Package evaluation to test VCFTools on Julia 1.13.0-DEV.1319 (9cddfda8ef*) started at 2025-10-16T18:21:01.532 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 11.85s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed CompositionsBase ──────── v0.1.2 Installed CommonSolve ───────────── v0.2.4 Installed Rmath_jll ─────────────── v0.5.1+0 Installed DelimitedFiles ────────── v1.9.1 Installed MacroTools ────────────── v0.5.16 Installed FillArrays ────────────── v1.14.0 Installed DataStructures ────────── v0.19.1 Installed VCFTools ──────────────── v0.2.10 Installed HypergeometricFunctions ─ v0.3.28 Installed ConstructionBase ──────── v1.6.0 Installed AliasTables ───────────── v1.1.3 Installed CodecZlib ─────────────── v0.7.8 Installed StatsBase ─────────────── v0.34.6 Installed TranscodingStreams ────── v0.11.3 Installed OrderedCollections ────── v1.8.1 Installed HypothesisTests ───────── v0.11.5 Installed SIMD ──────────────────── v3.7.2 Installed Combinatorics ─────────── v1.0.3 Installed DataAPI ───────────────── v1.16.0 Installed Statistics ────────────── v1.11.1 Installed StatsAPI ──────────────── v1.7.1 Installed ProgressMeter ─────────── v1.11.0 Installed IrrationalConstants ───── v0.2.6 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed PrecompileTools ───────── v1.3.3 Installed QuadGK ────────────────── v2.11.2 Installed LogExpFunctions ───────── v0.3.29 Installed BufferedStreams ───────── v1.2.2 Installed Rmath ─────────────────── v0.8.0 Installed BioGenerics ───────────── v0.1.5 Installed Roots ─────────────────── v2.2.10 Installed PtrArrays ─────────────── v1.3.0 Installed StatsFuns ─────────────── v1.5.0 Installed Distributions ─────────── v0.25.122 Installed InverseFunctions ──────── v0.1.17 Installed Reexport ──────────────── v1.2.2 Installed SpecialFunctions ──────── v2.6.1 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.1 Installed Preferences ───────────── v1.5.0 Installed SortingAlgorithms ─────── v1.2.2 Installed PDMats ────────────────── v0.11.35 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.42 Installed Automa ────────────────── v1.1.0 Installed BGZFStreams ───────────── v0.3.2 Installed VariantCallFormat ─────── v0.5.8 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.13/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.13/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 v0.19.1 [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 v0.11.5 [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 v0.11.35 [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 v0.8.0 [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 v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.8 [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 v0.7.0 [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 9.08s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4465.4 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 407.07s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_xi1Ch0/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.6 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.8 [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_xi1Ch0/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 v1.8.0 [864edb3b] DataStructures v0.19.1 [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 v0.11.5 [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 v0.11.35 [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 v0.8.0 [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 v0.34.6 [4c63d2b9] StatsFuns v1.5.0 [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 v0.5.8 [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 v0.6.4 [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 v0.7.0 [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 8.7s Test Summary: | Pass Total Time openvcf | 4 4 2.6s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.7s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.6s ┌ 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: 0:35:48 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 14.562077 seconds (10.36 M allocations: 582.586 MiB, 2.11% gc time, 95.87% compilation time: 19% of which was recompilation) 0.520933 seconds (2.40 M allocations: 143.572 MiB, 13.51% gc time, 17.55% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:32:19 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.308572 seconds (4.11 M allocations: 242.851 MiB, 1.59% gc time, 87.84% compilation time) 0.425630 seconds (2.38 M allocations: 143.285 MiB, 5.28% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.3s 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 1.8s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.0s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 6.0s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:08 Progress: 0%|▏ | ETA: 0:17:40 Progress: 0%|▏ | ETA: 0:17:22 Progress: 0%|▏ | ETA: 0:17:08 Progress: 0%|▎ | ETA: 0:16:59 Progress: 1%|▎ | ETA: 0:16:49 Progress: 1%|▎ | ETA: 0:16:43 Progress: 1%|▍ | ETA: 0:16:36 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0:01:41 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 17:43:58 Progress: 21%|████████▋ | ETA: 0:05:58 Progress: 43%|█████████████████▊ | ETA: 0:02:07 Progress: 67%|███████████████████████████▎ | ETA: 0:00:49 Progress: 91%|█████████████████████████████████████▍ | ETA: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:01:38 [ Info: 823 records are matched 210.843318 seconds (2.01 G allocations: 106.139 GiB, 5.95% gc time, 0.64% compilation time: 6% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:23 Progress: 0%|▏ | ETA: 0:16:47 Progress: 0%|▏ | ETA: 0:16:53 Progress: 0%|▏ | ETA: 0:16:57 Progress: 0%|▎ | ETA: 0:16:58 Progress: 1%|▎ | ETA: 0:16:54 Progress: 1%|▎ | ETA: 0:16:48 Progress: 1%|▍ | ETA: 0:16:48 Progress: 1%|▍ | ETA: 0:16:47 Progress: 1%|▍ | ETA: 0:16:47 Progress: 1%|▌ | ETA: 0:16:46 Progress: 1%|▌ | ETA: 0:16:41 Progress: 1%|▌ | ETA: 0:16:36 Progress: 1%|▋ | ETA: 0:16:37 Progress: 2%|▋ | ETA: 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Progress: 64%|██████████████████████████▍ | ETA: 0:00:56 Progress: 88%|███████████████████████████████████▉ | ETA: 0:00:15 Progress: 100%|█████████████████████████████████████████| Time: 0:01:42 [ Info: 488 records are matched 215.188097 seconds (2.01 G allocations: 106.121 GiB, 5.89% gc time, 0.34% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:03 Progress: 0%|▏ | ETA: 0:17:31 Progress: 0%|▏ | ETA: 0:17:03 Progress: 0%|▏ | ETA: 0:16:53 Progress: 1%|▎ | ETA: 0:16:40 Progress: 1%|▎ | ETA: 0:16:33 Progress: 1%|▎ | ETA: 0:16:28 Progress: 1%|▍ | ETA: 0:16:27 Progress: 1%|▍ | ETA: 0:16:26 Progress: 1%|▍ | ETA: 0:16:23 Progress: 1%|▌ | ETA: 0:16:22 Progress: 1%|▌ | ETA: 0:16:21 Progress: 1%|▌ | ETA: 0:16:19 Progress: 1%|▋ | ETA: 0:16:17 Progress: 2%|▋ | ETA: 0:16:15 Progress: 2%|▋ | ETA: 0:16:13 Progress: 2%|▊ | ETA: 0:16:12 Progress: 2%|▊ | ETA: 0:16:11 Progress: 2%|▊ | ETA: 0:16:09 Progress: 2%|▉ | ETA: 0:16:09 Progress: 2%|▉ | ETA: 0:16:10 Progress: 2%|▉ | 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ETA: 0:14:59 Progress: 9%|███▋ | ETA: 0:14:57 Progress: 9%|███▋ | ETA: 0:14:56 Progress: 9%|███▊ | ETA: 0:14:55 Progress: 9%|███▊ | ETA: 0:14:54 Progress: 9%|███▊ | ETA: 0:14:52 Progress: 9%|███▉ | ETA: 0:14:51 Progress: 9%|███▉ | ETA: 0:14:49 Progress: 10%|███▉ | ETA: 0:14:48 Progress: 10%|████ | ETA: 0:14:46 Progress: 10%|████ | ETA: 0:14:45 Progress: 10%|████ | ETA: 0:14:44 Progress: 10%|████▏ | ETA: 0:14:43 Progress: 10%|████▏ | ETA: 0:14:41 Progress: 10%|████▏ | ETA: 0:14:40 Progress: 10%|████▎ | ETA: 0:14:39 Progress: 100%|█████████████████████████████████████████| Time: 0:01:41 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:42:20 Progress: 20%|████████▎ | ETA: 0:06:39 Progress: 41%|████████████████▉ | ETA: 0:02:25 Progress: 64%|██████████████████████████▍ | ETA: 0:00:57 Progress: 88%|███████████████████████████████████▉ | ETA: 0:00:15 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: 0 records are matched 215.733545 seconds (2.01 G allocations: 106.120 GiB, 5.85% gc time, 0.40% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 10m49.1s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:31:59 Progress: 20%|████████▏ | ETA: 0:06:42 Progress: 41%|████████████████▉ | ETA: 0:02:24 Progress: 63%|█████████████████████████▉ | ETA: 0:00:59 Progress: 86%|███████████████████████████████████▍ | ETA: 0:00:17 Progress: 100%|█████████████████████████████████████████| Time: 0:01:43 [ Info: 833 records are matched 113.235860 seconds (1.02 G allocations: 53.885 GiB, 5.80% gc time, 0.50% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:39:51 Progress: 21%|████████▋ | ETA: 0:06:17 Progress: 43%|█████████████████▊ | ETA: 0:02:13 Progress: 66%|███████████████████████████ | ETA: 0:00:53 Progress: 90%|█████████████████████████████████████ | ETA: 0:00:11 Progress: 100%|█████████████████████████████████████████| Time: 0:01:43 [ Info: 493 records are matched 114.130086 seconds (1.02 G allocations: 53.885 GiB, 5.81% gc time, 0.56% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 17:46:57 Progress: 21%|████████▊ | ETA: 0:05:53 Progress: 44%|██████████████████▎ | ETA: 0:02:01 Progress: 69%|████████████████████████████▍ | ETA: 0:00:44 Progress: 100%|█████████████████████████████████████████| Time: 0:01:38 [ Info: 0 records are matched 108.727424 seconds (1.02 G allocations: 53.885 GiB, 5.88% gc time, 0.53% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m38.2s 1.042456 seconds (1.29 M allocations: 69.681 MiB, 4.67% gc time, 82.72% compilation time) 0.798575 seconds (1.19 M allocations: 66.188 MiB, 79.19% compilation time) 0.879152 seconds (1.19 M allocations: 65.212 MiB, 4.09% gc time, 76.60% compilation time) 0.354943 seconds (212.12 k allocations: 11.129 MiB, 99.96% compilation time) 0.009786 seconds (6.38 k allocations: 392.211 KiB, 96.71% compilation time) 0.008793 seconds (2.65 k allocations: 165.508 KiB, 96.27% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 8.4s 0.902465 seconds (979.71 k allocations: 54.670 MiB, 81.40% compilation time) 0.854000 seconds (878.78 k allocations: 51.627 MiB, 3.88% gc time, 76.52% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.8s Test Summary: | Pass Total Time convert_ds | 5 5 0.9s 0.117282 seconds (525.56 k allocations: 30.681 MiB, 16.23% gc time, 27.00% compilation time) 0.634341 seconds (651.56 k allocations: 37.708 MiB, 89.25% 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 0.090789 seconds (520.58 k allocations: 32.160 MiB, 16.86% gc time) 0.475358 seconds (594.70 k allocations: 36.353 MiB, 87.88% 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 0.129655 seconds (1.56 M allocations: 62.080 MiB, 12.45% gc time, 6.15% compilation time) 0.573275 seconds (1.71 M allocations: 70.291 MiB, 2.73% gc time, 78.45% 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 6.7s Test Summary: | Pass Total Time record info | 14 14 4.4s Test Summary: | Pass Total Time write VCF | 3 3 4.0s 2.159891 seconds (4.80 M allocations: 296.556 MiB, 3.54% gc time, 55.29% compilation time) 1.005361 seconds (2.39 M allocations: 142.649 MiB, 3.56% gc time, 22.60% compilation time) 0.941189 seconds (4.42 M allocations: 276.520 MiB, 4.70% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.0s 1.000561 seconds (610.43 k allocations: 33.742 MiB, 46.34% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.9s Test Summary: | Pass Total Time filter_chr | 4 4 1.5s Progress: 0%|▏ | ETA: 0:18:35 Progress: 1%|▍ | ETA: 0:18:37 Progress: 1%|▌ | ETA: 0:18:36 Progress: 2%|▊ | ETA: 0:18:10 Progress: 2%|█ | ETA: 0:18:18 Progress: 3%|█▏ | ETA: 0:18:22 Progress: 3%|█▎ | ETA: 0:18:24 Progress: 4%|█▌ | ETA: 0:18:20 Progress: 4%|█▋ | ETA: 0:18:18 Progress: 4%|█▉ | ETA: 0:18:18 Progress: 5%|██ | ETA: 0:18:12 Progress: 5%|██▏ | ETA: 0:18:08 Progress: 6%|██▍ | ETA: 0:17:51 Progress: 6%|██▋ | ETA: 0:17:48 Progress: 7%|██▊ | ETA: 0:17:45 Progress: 7%|███ | ETA: 0:17:42 Progress: 8%|███▏ | ETA: 0:17:39 Progress: 8%|███▎ | ETA: 0:17:31 Progress: 9%|███▌ | ETA: 0:17:26 Progress: 9%|███▋ | ETA: 0:17:23 Progress: 9%|███▉ | ETA: 0:17:18 Progress: 10%|████ | ETA: 0:17:14 Progress: 10%|████▎ | 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0:01:03 Progress: 95%|██████████████████████████████████████▉ | ETA: 0:00:58 ====================================================================================== 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 433 running 1 of 1 signal (10): User defined signal 1 ijl_get_pgcstack at /source/src/threading.c:266 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x7475de1c0d16) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _deepcopy_memory_t at ./deepcopy.jl:120 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/wA0VH/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [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: 0x7475bf51ca46) 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/v1.13/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:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x7475de1028e2) 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:2275 [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:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_59871.1 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:2275 [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_71179.1 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:2275 [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: 0x7475e7581249) 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: 95%|███████████████████████████████████████▏ | ETA: 0:00:53 ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ====================================================================================== 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 Progress: 96%|███████████████████████████████████████▎ | ETA: 0:00:48wait at ./task.jl:1217 wait_forever at ./task.jl:1139 jfptr_wait_forever_42350.1 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:2275 [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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000077d29be254b0 Total snapshots: 402. Utilization: 0% ╎402 @Base/task.jl:1139 wait_forever() 401╎ 402 @Base/task.jl:1217 wait() ┌ 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007475cd5fc010 Total snapshots: 563. Utilization: 100% ╎562 @Base/client.jl:577 _start() ╎ 562 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 562 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 562 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 562 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 562 @Base/loading.jl:3014 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 562 @Base/loading.jl:2954 include_string(mapexpr::typeof(identity), m… ╎ ╎ 562 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 562 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 562 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 562 @Base/loading.jl:3014 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 562 @Base/loading.jl:2954 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 562 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 562 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 562 @Test/src/Test.jl:1961 macro expansion ╎ ╎ ╎ 562 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 562 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 80 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:0 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 8 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 8 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 5 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ators.jl:424 > 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 2 @VCFTools/…t.jl:225 geno_ismissing 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == ╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ 63 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 62 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ 61 @Base/array.jl:2449 findnext 7╎ ╎ ╎ ╎ ╎ 7 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 54 @Base/…ators.jl:1202 Fix ╎ ╎ ╎ ╎ ╎ 54 @Base/…tors.jl:1202 #_#59 ╎ ╎ ╎ ╎ ╎ 54 @Base/…tors.jl:178 isequal 54╎ ╎ ╎ ╎ ╎ 54 @Base/…ring.jl:187 == ╎ ╎ ╎ ╎ 1 @Base/array.jl:2450 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 3 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:2449 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:673 isequaldata 2╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:86 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:99 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…al/log.jl:261 log(x::Float64) ╎ ╎ ╎ ╎ 1 @Base/…al/log.jl:289 _log ╎ ╎ ╎ ╎ ╎ 1 @Base/…l/log.jl:163 log_proc1 1╎ ╎ ╎ ╎ ╎ 1 @Base/float.jl:492 + ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:45 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:483 next! ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:484 #next!#15 ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:470 lock_if_threading ╎ ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:486 #17 ╎ ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:211 updateProgress! ╎ ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:213 #updateProgress!#9 ╎ ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:217 _updateProgress! 1╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:0 _updateProgress!(p::Progres… ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:289 _updateProgress!(p::Progr… ╎ ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:617 printover(io::Base.PipeE… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…/io.jl:239 print ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…io.jl:237 write ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:1150 unsafe_write(s::Base.Pip… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:1065 uv_write(s::Base.PipeEn… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:1110 uv_write_async(s::Base… ╎ ╎ ╎ ╎ 480 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 480 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 80 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 80 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 80 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:156 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:2125 empty! ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1288 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:211 _unsetindex! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:596 memoryref ╎ ╎ ╎ ╎ ╎ 53 @VariantCallFormat/…:165 _read!(reader::VariantCa… 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 macro expansion ╎ ╎ ╎ ╎ ╎ 40 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 10 @Base/array.jl:436 getindex 10╎ ╎ ╎ ╎ ╎ 10 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 27 @Base/array.jl:1345 push! ╎ ╎ ╎ ╎ ╎ 27 @Base/…ray.jl:1348 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1197 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1204 _growend! 4╎ ╎ ╎ ╎ ╎ ╎ 25 @Base/…ray.jl:1205 _growend! ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ay.jl:1181 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ay.jl:1101 array_new_memory 13╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ot.jl:588 GenericMemory 8╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ay.jl:1190 _growend_internal!(a::Vect… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:215 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:49 resize_and_copy! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:55 resize_and_copy! 2╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:503 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:572 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…yops.jl:51 vload ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…sics.jl:477 load 2╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:486 macro expansion 2╎ ╎ ╎ ╎ ╎ 5 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…dvec.jl:491 all ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…dvec.jl:486 reduce ╎ ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…ics.jl:1050 reduce_and 3╎ ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…cs.jl:1065 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:583 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:56 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:49 checkbounds ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:57 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…nter.jl:151 unsafe_load ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:584 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1454 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ ╎ 24 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 24 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 24 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 24 @BufferedStreams/…:5 readbytes! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:0 readbytes!(s::TranscodingStream… ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/io.jl:1167 readbytes!(s::TranscodingStr… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:212 eof ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @CodecZlib/…:195 process(codec::GzipDec… 5╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/io.jl:1168 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/io.jl:366 peek ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:302 peek ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ls.jl:964 getindex 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ls.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:381 checkbounds 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ls.jl:965 getindex ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:307 read ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:97 consumed! ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:98 #consumed!#1 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1170 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ors.jl:424 > 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/io.jl:1174 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ray.jl:400 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ay.jl:1020 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1024 _setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:1025 _setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ 400 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 400 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:384 copy 3╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:588 GenericMemory 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:386 copy ╎ ╎ ╎ ╎ ╎ 395 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 395 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:138 deepcopy_internal(x::MemoryRe… ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:182 in 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:92 get ╎ ╎ ╎ ╎ ╎ 394 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 4╎ ╎ ╎ ╎ ╎ 394 @Base/…copy.jl:104 deepcopy_internal 39╎ ╎ ╎ ╎ ╎ 39 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 7╎ ╎ ╎ ╎ ╎ 7 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 5╎ ╎ ╎ ╎ ╎ 5 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 15╎ ╎ ╎ ╎ ╎ 284 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::Vector{U… ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:182 in 23╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 47 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/boot.jl:661 Array 13╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ot.jl:649 Array 33╎ ╎ ╎ ╎ ╎ ╎ 34 @Base/…ict.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:61 setproperty! 5╎ ╎ ╎ ╎ ╎ ╎ 196 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ct.jl:182 in 64╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 121 @Base/…opy.jl:142 deepcopy_internal(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:0 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…ct.jl:182 in 17╎ ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…ct.jl:92 get 8╎ ╎ ╎ ╎ ╎ ╎ 102 @Base/…py.jl:104 deepcopy_internal 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:108 _deepcopy_memory_t(x::Mem… 12╎ ╎ ╎ ╎ ╎ ╎ 89 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:189 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ry.jl:193 copy(a::Memory{UnitRange… 23╎ ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ry.jl:194 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ry.jl:157 unsafe_copyto! 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ry.jl:139 unsafe_copyto! 5╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…em.jl:28 memmove 43╎ ╎ ╎ ╎ ╎ ╎ 43 @Base/…ct.jl:86 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:87 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:145 deepcopy_internal(x::Memor… 36╎ ╎ ╎ ╎ ╎ 37 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 18╎ ╎ ╎ ╎ ╎ 18 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:3 Record [433] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 ijl_eqtable_get at /source/src/iddict.c:159 get at ./iddict.jl:92 [inlined] in at ./iddict.jl:182 [inlined] haskey at ./abstractdict.jl:19 [inlined] deepcopy_internal at ./deepcopy.jl:138 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x7475de1c0d16) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _deepcopy_memory_t at ./deepcopy.jl:120 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/wA0VH/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [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: 0x7475bf51ca46) 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/v1.13/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:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x7475de1028e2) 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:2275 [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:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_59871.1 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:2275 [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_71179.1 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:2275 [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: 0x7475e7581249) 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: 18503385281 (Pool: 18503369761; Big: 15520); GC: 22213 PkgEval terminated after 2723.33s: test duration exceeded the time limit