Package evaluation of VCFTools on Julia 1.13.0-DEV.853 (3e868b27cf*) started at 2025-07-17T03:14:53.961 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.81s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed MacroTools ────────────── v0.5.16 Installed FillArrays ────────────── v1.13.0 Installed CompositionsBase ──────── v0.1.2 Installed CommonSolve ───────────── v0.2.4 Installed DataStructures ────────── v0.18.22 Installed DelimitedFiles ────────── v1.9.1 Installed VCFTools ──────────────── v0.2.10 Installed ConstructionBase ──────── v1.6.0 Installed AliasTables ───────────── v1.1.3 Installed HypergeometricFunctions ─ v0.3.28 Installed CodecZlib ─────────────── v0.7.8 Installed OrderedCollections ────── v1.8.1 Installed StatsBase ─────────────── v0.34.5 Installed Compat ────────────────── v4.17.0 Installed TranscodingStreams ────── v0.9.13 Installed DataAPI ───────────────── v1.16.0 Installed Combinatorics ─────────── v1.0.3 Installed HypothesisTests ───────── v0.11.5 Installed StatsAPI ──────────────── v1.7.1 Installed Statistics ────────────── v1.11.1 Installed IrrationalConstants ───── v0.2.4 Installed ProgressMeter ─────────── v1.10.4 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed QuadGK ────────────────── v2.11.2 Installed Rmath ─────────────────── v0.8.0 Installed LogExpFunctions ───────── v0.3.29 Installed BufferedStreams ───────── v1.2.2 Installed Roots ─────────────────── v2.2.8 Installed StatsFuns ─────────────── v1.5.0 Installed PtrArrays ─────────────── v1.3.0 Installed BioGenerics ───────────── v0.1.5 Installed Distributions ─────────── v0.25.120 Installed InverseFunctions ──────── v0.1.17 Installed Reexport ──────────────── v1.2.2 Installed Missings ──────────────── v1.2.0 Installed SpecialFunctions ──────── v2.5.1 Installed Preferences ───────────── v1.4.3 Installed JLLWrappers ───────────── v1.7.0 Installed PDMats ────────────────── v0.11.35 Installed Accessors ─────────────── v0.1.42 Installed DocStringExtensions ───── v0.9.5 Installed SortingAlgorithms ─────── v1.2.1 Installed BGZFStreams ───────────── v0.3.2 Installed VariantCallFormat ─────── v0.5.6 Installed Automa ────────────────── v0.8.4 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 v0.8.4 [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 [34da2185] + Compat v4.17.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [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 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.8 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.6 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [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 v1.12.0 [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 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+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 7.24s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4528.8 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 353.65s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_gPZYSJ/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.10.4 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.5 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_gPZYSJ/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [66dad0bd] AliasTables v1.1.3 ⌅ [67c07d97] Automa v0.8.4 [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 v4.17.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.4 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [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 v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.8 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [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 v1.12.0 [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 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [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 v8.14.1+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+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 3.6s Test Summary: | Pass Total Time openvcf | 4 4 2.6s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.3s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.3s ┌ 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: 0:24:39 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 13.657147 seconds (10.61 M allocations: 665.184 MiB, 5.14% gc time, 92.84% compilation time: 21% of which was recompilation) 0.445722 seconds (2.86 M allocations: 195.852 MiB, 10.07% gc time, 19.58% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:22:16 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.370430 seconds (4.37 M allocations: 297.947 MiB, 3.10% gc time, 83.20% compilation time) 0.383419 seconds (2.85 M allocations: 195.344 MiB, 6.63% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 20.6s Test Summary: | Pass Total Time get sampleID | 4 4 0.0s 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 1.8s 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 5.1s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:17 Progress: 0%|▏ | ETA: 0:17:25 Progress: 0%|▏ | ETA: 0:16:37 Progress: 0%|▏ | ETA: 0:16:37 Progress: 1%|▎ | ETA: 0:16:41 Progress: 1%|▎ | ETA: 0:16:44 Progress: 1%|▎ | ETA: 0:16:47 Progress: 1%|▍ | ETA: 0:16:45 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100%|█████████████████████████████████████████| Time: 0:01:43 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:51:38 Progress: 19%|███████▉ | ETA: 0:07:05 Progress: 39%|████████████████ | ETA: 0:02:40 Progress: 61%|█████████████████████████ | ETA: 0:01:06 Progress: 83%|██████████████████████████████████ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 823 records are matched 220.510352 seconds (2.19 G allocations: 143.742 GiB, 6.41% gc time, 0.60% compilation time: 5% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:39 Progress: 0%|▏ | ETA: 0:17:13 Progress: 0%|▏ | ETA: 0:17:01 Progress: 0%|▏ | ETA: 0:16:51 Progress: 1%|▎ | ETA: 0:16:35 Progress: 1%|▎ | ETA: 0:16:33 Progress: 1%|▎ | ETA: 0:16:24 Progress: 1%|▍ | ETA: 0:16:15 Progress: 1%|▍ | ETA: 0:16:04 Progress: 1%|▍ | ETA: 0:15:56 Progress: 1%|▌ | ETA: 0:15:56 Progress: 1%|▌ | ETA: 0:16:02 Progress: 1%|▌ | ETA: 0:15:58 Progress: 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100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 488 records are matched 217.431194 seconds (2.19 G allocations: 143.726 GiB, 6.58% gc time, 0.38% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:56 Progress: 0%|▏ | ETA: 0:17:28 Progress: 0%|▏ | ETA: 0:17:14 Progress: 0%|▏ | ETA: 0:17:01 Progress: 0%|▎ | ETA: 0:16:53 Progress: 1%|▎ | ETA: 0:16:48 Progress: 1%|▎ | ETA: 0:16:48 Progress: 1%|▍ | ETA: 0:16:53 Progress: 1%|▍ | ETA: 0:16:50 Progress: 1%|▍ | ETA: 0:16:56 Progress: 1%|▌ | ETA: 0:16:54 Progress: 1%|▌ | ETA: 0:16:54 Progress: 1%|▌ | ETA: 0:16:55 Progress: 1%|▋ | ETA: 0:16:54 Progress: 1%|▋ | ETA: 0:16:51 Progress: 2%|▋ | ETA: 0:16:51 Progress: 2%|▋ | ETA: 0:16:51 Progress: 2%|▊ | ETA: 0:16:51 Progress: 2%|▊ | ETA: 0:16:51 Progress: 2%|▊ | ETA: 0:16:50 Progress: 2%|▉ | ETA: 0:16:48 Progress: 2%|▉ | ETA: 0:16:47 Progress: 2%|▉ | ETA: 0:16:46 Progress: 2%|█ | ETA: 0:16:45 Progress: 2%|█ | ETA: 0:16:44 Progress: 3%|█ | ETA: 0:16:44 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0:15:18 Progress: 9%|███▊ | ETA: 0:15:17 Progress: 9%|███▊ | ETA: 0:15:16 Progress: 9%|███▊ | ETA: 0:15:15 Progress: 9%|███▉ | ETA: 0:15:15 Progress: 9%|███▉ | ETA: 0:15:14 Progress: 10%|███▉ | ETA: 0:15:13 Progress: 10%|████ | ETA: 0:15:12 Progress: 10%|████ | ETA: 0:15:11 Progress: 10%|████ | ETA: 0:15:10 Progress: 10%|████▏ | ETA: 0:15:09 Progress: 10%|████▏ | ETA: 0:15:08 Progress: 10%|████▏ | ETA: 0:15:07 Progress: 10%|████▎ | ETA: 0:15:06 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:44:05 Progress: 21%|████████▋ | ETA: 0:06:17 Progress: 42%|█████████████████ | ETA: 0:02:23 Progress: 64%|██████████████████████████▍ | ETA: 0:00:57 Progress: 89%|████████████████████████████████████▍ | ETA: 0:00:13 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: 0 records are matched 218.575585 seconds (2.19 G allocations: 143.726 GiB, 6.55% gc time, 0.38% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m03.3s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 17:48:17 Progress: 20%|████████▎ | ETA: 0:06:23 Progress: 40%|████████████████▋ | ETA: 0:02:22 Progress: 62%|█████████████████████████▌ | ETA: 0:00:59 Progress: 85%|███████████████████████████████████ | ETA: 0:00:17 Progress: 100%|█████████████████████████████████████████| Time: 0:01:39 [ Info: 833 records are matched 109.280003 seconds (1.11 G allocations: 72.817 GiB, 6.45% gc time, 0.46% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:10:12 Progress: 21%|████████▍ | ETA: 0:06:37 Progress: 42%|█████████████████▍ | ETA: 0:02:21 Progress: 64%|██████████████████████████▍ | ETA: 0:00:58 Progress: 88%|███████████████████████████████████▉ | ETA: 0:00:15 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 493 records are matched 116.493982 seconds (1.11 G allocations: 72.816 GiB, 6.19% gc time, 0.48% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:25:17 Progress: 20%|████████▍ | ETA: 0:06:50 Progress: 42%|█████████████████▏ | ETA: 0:02:27 Progress: 64%|██████████████████████████▎ | ETA: 0:00:59 Progress: 87%|███████████████████████████████████▌ | ETA: 0:00:16 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 0 records are matched 117.952607 seconds (1.11 G allocations: 72.816 GiB, 6.20% gc time, 0.48% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m45.9s 1.139067 seconds (1.28 M allocations: 91.360 MiB, 2.09% gc time, 87.56% compilation time) 0.914803 seconds (1.16 M allocations: 86.629 MiB, 2.54% gc time, 83.63% compilation time) 0.915423 seconds (1.16 M allocations: 85.888 MiB, 2.28% gc time, 84.56% compilation time) 0.460440 seconds (203.61 k allocations: 11.563 MiB, 99.97% compilation time) 0.012307 seconds (6.18 k allocations: 483.492 KiB, 96.89% compilation time) 0.009529 seconds (2.65 k allocations: 247.586 KiB, 96.63% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.4s 0.912898 seconds (952.92 k allocations: 74.545 MiB, 4.01% gc time, 87.15% compilation time) 0.807917 seconds (861.52 k allocations: 71.598 MiB, 3.25% gc time, 81.87% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.7s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.145871 seconds (525.31 k allocations: 50.449 MiB, 22.73% compilation time) 0.711423 seconds (647.53 k allocations: 57.716 MiB, 7.97% gc time, 81.85% 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 0.090220 seconds (520.43 k allocations: 51.916 MiB, 22.58% gc time) 0.540945 seconds (589.76 k allocations: 56.017 MiB, 2.87% gc time, 84.38% 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 0.134652 seconds (1.56 M allocations: 81.839 MiB, 12.89% gc time, 7.16% compilation time) 0.599465 seconds (1.70 M allocations: 90.369 MiB, 3.36% gc time, 77.76% 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 6.4s Test Summary: | Pass Total Time record info | 14 14 5.1s Test Summary: | Pass Total Time write VCF | 3 3 4.3s 2.561942 seconds (5.25 M allocations: 378.537 MiB, 18.89% gc time, 47.43% compilation time) 0.950859 seconds (2.86 M allocations: 195.046 MiB, 4.82% gc time, 21.43% compilation time) 0.908462 seconds (4.89 M allocations: 358.252 MiB, 6.61% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.9s 0.972358 seconds (618.95 k allocations: 54.418 MiB, 1.75% gc time, 49.79% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.5s Test Summary: | Pass Total Time filter_chr | 4 4 1.3s Progress: 0%|▏ | ETA: 0:21:46 Progress: 1%|▍ | ETA: 0:19:55 Progress: 1%|▌ | ETA: 0:19:55 Progress: 2%|▊ | ETA: 0:19:45 Progress: 2%|▉ | ETA: 0:19:35 Progress: 3%|█ | ETA: 0:19:30 Progress: 3%|█▎ | ETA: 0:19:24 Progress: 3%|█▍ | ETA: 0:19:19 Progress: 4%|█▌ | ETA: 0:19:12 Progress: 4%|█▊ | ETA: 0:19:09 Progress: 5%|█▉ | ETA: 0:19:05 Progress: 5%|██▏ | ETA: 0:19:02 Progress: 5%|██▎ | ETA: 0:18:58 Progress: 6%|██▍ | ETA: 0:18:53 Progress: 6%|██▋ | ETA: 0:18:50 Progress: 7%|██▊ | ETA: 0:18:44 Progress: 7%|██▉ | ETA: 0:18:40 Progress: 8%|███▏ | ETA: 0:18:35 Progress: 8%|███▎ | ETA: 0:18:28 Progress: 8%|███▌ | ETA: 0:18:22 Progress: 9%|███▋ | ETA: 0:18:16 Progress: 9%|███▊ | ETA: 0:18:10 Progress: 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A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 426 running 1 of 1 signal (10): User defined signal 1 isbits at ./runtime_internals.jl:834 [inlined] _deepcopy_memory_t at ./deepcopy.jl:119 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/YgfJC/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: 0x7ba3bd11e666) at (unknown file) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 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:1855 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_invoke at /source/src/gf.c:3800 jl_toplevel_eval_flex at /source/src/toplevel.c:762 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2848 _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 _include at ./loading.jl:2908 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_44279.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 jl_apply at /source/src/julia.h:2345 [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:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2848 _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 _include at ./loading.jl:2908 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_44279.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 jl_apply at /source/src/julia.h:2345 [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:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 exec_options at ./client.jl:286 _start at ./client.jl:553 jfptr__start_68801.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 jl_apply at /source/src/julia.h:2345 [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: 0x7ba3df62d249) 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 ============================================================== Progress: 97%|███████████████████████████████████████▊ | ETA: 0:00:35┌ 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 0x00007ba3c5400010 Total snapshots: 682. Utilization: 100% ╎681 @Base/client.jl:553 _start() ╎ 681 @Base/client.jl:286 exec_options(opts::Base.JLOptions) ╎ 681 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 681 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 681 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 681 @Base/loading.jl:2908 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 681 @Base/loading.jl:2848 include_string(mapexpr::typeof(identity), m… ╎ ╎ 681 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 681 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 681 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 681 @Base/loading.jl:2908 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 681 @Base/loading.jl:2848 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 681 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 681 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 681 @Test/src/Test.jl:1855 macro expansion ╎ ╎ ╎ 681 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 681 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 2╎ ╎ ╎ ╎ 110 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:0 aim_select(record::VariantCallFor… 1╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:0 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 24 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 24 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 11 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 6╎ ╎ ╎ ╎ ╎ 6 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ators.jl:425 > 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 4 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 4 @Base/…tials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 4 @Base/…ials.jl:387 checkbounds ╎ ╎ ╎ ╎ ╎ 4 @Base/…ials.jl:383 checkbounds 4╎ ╎ ╎ ╎ ╎ 4 @Base/…ials.jl:11 length 2╎ ╎ ╎ ╎ 8 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:3151 getindex ╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:960 _getindex ╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:947 _in_unit_range 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:522 <= ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:387 checkbounds 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + 2╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:134 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:146 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 2 @VCFTools/…s.jl:169 hwe(n00::Int64, n01::Int64, n1… ╎ ╎ ╎ ╎ ╎ 2 @Distributions/…:102 ccdf ╎ ╎ ╎ ╎ ╎ 2 @Distributions/…:649 ccdf ╎ ╎ ╎ ╎ ╎ 2 @StatsFuns/….jl:9 chisqccdf ╎ ╎ ╎ ╎ ╎ 2 @StatsFuns/…jl:50 gammaccdf ╎ ╎ ╎ ╎ ╎ ╎ 2 @StatsFuns/…jl:48 gammaccdf ╎ ╎ ╎ ╎ ╎ ╎ 2 @SpecialFunctions/…:855 gamma_inc 1╎ ╎ ╎ ╎ ╎ ╎ 2 @SpecialFunctions/…:855 gamma_inc ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:859 _gamma_inc(a::Floa… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:966 getindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:387 checkbounds ╎ ╎ ╎ ╎ 77 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 76 @Base/array.jl:2458 findfirst ╎ ╎ ╎ ╎ 73 @Base/array.jl:2407 findnext ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:387 checkbounds 4╎ ╎ ╎ ╎ ╎ 4 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 68 @Base/…ators.jl:1195 Fix ╎ ╎ ╎ ╎ ╎ 68 @Base/…tors.jl:1195 #_#59 ╎ ╎ ╎ ╎ ╎ 68 @Base/…tors.jl:178 isequal 68╎ ╎ ╎ ╎ ╎ 68 @Base/…ring.jl:186 == ╎ ╎ ╎ ╎ 3 @Base/array.jl:2408 findnext 3╎ ╎ ╎ ╎ ╎ 3 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 1 @Base/array.jl:2458 findfirst ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2405 findnext ╎ ╎ ╎ ╎ ╎ 1 @Base/…ators.jl:425 > 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:78 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:966 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:387 checkbounds ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:85 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 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 + ╎ ╎ ╎ ╎ 571 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 571 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 63 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 63 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 63 @VariantCallFormat/…:147 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:160 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:2083 empty! ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:1246 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:219 _unsetindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:596 memoryref ╎ ╎ ╎ ╎ ╎ 53 @VariantCallFormat/…:169 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 48 @Automa/…en.jl:263 macro expansion ╎ ╎ ╎ ╎ ╎ 12 @Base/array.jl:411 getindex 12╎ ╎ ╎ ╎ ╎ 12 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 34 @Base/array.jl:1303 push! ╎ ╎ ╎ ╎ ╎ 31 @Base/…ray.jl:1306 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1165 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1168 _growend! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…als.jl:11 length ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1173 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 2╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ray.jl:1174 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1126 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1127 _growend_internal!(a::Vect… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ay.jl:1149 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ay.jl:1069 array_new_memory 14╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1152 _growend_internal!(a::Vect… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1153 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:118 unsafe_copyto! 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:1158 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:1307 _push! 2╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:1012 __safe_setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:387 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:383 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:967 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:264 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:291 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:56 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:49 checkbounds ╎ ╎ ╎ ╎ ╎ 2 @Automa/…ry.jl:57 getindex 2╎ ╎ ╎ ╎ ╎ 2 @Base/…nter.jl:151 unsafe_load 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:292 macro expansion ╎ ╎ ╎ ╎ ╎ 7 @VariantCallFormat/…:185 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 7 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 7 @BufferedStreams/…:71 fillbuffer! ╎ ╎ ╎ ╎ ╎ 7 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:387 readbytes!(stream::… ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:201 eof(stream::Transc… ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:582 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:596 fillbuffer(strea… ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:656 callprocess(str… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @CodecZlib/…:195 process(codec::GzipDeco… 7╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ 508 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 508 @VariantCallFormat/…:309 copy(record::VariantCallFo… 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 copy ╎ ╎ ╎ ╎ ╎ 5 @Base/array.jl:360 copy 5╎ ╎ ╎ ╎ ╎ 5 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:361 copy ╎ ╎ ╎ ╎ ╎ 1 @Base/…emory.jl:125 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ 1 @Base/cmem.jl:28 memmove ╎ ╎ ╎ ╎ ╎ 501 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 501 @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 ╎ ╎ ╎ ╎ ╎ 500 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 2╎ ╎ ╎ ╎ ╎ 500 @Base/…copy.jl:104 deepcopy_internal 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:0 _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 6 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:113 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:594 memoryref 64╎ ╎ ╎ ╎ ╎ 64 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 16╎ ╎ ╎ ╎ ╎ 16 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 17╎ ╎ ╎ ╎ ╎ 17 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 4╎ ╎ ╎ ╎ ╎ 5 @Base/…copy.jl:119 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:834 isbits 21╎ ╎ ╎ ╎ ╎ 329 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ct.jl:182 in 30╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 48 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/boot.jl:661 Array 13╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ot.jl:649 Array ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ict.jl:81 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:88 * 31╎ ╎ ╎ ╎ ╎ ╎ 32 @Base/…ict.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:61 setproperty! 6╎ ╎ ╎ ╎ ╎ ╎ 225 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 74 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 74 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 74 @Base/…ct.jl:182 in 73╎ ╎ ╎ ╎ ╎ ╎ 74 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 142 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…ct.jl:182 in 31╎ ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…ct.jl:92 get 11╎ ╎ ╎ ╎ ╎ ╎ 111 @Base/…py.jl:104 deepcopy_internal 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:108 _deepcopy_memory_t(x::Mem… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:827 isbitstype 14╎ ╎ ╎ ╎ ╎ ╎ 92 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ry.jl:179 copy(a::Memory{UnitRange… 14╎ ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ry.jl:180 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ry.jl:143 unsafe_copyto! 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ry.jl:125 unsafe_copyto! 8╎ ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…em.jl:28 memmove 50╎ ╎ ╎ ╎ ╎ ╎ 51 @Base/…ct.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:87 setindex! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ue.jl:59 getindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:0 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:144 deepcopy_internal(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…on.jl:637 == 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…opy.jl:134 deepcopy_internal(x::Vector… 41╎ ╎ ╎ ╎ ╎ 42 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 15╎ ╎ ╎ ╎ ╎ 15 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:125 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…nge.jl:929 iterate 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ion.jl:637 == ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== 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:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_36162.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ 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 0x0000796f288b15a0 Total snapshots: 418. Utilization: 0% ╎418 @Base/task.jl:1129 wait_forever() 417╎ 418 @Base/task.jl:1192 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:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_36162.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 20188049 (Pool: 20187492; Big: 557); GC: 22 [426] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 jl_egal_ at /source/src/julia.h:1852 [inlined] jl_table_assign_bp at /source/src/iddict.c:62 [inlined] ijl_eqtable_put at /source/src/iddict.c:146 setindex! at ./iddict.jl:86 [inlined] _deepcopy_memory_t at ./deepcopy.jl:109 _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_invoke at /source/src/gf.c:3800 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x7ba3de2f0fb6) at (unknown file) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 _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/YgfJC/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: 0x7ba3bd11e666) at (unknown file) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 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:1855 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_invoke at /source/src/gf.c:3800 jl_toplevel_eval_flex at /source/src/toplevel.c:762 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2848 _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 _include at ./loading.jl:2908 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_44279.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 jl_apply at /source/src/julia.h:2345 [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:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2848 _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 _include at ./loading.jl:2908 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_44279.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 jl_apply at /source/src/julia.h:2345 [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:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 exec_options at ./client.jl:286 _start at ./client.jl:553 jfptr__start_68801.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3793 [inlined] ijl_apply_generic at /source/src/gf.c:3993 jl_apply at /source/src/julia.h:2345 [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: 0x7ba3df62d249) 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: 20312992488 (Pool: 20312976998; Big: 15490); GC: 35722 PkgEval terminated after 2723.7s: test duration exceeded the time limit