%|▎ | ETA: 0:16:39 Progress: 1%|▍ | ETA: 0:16:38 Progress: 1%|▍ | ETA: 0:16:36 Progress: 1%|▍ | ETA: 0:16:34 Progress: 1%|▌ | ETA: 0:16:34 Progress: 1%|▌ | ETA: 0:16:32 Progress: 1%|▌ | ETA: 0:16:31 Progress: 1%|▋ | ETA: 0:16:31 Progress: 1%|▋ | ETA: 0:16:30 Progress: 2%|▋ | ETA: 0:16:29 Progress: 2%|▊ | ETA: 0:16:28 Progress: 2%|▊ | ETA: 0:16:27 Progress: 2%|▊ | ETA: 0:16:26 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8%|███▌ | ETA: 0:15:16 Progress: 9%|███▌ | ETA: 0:15:15 Progress: 9%|███▌ | ETA: 0:15:14 Progress: 9%|███▋ | ETA: 0:15:12 Progress: 9%|███▋ | ETA: 0:15:11 Progress: 9%|███▋ | ETA: 0:15:10 Progress: 9%|███▊ | ETA: 0:15:10 Progress: 9%|███▊ | ETA: 0:15:09 Progress: 9%|███▊ | ETA: 0:15:08 Progress: 9%|███▉ | ETA: 0:15:07 Progress: 9%|███▉ | ETA: 0:15:06 Progress: 10%|███▉ | ETA: 0:15:05 Progress: 10%|████ | ETA: 0:15:03 Progress: 10%|████ | ETA: 0:15:02 Progress: 10%|████ | ETA: 0:15:01 Progress: 10%|████▏ | ETA: 0:15:00 Progress: 10%|████▏ | ETA: 0:14:59 Progress: 10%|████▏ | ETA: 0:14:58 Progress: 10%|████▎ | ETA: 0:14:56 Progress: 100%|█████████████████████████████████████████| Time: 0:01:43 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:57:34 Progress: 20%|████████▎ | ETA: 0:06:48 Progress: 41%|████████████████▊ | ETA: 0:02:28 Progress: 63%|█████████████████████████▉ | ETA: 0:01:01 Progress: 85%|██████████████████████████████████▉ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 0 records are matched 218.835319 seconds (2.01 G allocations: 106.120 GiB, 6.51% gc time, 0.38% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m03.7s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:52:12 Progress: 19%|███████▉ | ETA: 0:07:05 Progress: 39%|████████████████▏ | ETA: 0:02:38 Progress: 61%|████████████████████████▉ | ETA: 0:01:07 Progress: 83%|██████████████████████████████████▏ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 833 records are matched 115.142637 seconds (1.02 G allocations: 53.885 GiB, 6.46% gc time, 0.49% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:59:49 Progress: 20%|████████▎ | ETA: 0:06:45 Progress: 42%|█████████████████▏ | ETA: 0:02:23 Progress: 63%|██████████████████████████ | ETA: 0:01:00 Progress: 85%|███████████████████████████████████ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 493 records are matched 115.805218 seconds (1.02 G allocations: 53.885 GiB, 6.37% gc time, 0.51% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:47:49 Progress: 20%|████████▍ | ETA: 0:06:33 Progress: 42%|█████████████████▎ | ETA: 0:02:20 Progress: 65%|██████████████████████████▌ | ETA: 0:00:57 Progress: 88%|████████████████████████████████████▏ | ETA: 0:00:14 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: 0 records are matched 114.458249 seconds (1.02 G allocations: 53.885 GiB, 6.39% gc time, 0.49% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m47.6s 1.165809 seconds (1.29 M allocations: 69.649 MiB, 4.61% gc time, 84.35% compilation time) 0.922015 seconds (1.19 M allocations: 66.173 MiB, 79.28% compilation time) 1.007098 seconds (1.19 M allocations: 65.201 MiB, 3.72% gc time, 76.39% compilation time) 0.418952 seconds (211.94 k allocations: 11.126 MiB, 99.92% compilation time) 0.009925 seconds (6.38 k allocations: 392.211 KiB, 95.48% compilation time) 0.008599 seconds (2.65 k allocations: 165.508 KiB, 95.98% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.4s 0.878116 seconds (979.59 k allocations: 54.659 MiB, 80.38% compilation time) 0.865609 seconds (877.98 k allocations: 51.620 MiB, 4.05% gc time, 74.72% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.2s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.116475 seconds (525.56 k allocations: 30.681 MiB, 16.53% gc time, 25.26% compilation time) 0.627971 seconds (651.33 k allocations: 37.705 MiB, 88.51% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:72 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:176 0.080652 seconds (520.58 k allocations: 32.160 MiB, 18.78% gc time) 0.502636 seconds (594.53 k allocations: 36.350 MiB, 86.38% compilation time) ┌ Warning: Reached end of record! Columns 1357-1400 are filled with 0.0s and are NOT haplotypes! └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:414 ┌ Warning: Reached end of record! Rows 1357-1400 are filled with 0.0s and are NOT haplotypes! └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:501 0.621939 seconds (1.56 M allocations: 62.084 MiB, 79.94% gc time, 2.75% compilation time: <1% of which was recompilation) 0.568216 seconds (1.71 M allocations: 70.291 MiB, 80.71% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:672 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:787 Test Summary: | Pass Total Time convert to transpose functions | 13 13 6.9s Test Summary: | Pass Total Time record info | 14 14 4.8s Test Summary: | Pass Total Time write VCF | 3 3 4.3s 2.127656 seconds (4.80 M allocations: 296.487 MiB, 3.16% gc time, 56.18% compilation time) 1.041836 seconds (2.39 M allocations: 142.653 MiB, 3.42% gc time, 21.49% compilation time) 0.966952 seconds (4.42 M allocations: 276.461 MiB, 4.19% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.0s 1.009311 seconds (610.43 k allocations: 33.747 MiB, 1.76% gc time, 44.60% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.9s Test Summary: | Pass Total Time filter_chr | 4 4 1.6s Progress: 0%|▏ | ETA: 0:22:31 Progress: 1%|▍ | ETA: 0:20:35 Progress: 1%|▌ | ETA: 0:20:07 Progress: 2%|▊ | ETA: 0:19:38 Progress: 2%|▉ | ETA: 0:19:18 Progress: 3%|█ | ETA: 0:19:12 Progress: 3%|█▎ | ETA: 0:19:09 Progress: 3%|█▍ | ETA: 0:19:06 Progress: 4%|█▋ | ETA: 0:18:58 Progress: 4%|█▊ | ETA: 0:18:42 Progress: 5%|██ | ETA: 0:18:39 Progress: 5%|██▏ | ETA: 0:18:35 Progress: 6%|██▎ | ETA: 0:18:30 Progress: 6%|██▌ | ETA: 0:18:26 Progress: 7%|██▋ | ETA: 0:18:10 Progress: 7%|██▉ | ETA: 0:18:07 Progress: 7%|███ | ETA: 0:18:04 Progress: 8%|███▎ | ETA: 0:18:00 Progress: 8%|███▍ | ETA: 0:17:56 Progress: 9%|███▋ | ETA: 0:17:44 Progress: 9%|███▊ | ETA: 0:17:34 Progress: 10%|████ | ETA: 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A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 331 running 1 of 1 signal (10): User defined signal 1 == at ./strings/string.jl:187 [inlined] isequal at ./operators.jl:178 [inlined] #_#59 at ./operators.jl:1203 [inlined] Fix at ./operators.jl:1203 [inlined] findnext at ./array.jl:2449 [inlined] findfirst at ./array.jl:2500 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:74 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:44 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x73701751c0a6) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_invoke at /source/src/gf.c:4123 jl_toplevel_eval_flex at /source/src/toplevel.c:731 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2994 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3054 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x7370351fea42) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2994 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3054 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_36779.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:577 jfptr__start_63030.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x73703e67c249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Progress: 97%|███████████████████████████████████████▋ | ETA: 0:00:36┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007370245fc010 Total snapshots: 605. Utilization: 100% ╎605 @Base/client.jl:577 _start() ╎ 605 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 605 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 605 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 605 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 605 @Base/loading.jl:3054 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 605 @Base/loading.jl:2994 include_string(mapexpr::typeof(identity), m… ╎ ╎ 605 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 605 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 605 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 605 @Base/loading.jl:3054 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 605 @Base/loading.jl:2994 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 605 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 605 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 605 @Test/src/Test.jl:1961 macro expansion ╎ ╎ ╎ 605 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 605 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 80 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 13 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 13 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 7 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:964 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ators.jl:424 > 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 4 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:964 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:385 checkbounds 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:965 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + 1╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:134 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:3196 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:943 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:146 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @VCFTools/…s.jl:169 hwe(n00::Int64, n01::Int64, n1… ╎ ╎ ╎ ╎ ╎ 1 @Distributions/…:102 ccdf ╎ ╎ ╎ ╎ ╎ 1 @Distributions/…:649 ccdf ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/….jl:9 chisqccdf ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/…jl:50 gammaccdf ╎ ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/…jl:48 gammaccdf ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:856 gamma_inc ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:856 gamma_inc ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:932 _gamma_inc(a::Floa… ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:13 erfc 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:15 _erfc ╎ ╎ ╎ ╎ 56 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 55 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ 54 @Base/array.jl:2449 findnext 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 51 @Base/…ators.jl:1203 Fix ╎ ╎ ╎ ╎ ╎ 51 @Base/…tors.jl:1203 #_#59 ╎ ╎ ╎ ╎ ╎ 51 @Base/…tors.jl:178 isequal 51╎ ╎ ╎ ╎ ╎ 51 @Base/…ring.jl:187 == ╎ ╎ ╎ ╎ 1 @Base/array.jl:2450 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 4 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 4 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 4 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ ╎ 4 @Base/array.jl:2449 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:673 isequaldata 3╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 2 @VCFTools/…rt.jl:225 geno_ismissing ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:964 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:385 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:82 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3196 getindex ╎ ╎ ╎ ╎ 1 @Base/range.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:943 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:86 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/array.jl:1020 setindex! 1╎ ╎ ╎ ╎ 1 @Base/array.jl:1025 _setindex! 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 525 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 525 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 88 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 88 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 4╎ ╎ ╎ ╎ ╎ 88 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 63 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 59 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 14 @Base/array.jl:436 getindex 14╎ ╎ ╎ ╎ ╎ 14 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 42 @Base/array.jl:1345 push! ╎ ╎ ╎ ╎ ╎ 38 @Base/…ray.jl:1348 _push! 5╎ ╎ ╎ ╎ ╎ ╎ 38 @Base/…ray.jl:1205 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1158 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ay.jl:1181 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ay.jl:1101 array_new_memory 21╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1184 _growend_internal!(a::Vect… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:595 memoryref 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1186 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1189 _growend_internal!(a::Vect… 7╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ay.jl:1190 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 4 @Base/…ray.jl:1349 _push! 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ray.jl:1044 __safe_setindex! 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:215 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:49 resize_and_copy! ╎ ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:55 resize_and_copy! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1540 resize!(a::Vector{UInt8}, … ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1204 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:502 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:56 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:49 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:503 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…dvec.jl:491 all ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…dvec.jl:486 reduce ╎ ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…ics.jl:1050 reduce_and 1╎ ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…cs.jl:1065 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:584 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1454 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ ╎ 21 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 21 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 21 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 21 @BufferedStreams/…:5 readbytes! 1╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/io.jl:1167 readbytes!(s::TranscodingStr… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:209 eof 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:212 eof ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:622 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:123 makemargin! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:140 makemargin!(b… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:291 copyto! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:300 _copyto_impl! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:139 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…em.jl:28 memmove ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @CodecZlib/…:195 process(codec::GzipDec… 5╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/io.jl:1168 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 9 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/io.jl:366 peek ╎ ╎ ╎ ╎ ╎ ╎ 9 @TranscodingStreams/…:302 peek 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 8╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ls.jl:965 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:307 read ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:97 consumed! ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:98 #consumed!#1 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/io.jl:1174 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:393 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1020 setindex! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1025 _setindex! ╎ ╎ ╎ ╎ 437 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 437 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 6 @Base/array.jl:384 copy 6╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 431 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 431 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 431 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 3╎ ╎ ╎ ╎ ╎ 431 @Base/…copy.jl:104 deepcopy_internal ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:114 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:594 memoryref 44╎ ╎ ╎ ╎ ╎ 44 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 11╎ ╎ ╎ ╎ ╎ 11 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 13╎ ╎ ╎ ╎ ╎ 13 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 23╎ ╎ ╎ ╎ ╎ 300 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…opy.jl:128 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 40 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 40 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 40 @Base/…ct.jl:182 in 39╎ ╎ ╎ ╎ ╎ ╎ 40 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 44 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/boot.jl:661 Array 6╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ot.jl:649 Array 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:594 memoryref 37╎ ╎ ╎ ╎ ╎ ╎ 37 @Base/…ict.jl:86 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 187 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 57 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 57 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 57 @Base/…ct.jl:182 in 55╎ ╎ ╎ ╎ ╎ ╎ 57 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 125 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ct.jl:182 in 21╎ ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ct.jl:92 get 6╎ ╎ ╎ ╎ ╎ ╎ 104 @Base/…py.jl:104 deepcopy_internal 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 2╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…py.jl:108 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:876 isbitstype 16╎ ╎ ╎ ╎ ╎ ╎ 92 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 25 @Base/…ry.jl:193 copy(a::Memory{UnitRange… 25╎ ╎ ╎ ╎ ╎ ╎ ╎ 25 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ry.jl:194 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ry.jl:157 unsafe_copyto! 3╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ry.jl:139 unsafe_copyto! 11╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…em.jl:28 memmove 36╎ ╎ ╎ ╎ ╎ ╎ 36 @Base/…ct.jl:86 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:87 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:134 deepcopy_internal(x::Vector… 42╎ ╎ ╎ ╎ ╎ 42 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 14╎ ╎ ╎ ╎ ╎ 14 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ 3 @Base/…copy.jl:125 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…nge.jl:925 iterate 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ion.jl:637 == ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1223 wait_forever at ./task.jl:1145 jfptr_wait_forever_57186.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007a0bc52724a0 Total snapshots: 452. Utilization: 0% ╎452 @Base/task.jl:1145 wait_forever() 451╎ 452 @Base/task.jl:1223 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1223 wait_forever at ./task.jl:1145 jfptr_wait_forever_57186.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) Allocations: 23163226 (Pool: 23162518; Big: 708); GC: 21 [331] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 inflate_fast at /opt/julia/bin/../lib/julia/libz.so.1 (unknown line) inflate at /opt/julia/bin/../lib/julia/libz.so.1 (unknown line) inflate! at /home/pkgeval/.julia/packages/CodecZlib/lEc2s/src/libz.jl:127 [inlined] process at /home/pkgeval/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:195 callprocess at /home/pkgeval/.julia/packages/TranscodingStreams/O3BYF/src/stream.jl:685 #fillbuffer#7 at /home/pkgeval/.julia/packages/TranscodingStreams/O3BYF/src/stream.jl:624 fillbuffer at /home/pkgeval/.julia/packages/TranscodingStreams/O3BYF/src/stream.jl:610 [inlined] sloweof at /home/pkgeval/.julia/packages/TranscodingStreams/O3BYF/src/stream.jl:222 eof at /home/pkgeval/.julia/packages/TranscodingStreams/O3BYF/src/stream.jl:213 [inlined] readbytes! at ./io.jl:1167 readbytes! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/io.jl:5 [inlined] fillbuffer! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/bufferedinputstream.jl:71 fillbuffer! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/bufferedinputstream.jl:61 [inlined] _read! at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/ReaderHelper.jl:181 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 read! at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/ReaderHelper.jl:142 tryread! at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:76 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:87 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x73701751c0a6) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_invoke at /source/src/gf.c:4123 jl_toplevel_eval_flex at /source/src/toplevel.c:731 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2994 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3054 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x7370351fea42) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2994 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3054 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_36779.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:577 jfptr__start_63030.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x73703e67c249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Allocations: 18698896406 (Pool: 18698880583; Big: 15823); GC: 22996 PkgEval terminated after 2734.14s: test duration exceeded the time limit