Package evaluation to test VCFTools on Julia 1.14.0-DEV.2457 (6e8868916a*) started at 2026-06-28T20:16:31.291 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.66s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed CommonSolve ───────────── v0.2.9 Installed FillArrays ────────────── v1.16.0 Installed DataStructures ────────── v0.19.5 Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed DelimitedFiles ────────── v1.9.1 Installed ConstructionBase ──────── v1.6.0 Installed MacroTools ────────────── v0.5.16 Installed CodecZlib ─────────────── v0.7.8 Installed OrderedCollections ────── v1.8.2 Installed AliasTables ───────────── v1.1.3 Installed HypergeometricFunctions ─ v0.3.28 Installed TranscodingStreams ────── v0.11.3 Installed VCFTools ──────────────── v0.2.10 Installed StatsBase ─────────────── v0.34.12 Installed HypothesisTests ───────── v0.11.8 Installed DataAPI ───────────────── v1.16.0 Installed Statistics ────────────── v1.11.1 Installed Combinatorics ─────────── v1.1.0 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed LogExpFunctions ───────── v1.0.1 Installed StatsAPI ──────────────── v1.8.0 Installed PrecompileTools ───────── v1.3.4 Installed IrrationalConstants ───── v0.2.6 Installed ProgressMeter ─────────── v1.11.0 Installed QuadGK ────────────────── v2.11.3 Installed BufferedStreams ───────── v1.2.2 Installed Rmath ─────────────────── v0.9.0 Installed BioGenerics ───────────── v0.1.5 Installed Roots ─────────────────── v3.0.0 Installed InverseFunctions ──────── v0.1.17 Installed PtrArrays ─────────────── v1.4.0 Installed StatsFuns ─────────────── v2.2.0 Installed Reexport ──────────────── v1.2.2 Installed SpecialFunctions ──────── v2.8.0 Installed Distributions ─────────── v0.25.129 Installed Missings ──────────────── v1.2.0 Installed PDMats ────────────────── v0.11.40 Installed Automa ────────────────── v1.2.0 Installed DocStringExtensions ───── v0.9.5 Installed JLLWrappers ───────────── v1.8.0 Installed Preferences ───────────── v1.5.2 Installed BGZFStreams ───────────── v0.3.2 Installed SortingAlgorithms ─────── v1.2.3 Installed Accessors ─────────────── v0.1.45 Installed VariantCallFormat ─────── v0.5.9 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 v0.1.45 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.2.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.9 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.5 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.129 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.8 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.8.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [90014a1f] + PDMats v0.11.40 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.0 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.2.0 [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 v1.14.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [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 v1.5.5+2 [4536629a] + OpenBLAS_jll v0.3.33+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 9.46s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 4.9 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 3.5 s ✓ MacroTools 1.5 s ✓ InlineStrings 0.5 s ✓ Reexport 0.9 s ✓ Statistics 0.6 s ✓ DataAPI 0.9 s ✓ ConstructionBase 1.9 s ✓ IrrationalConstants 0.5 s ✓ DataValueInterfaces 0.6 s ✓ StatsAPI 1.1 s ✓ OrderedCollections 0.6 s ✓ InvertedIndices 0.6 s ✓ InverseFunctions 0.5 s ✓ CompositionsBase 0.8 s ✓ DocStringExtensions 1.7 s ✓ Combinatorics 0.7 s ✓ WorkerUtilities 2.1 s ✓ FillArrays 0.8 s ✓ BufferedStreams 0.5 s ✓ PtrArrays 0.5 s ✓ CommonSolve 1.1 s ✓ TranscodingStreams 0.5 s ✓ IteratorInterfaceExtensions 0.6 s ✓ LaTeXStrings 1.7 s ✓ Crayons 0.7 s ✓ DelimitedFiles 2.5 s ✓ PDMats 2.3 s ✓ ProgressMeter 1.6 s ✓ SentinelArrays 0.9 s ✓ Compat 1.2 s ✓ Preferences 1.9 s ✓ Statistics → SparseArraysExt 0.7 s ✓ Missings 0.9 s ✓ PooledArrays 0.5 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3.7 s ✓ DataStructures 1.6 s ✓ InverseFunctions → InverseFunctionsTestExt 1.0 s ✓ InverseFunctions → InverseFunctionsDatesExt 0.5 s ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1.1 s ✓ LogExpFunctions 2.3 s ✓ FillArrays → FillArraysSparseArraysExt 0.9 s ✓ FillArrays → FillArraysStatisticsExt 0.7 s ✓ AliasTables 0.7 s ✓ BioGenerics 0.8 s ✓ CodecZlib 0.5 s ✓ TableTraits 2.2 s ✓ FillArrays → FillArraysPDMatsExt 0.5 s ✓ Compat → CompatLinearAlgebraExt 2.0 s ✓ JLLWrappers 1.7 s ✓ PrecompileTools 1.0 s ✓ SortingAlgorithms 2.0 s ✓ QuadGK 4.6 s ✓ Accessors 0.6 s ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 0.8 s ✓ BGZFStreams 1.8 s ✓ Tables 2.2 s ✓ FilePathsBase 1.9 s ✓ Rmath_jll 1.9 s ✓ OpenSpecFun_jll 17.9 s ✓ Automa 3.6 s ✓ StringManipulation 11.2 s ✓ Parsers 5.7 s ✓ StatsBase 2.6 s ✓ Accessors → LinearAlgebraExt 2.5 s ✓ Accessors → TestExt 3.7 s ✓ FilePathsBase → FilePathsBaseTestExt 1.2 s ✓ FilePathsBase → FilePathsBaseMmapExt 2.0 s ✓ Rmath 6.2 s ✓ SpecialFunctions [ Info: Compiling VCF parser... 18.1 s ✓ VariantCallFormat 50.8 s ✓ PrettyTables 1.2 s ✓ InlineStrings → ParsersExt 2.3 s ✓ PDMats → StatsBaseExt 7.8 s ✓ Roots 2.7 s ✓ HypergeometricFunctions 104.6 s ✓ DataFrames 3.6 s ✓ WeakRefStrings 2.8 s ✓ StatsFuns 26.5 s ✓ CSV 1.3 s ✓ StatsFuns → StatsFunsInverseFunctionsExt 11.8 s ✓ Distributions 5.4 s ✓ Distributions → DistributionsTestExt 5.5 s ✓ HypothesisTests 6.6 s ✓ VCFTools 83 dependencies successfully precompiled in 383 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 420.01s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_mKHMFr/Project.toml` [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.129 [09f84164] HypothesisTests v0.11.8 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_mKHMFr/Manifest.toml` [7d9f7c33] Accessors v0.1.45 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.2.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.9 [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 v1.8.2 [864edb3b] DataStructures v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.129 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.8 [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 v1.8.0 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v1.0.1 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 ⌅ [bac558e1] OrderedCollections v1.8.2 [90014a1f] PDMats v0.11.40 [69de0a69] Parsers v2.8.6 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v3.0.0 [91c51154] SentinelArrays v1.4.10 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.8.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [4c63d2b9] StatsFuns v2.2.0 [892a3eda] StringManipulation v0.4.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.13.0 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.2.0 [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 v1.13.0 [b27032c2] LibCURL v1.0.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [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 v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.5.5+2 [deac9b47] LibCURL_jll v8.20.0+1 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.7+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 2.8s Test Summary: | Pass Total Time openvcf | 4 4 2.5s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 3.0s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 4.7s ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 ┌ 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: 1:03:21 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 19.897517 seconds (7.05 M allocations: 444.489 MiB, 2.35% gc time, 93.79% compilation time: 6% of which was recompilation) 0.576241 seconds (2.37 M allocations: 141.430 MiB, 18.57% gc time, 11.68% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:55:05 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 5.595655 seconds (3.20 M allocations: 196.619 MiB, 4.58% gc time, 87.44% compilation time: <1% of which was recompilation) 0.500288 seconds (2.37 M allocations: 141.437 MiB, 4.14% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 30.7s 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 2.0s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.5s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.2s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 1.2s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:15:27 Progress: 0%|▏ | ETA: 0:17:13 Progress: 0%|▏ | ETA: 0:17:28 Progress: 0%|▏ | ETA: 0:18:02 Progress: 0%|▎ | ETA: 0:18:17 Progress: 1%|▎ | ETA: 0:19:02 Progress: 1%|▎ | ETA: 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282.760348 seconds (2.01 G allocations: 106.048 GiB, 8.53% gc time, 0.42% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 14m15.4s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:24:10 Progress: 16%|██████▊ | ETA: 0:09:47 Progress: 35%|██████████████▍ | ETA: 0:03:36 Progress: 55%|██████████████████████▋ | ETA: 0:01:35 Progress: 75%|██████████████████████████████▉ | ETA: 0:00:39 Progress: 97%|███████████████████████████████████████▉ | ETA: 0:00:04 Progress: 100%|█████████████████████████████████████████| Time: 0:01:59 [ Info: 833 records are matched 129.630357 seconds (1.01 G allocations: 53.814 GiB, 7.24% gc time, 0.49% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:06:30 Progress: 17%|███████ | ETA: 0:09:06 Progress: 35%|██████████████▌ | ETA: 0:03:29 Progress: 57%|███████████████████████▍ | ETA: 0:01:27 Progress: 78%|████████████████████████████████▏ | ETA: 0:00:32 Progress: 99%|████████████████████████████████████████▉| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:01:57 [ Info: 493 records are matched 128.061637 seconds (1.01 G allocations: 53.813 GiB, 6.97% gc time, 0.51% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:24:43 Progress: 15%|██████▏ | ETA: 0:10:56 Progress: 35%|██████████████▏ | ETA: 0:03:40 Progress: 55%|██████████████████████▋ | ETA: 0:01:35 Progress: 74%|██████████████████████████████▏ | ETA: 0:00:42 Progress: 95%|███████████████████████████████████████ | ETA: 0:00:06 Progress: 100%|█████████████████████████████████████████| Time: 0:01:59 [ Info: 0 records are matched 129.706923 seconds (1.01 G allocations: 53.813 GiB, 6.84% gc time, 0.49% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m30.0s 1.190016 seconds (1.10 M allocations: 65.777 MiB, 1.90% gc time, 77.16% compilation time) 1.031432 seconds (1.02 M allocations: 62.853 MiB, 75.41% compilation time) 1.134821 seconds (1.02 M allocations: 61.911 MiB, 11.19% gc time, 78.45% compilation time) 0.417618 seconds (163.61 k allocations: 10.204 MiB, 99.95% compilation time) 0.011070 seconds (5.42 k allocations: 364.711 KiB, 94.57% compilation time) 0.009010 seconds (2.60 k allocations: 164.852 KiB, 92.51% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.3s 1.127291 seconds (910.99 k allocations: 55.241 MiB, 3.93% gc time, 77.13% compilation time) 0.969005 seconds (779.26 k allocations: 49.410 MiB, 74.55% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.4s Test Summary: | Pass Total Time convert_ds | 5 5 1.2s 0.190137 seconds (523.99 k allocations: 30.649 MiB, 11.90% gc time, 15.93% compilation time) 0.658101 seconds (616.67 k allocations: 37.108 MiB, 2.57% gc time, 76.77% 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 0.138302 seconds (520.01 k allocations: 32.143 MiB) 0.637930 seconds (575.18 k allocations: 35.894 MiB, 2.36% gc time, 75.78% 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 0.212699 seconds (1.30 M allocations: 54.159 MiB, 11.37% gc time, 3.96% compilation time) 0.746290 seconds (1.41 M allocations: 61.647 MiB, 76.01% 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 6.6s Test Summary: | Pass Total Time record info | 14 14 6.0s Test Summary: | Pass Total Time write VCF | 3 3 3.9s 2.353206 seconds (4.70 M allocations: 294.519 MiB, 2.49% gc time, 56.07% compilation time) 1.111705 seconds (2.38 M allocations: 142.488 MiB, 2.95% gc time, 23.24% compilation time) 1.016204 seconds (4.42 M allocations: 276.480 MiB, 4.54% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.7s 1.108679 seconds (583.54 k allocations: 33.094 MiB, 1.54% gc time, 42.52% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.0s Test Summary: | Pass Total Time filter_chr | 4 4 1.8s Progress: 0%|▏ | ETA: 0:20:47 Progress: 1%|▍ | ETA: 0:20:32 Progress: 1%|▌ | ETA: 0:20:24 Progress: 2%|▋ | ETA: 0:20:15 Progress: 2%|▉ | ETA: 0:19:56 Progress: 2%|█ | ETA: 0:20:05 Progress: 3%|█▏ | ETA: 0:20:11 Progress: 3%|█▍ | ETA: 0:20:20 Progress: 4%|█▌ | ETA: 0:20:18 Progress: 4%|█▋ | ETA: 0:20:15 Progress: 4%|█▊ | ETA: 0:20:19 Progress: 5%|██ | ETA: 0:20:18 Progress: 5%|██▏ | ETA: 0:20:13 Progress: 6%|██▎ | ETA: 0:20:11 Progress: 6%|██▌ | ETA: 0:20:06 Progress: 6%|██▋ | ETA: 0:20:01 Progress: 7%|██▊ | ETA: 0:19:56 Progress: 7%|██▉ | ETA: 0:19:53 Progress: 8%|███▏ | ETA: 0:19:48 Progress: 8%|███▎ | ETA: 0:19:44 Progress: 8%|███▍ | ETA: 0:19:38 Progress: 9%|███▋ | ETA: 0:19:33 Progress: 9%|███▊ | ETA: 0:19:27 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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 336 running 1 of 1 signal (10): User defined signal 1 GenericMemory at ./boot.jl:659:0 [inlined] array_new_memory at ./array.jl:1129:0 [inlined] _growend_internal! at ./array.jl:1209:0 (pc: 41) _growend! at ./array.jl:1233:0 [inlined] _push! at ./array.jl:1376:0 [inlined] push! at ./array.jl:1373:0 [inlined] macro expansion at /home/pkgeval/.julia/packages/Automa/fzRJn/src/codegen.jl:449:0 [inlined] _read! at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/ReaderHelper.jl:165:0 (pc: 5564) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 read! at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/ReaderHelper.jl:142:0 (pc: 2) tryread! at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:76:0 (pc: 2) iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:87:0 [inlined] iterate at ./iterators.jl:209:0 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46:0 (pc: 346) aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26:0 (pc: 1) unknown function (ip: 0x7759e5f98eb6) at (unknown file) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19:0 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2246:0 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3:0 (pc: 359) jl_invoke_oneshot at /source/src/gf.c:4361:23 ijl_eval_thunk at /source/src/toplevel.c:756:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:326:0 (pc: 1) IncludeInto at ./Base.jl:327:0 (pc: 2) jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 jl_apply at /source/src/julia.h:2406:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:757:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:947:21 ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:326:0 (pc: 1) IncludeInto at ./Base.jl:327:0 (pc: 2) jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 jl_apply at /source/src/julia.h:2406:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:757:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:947:21 ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:522:0 (pc: 1) exec_options at ./client.jl:321:0 (pc: 426) _start at ./client.jl:596:0 (pc: 295) jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 jl_apply at /source/src/julia.h:2406:12 [inlined] true_main at /source/src/jlapi.c:985:29 jl_repl_entrypoint at /source/src/jlapi.c:1152:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x775a0e8ac249) 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) Progress: 65%|██████████████████████████▊ | ETA: 0:07:24 ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Progress: 66%|██████████████████████████▉ | ETA: 0:07:19┌ 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:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007759f3bfc010 Total snapshots: 621. Utilization: 100% ╎621 @Base/client.jl:596 _start() ╎ 621 @Base/client.jl:321 exec_options(opts::Base.JLOptions) ╎ 621 @Base/boot.jl:522 eval(m::Module, e::Any) ╎ 621 @Base/Base.jl:327 (::Base.IncludeInto)(fname::String) ╎ 621 @Base/Base.jl:326 include(mapexpr::Function, mod::Module, _path::St… ╎ 621 @Base/loading.jl:3192 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 621 @Base/loading.jl:3132 include_string(mapexpr::typeof(identity), m… ╎ ╎ 621 @Base/boot.jl:522 eval(m::Module, e::Any) ╎ ╎ 621 @Base/Base.jl:327 (::Base.IncludeInto)(fname::String) ╎ ╎ 621 @Base/Base.jl:326 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 621 @Base/loading.jl:3192 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 621 @Base/loading.jl:3132 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 621 @Base/boot.jl:522 eval(m::Module, e::Any) ╎ ╎ ╎ 621 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 621 @Test/src/Test.jl:2246 macro expansion ╎ ╎ ╎ 621 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 621 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 43 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 11 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 11 @VCFTools/…ts.jl:122 gtstats(record::VariantCallForm… ╎ ╎ ╎ ╎ 8 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 3 @VCFTools/…t.jl:225 geno_ismissing(record::Variant… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:1040 getindex(A::Vector{UInt8}, i:… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tion.jl:658 ==(x::UInt8, y::UInt8) 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:1040 getindex(A::Vector{UnitRange{… ╎ ╎ ╎ ╎ ╎ 2 @Base/…ators.jl:425 >(x::Int64, y::Int64) 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 <(x::Int64, y::Int64) 1╎ ╎ ╎ ╎ 3 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1039 getindex(A::Vector{UInt8}, i:… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:391 checkbounds(A::Vector{UInt8},… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:387 checkbounds(::Type{Bool}, A::… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1040 getindex(A::Vector{UnitRange{… ╎ ╎ ╎ ╎ 31 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 30 @Base/array.jl:2528 findfirst(testf::Base.Fix2{typeo… ╎ ╎ ╎ ╎ 29 @Base/array.jl:2477 findnext(testf::Base.Fix2{typeo… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1039 getindex(A::Vector{String}, i… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:391 checkbounds(A::Vector{String}… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:1040 getindex(A::Vector{String}, i… ╎ ╎ ╎ ╎ ╎ 26 @Base/…ators.jl:1206 (::Base.Fix2{typeof(isequal),… ╎ ╎ ╎ ╎ ╎ 26 @Base/…tors.jl:1206 (::Base.Fix2{typeof(isequal),… ╎ ╎ ╎ ╎ ╎ 26 @Base/…tors.jl:178 isequal(x::String, y::String) 25╎ ╎ ╎ ╎ ╎ 26 @Base/…ring.jl:238 ==(a::String, b::String) ╎ ╎ ╎ ╎ 1 @Base/array.jl:2478 findnext(testf::Base.Fix2{typeo… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:658 ==(x::Int64, y::Int64) 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1040 getindex(A::Vector{String}, i:… ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:613 findgenokey(record::Variant… ╎ ╎ ╎ ╎ 1 @Base/array.jl:2528 findfirst(testf::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2477 findnext(testf::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:1040 getindex(A::Vector{UnitRange{… ╎ ╎ ╎ ╎ 578 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 578 @Base/…rators.jl:209 iterate(e::Base.Iterators.Enumer… ╎ ╎ ╎ ╎ 128 @BioGenerics/…jl:87 iterate(reader::VariantCallForma… ╎ ╎ ╎ ╎ 128 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 128 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:156 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2153 empty!(a::Vector{Vector{Uni… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1316 _deleteend!(a::Vector{Vecto… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:211 _unsetindex!(A::Vector{Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:667 memoryref(ref::MemoryRef{V… ╎ ╎ ╎ ╎ ╎ 103 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 46 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/…rray.jl:429 lastindex(a::Vector{Vector{U… ╎ ╎ ╎ ╎ ╎ 1 @Base/…rray.jl:394 eachindex(::IndexLinear, A:… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:1255 length(a::Vector{Vector{Un… ╎ ╎ ╎ ╎ ╎ 13 @Base/array.jl:441 getindex(::Type{UnitRange{In… 13╎ ╎ ╎ ╎ ╎ 13 @Base/boot.jl:720 Vector{UnitRange{Int64}}(::U… ╎ ╎ ╎ ╎ ╎ 28 @Base/array.jl:1373 push!(a::Vector{UnitRange{I… ╎ ╎ ╎ ╎ ╎ 26 @Base/…ray.jl:1376 _push!(a::Vector{UnitRange{… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1230 _growend!(a::Vector{UnitRa… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1232 _growend!(a::Vector{Vector… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 <(x::Int64, y::Int64) 1╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ray.jl:1233 _growend!(a::Vector{UnitRa… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1186 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1197 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:341 div(x::Int64, y::Int64) ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ay.jl:1209 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ay.jl:1129 array_new_memory(mem::Mem… 13╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ot.jl:659 Memory{UnitRange{Int64}}(… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1214 _growend_internal!(a::Vect… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1217 _growend_internal!(a::Vect… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1218 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1377 _push!(a::Vector{UnitRange{… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1072 __safe_setindex!(A::Vector… ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:1039 getindex(A::Vector{Vector{U… 1╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:391 checkbounds(A::Vector{Vecto… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:387 checkbounds(::Type{Bool}, A… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:1040 getindex(A::Vector{Vector{U… ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:5 (::Colon)(start::Int64, stop::… ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:417 UnitRange{Int64}(start::Int… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:428 unitrange_last(start::Int64… 3╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:464 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:502 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:57 getindex(mem::Automa.SizedMem… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…nter.jl:151 unsafe_load(p::Ptr{UInt8}, … 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:503 macro expansion ╎ ╎ ╎ ╎ ╎ 22 @Automa/…en.jl:577 macro expansion ╎ ╎ ╎ ╎ ╎ 22 @Automa/…ry.jl:56 getindex(mem::Automa.SizedMem… 19╎ ╎ ╎ ╎ ╎ 22 @Automa/…ry.jl:49 checkbounds(mem::Automa.Size… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/int.jl:560 <=(x::Int64, y::Int64) ╎ ╎ ╎ ╎ ╎ 19 @Automa/…en.jl:578 macro expansion 16╎ ╎ ╎ ╎ ╎ 16 @Base/bool.jl:14 &(x::Bool, y::Bool) 3╎ ╎ ╎ ╎ ╎ 3 @Base/bool.jl:15 |(x::Bool, y::Bool) ╎ ╎ ╎ ╎ ╎ 6 @Automa/…en.jl:579 macro expansion ╎ ╎ ╎ ╎ ╎ 6 @Base/range.jl:928 iterate(r::UnitRange{Int64},… 6╎ ╎ ╎ ╎ ╎ 6 @Base/…tion.jl:658 ==(x::Int64, y::Int64) ╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:588 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Automa/…ry.jl:56 getindex(mem::Automa.SizedMem… 2╎ ╎ ╎ ╎ ╎ 2 @Automa/…ry.jl:49 checkbounds(mem::Automa.Size… ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:57 getindex(mem::Automa.SizedMem… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…nter.jl:151 unsafe_load(p::Ptr{UInt8}, … 1╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:589 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1468 in(x::UInt8, r::UnitRange{U… 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:14 &(x::Bool, y::Bool) ╎ ╎ ╎ ╎ ╎ 23 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 23 @BufferedStreams/…:61 fillbuffer!(stream::Buffer… ╎ ╎ ╎ ╎ ╎ 23 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 23 @BufferedStreams/…:5 readbytes!(source::Transc… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/io.jl:1185 readbytes!(s::TranscodingStr… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:209 eof(stream::Transc… ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:213 eof(stream::Transc… ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:610 fillbuffer(strea… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:622 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:123 makemargin!(bu… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:140 makemargin!(b… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:295 copyto!(dest::Vector{… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:300 _copyto_impl!(dest::… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @CodecZlib/…:195 process(codec::GzipDec… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @CodecZlib/…:127 inflate!(zstream::Cod… ╎ ╎ ╎ ╎ ╎ ╎ 16 @Base/io.jl:1186 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 16 @TranscodingStreams/…:306 read(stream::Trans… ╎ ╎ ╎ ╎ ╎ ╎ 16 @Base/io.jl:377 peek(s::TranscodingStreams.… ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:298 peek(stream::Tra… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:206 eof(stream::Tra… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:52 buffersize(buf:… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:58 getproperty(x::Transcod… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:209 eof(stream::Tra… ╎ ╎ ╎ ╎ ╎ ╎ 13 @TranscodingStreams/…:302 peek(stream::Tra… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:58 getproperty(x::Transcodin… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:1039 getindex(A::Vector{UInt… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:391 checkbounds(A::Vector{U… 9╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ls.jl:1040 getindex(A::Vector{UInt… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/io.jl:1192 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ray.jl:393 setindex!(V::SubArray{UInt… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:1048 setindex!(A::Vector{UInt8… 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:1053 _setindex!(A::Vector{UIn… ╎ ╎ ╎ ╎ 450 @BioGenerics/…jl:90 iterate(reader::VariantCallForma… ╎ ╎ ╎ ╎ 450 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:389 copy(a::Vector{UInt8}) 2╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:659 Memory{UInt8}(::UndefInitialize… ╎ ╎ ╎ ╎ ╎ 448 @Base/…pcopy.jl:34 deepcopy(x::Vector{Vector{UnitR… ╎ ╎ ╎ ╎ ╎ 448 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:138 deepcopy_internal(x::MemoryRe… ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:19 haskey(d::IdDict{Any, Any}, k… ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:185 in(k::MemoryRef{Vector{Unit… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:95 get(d::IdDict{Any, Any}, ke… ╎ ╎ ╎ ╎ ╎ 447 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… ╎ ╎ ╎ ╎ ╎ 447 @Base/…copy.jl:104 deepcopy_internal(x::Memory{… ╎ ╎ ╎ ╎ ╎ 5 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/boot.jl:659 (::Type{Memory{T}} where T)… 54╎ ╎ ╎ ╎ ╎ 54 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 9╎ ╎ ╎ ╎ ╎ 9 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 12╎ ╎ ╎ ╎ ╎ 12 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 16╎ ╎ ╎ ╎ ╎ 304 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…ict.jl:19 haskey(d::IdDict{Any, Any},… ╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…ct.jl:185 in(k::Vector{UnitRange{Int… 22╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…ct.jl:95 get(d::IdDict{Any, Any}, k… ╎ ╎ ╎ ╎ ╎ ╎ 47 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/boot.jl:732 Vector{UnitRange{Int64}}(:… 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ot.jl:720 Vector{UnitRange{Int64}}(:… 42╎ ╎ ╎ ╎ ╎ ╎ 43 @Base/…ict.jl:89 setindex!(d::IdDict{Any, An… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:62 setproperty!(x::IdDict{Any… 2╎ ╎ ╎ ╎ ╎ ╎ 219 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… ╎ ╎ ╎ ╎ ╎ ╎ 61 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 61 @Base/…ict.jl:19 haskey(d::IdDict{Any, Any}… ╎ ╎ ╎ ╎ ╎ ╎ 61 @Base/…ct.jl:185 in(k::MemoryRef{UnitRange… 58╎ ╎ ╎ ╎ ╎ ╎ 60 @Base/…ct.jl:95 get(d::IdDict{Any, Any}, … 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:58 getproperty(x::IdDict{An… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:96 get(d::IdDict{Any, Any}, … ╎ ╎ ╎ ╎ ╎ ╎ 152 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 32 @Base/…py.jl:101 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 32 @Base/…ct.jl:19 haskey(d::IdDict{Any, Any}… ╎ ╎ ╎ ╎ ╎ ╎ 32 @Base/…ct.jl:185 in(k::Memory{UnitRange{I… 31╎ ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…ct.jl:95 get(d::IdDict{Any, Any},… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:96 get(d::IdDict{Any, Any},… 9╎ ╎ ╎ ╎ ╎ ╎ 120 @Base/…py.jl:104 deepcopy_internal(x::Memor… 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 27╎ ╎ ╎ ╎ ╎ ╎ 106 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:166 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ry.jl:170 copy(a::Memory{UnitRange… 14╎ ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ot.jl:659 Memory{UnitRange{Int64}… ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ry.jl:171 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ry.jl:134 unsafe_copyto!(dest::Me… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:666 memoryref(mem::Memory{… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ry.jl:116 unsafe_copyto!(dest::M… 11╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…em.jl:28 memmove(dst::Ptr{Nothi… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:84 setindex!(d::IdDict{Any, … ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:580 >>(x::Int64, y::Int64) 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:573 >>(x::Int64, y::UInt64) 50╎ ╎ ╎ ╎ ╎ ╎ 50 @Base/…ct.jl:89 setindex!(d::IdDict{Any, … ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:90 setindex!(d::IdDict{Any, … 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:62 setproperty!(x::IdDict{A… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:144 deepcopy_internal(x::Memor… 50╎ ╎ ╎ ╎ ╎ 50 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 13╎ ╎ ╎ ╎ ╎ 13 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ====================================================================================== 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:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 jl_apply at /source/src/julia.h:2406:12 [inlined] start_task at /source/src/task.c:1276:19 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:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007e1cfeb04100 Total snapshots: 380. Utilization: 0% ╎380 @Base/task.jl:1170 wait_forever() 379╎ 380 @Base/task.jl:1248 wait() Progress: 66%|███████████████████████████▏ | ETA: 0:07:11 Progress: 67%|███████████████████████████▍ | ETA: 0:07:05 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404:0 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430:0 ijl_task_get_next at /source/src/scheduler.c:524:34 wait at ./task.jl:1248:0 (pc: 107) wait_forever at ./task.jl:1170:0 (pc: 4) jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 jl_apply at /source/src/julia.h:2406:12 [inlined] start_task at /source/src/task.c:1276:19 unknown function (ip: (nil)) at (unknown file) Allocations: 19291782 (Pool: 19291015; Big: 767); GC: 20 [336] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 checkbounds at /home/pkgeval/.julia/packages/Automa/fzRJn/src/memory.jl:49:0 [inlined] getindex at /home/pkgeval/.julia/packages/Automa/fzRJn/src/memory.jl:56:0 [inlined] macro expansion at /home/pkgeval/.julia/packages/Automa/fzRJn/src/codegen.jl:577:0 [inlined] _read! at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/ReaderHelper.jl:165:0 (pc: 5406) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 read! at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/ReaderHelper.jl:142:0 (pc: 2) tryread! at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:76:0 (pc: 2) iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:87:0 [inlined] iterate at ./iterators.jl:209:0 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46:0 (pc: 346) aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26:0 (pc: 1) unknown function (ip: 0x7759e5f98eb6) at (unknown file) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19:0 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2246:0 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3:0 (pc: 359) jl_invoke_oneshot at /source/src/gf.c:4361:23 ijl_eval_thunk at /source/src/toplevel.c:756:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:326:0 (pc: 1) IncludeInto at ./Base.jl:327:0 (pc: 2) jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 jl_apply at /source/src/julia.h:2406:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:757:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:947:21 ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:522:0 (pc: 1) include_string at ./loading.jl:3132:0 (pc: 208) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 _include at ./loading.jl:3192:0 (pc: 122) include at ./Base.jl:326:0 (pc: 1) IncludeInto at ./Base.jl:327:0 (pc: 2) jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 jl_apply at /source/src/julia.h:2406:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:259:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:757:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:947:21 ijl_eval_thunk at /source/src/toplevel.c:764:18 jl_toplevel_eval_flex at /source/src/toplevel.c:708:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:598:15 jl_toplevel_eval_flex at /source/src/toplevel.c:680:27 ijl_toplevel_eval at /source/src/toplevel.c:778:12 ijl_toplevel_eval_in at /source/src/toplevel.c:823:13 eval at ./boot.jl:522:0 (pc: 1) exec_options at ./client.jl:321:0 (pc: 426) _start at ./client.jl:596:0 (pc: 295) jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4326:23 [inlined] ijl_apply_generic at /source/src/gf.c:4564:12 jl_apply at /source/src/julia.h:2406:12 [inlined] true_main at /source/src/jlapi.c:985:29 jl_repl_entrypoint at /source/src/jlapi.c:1152:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x775a0e8ac249) 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: 15628173651 (Pool: 15628158215; Big: 15436); GC: 16757 PkgEval terminated after 2750.63s: test duration exceeded the time limit