Package evaluation of VCFTools on Julia 1.13.0-DEV.1022 (6a783956c1*) started at 2025-08-21T17:46:44.451 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.0s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... 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 v0.19.0 [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 v1.7.1 [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 v1.3.2 [21216c6a] + Preferences v1.5.0 [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 v2.2.9 [fdea26ae] + SIMD v3.7.1 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [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 v0.5.7 [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 v5.13.1+0 Installation completed after 4.65s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 57.37s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_zxLXB8/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 ⌃ [a93c6f00] DataFrames v1.5.0 [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 v0.34.6 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.7 [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_zxLXB8/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 v4.18.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 ⌃ [a93c6f00] DataFrames v1.5.0 [864edb3b] DataStructures v0.19.0 [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 v1.7.1 [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 v1.3.2 [21216c6a] Preferences v1.5.0 [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 v2.2.9 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [66db9d55] SnoopPrecompile v1.0.3 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.5.1 [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 v0.5.7 [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 v8.15.0+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.8.12 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.2+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 v5.13.1+0 [8e850ede] nghttp2_jll v1.66.0+0 Info Packages marked with ⌃ have new versions available and may be upgradable. Testing Running tests... Precompiling packages... 85921.0 ms ✓ DataFrames 1 dependency successfully precompiled in 87 seconds. 36 already precompiled. Test Summary: | Pass Total Time H-W test | 1 1 3.9s Test Summary: | Pass Total Time openvcf | 4 4 2.9s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.5s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.6s ┌ 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: 0:31:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 14.168147 seconds (10.90 M allocations: 686.200 MiB, 2.31% gc time, 95.22% compilation time: 20% of which was recompilation) 0.515939 seconds (2.86 M allocations: 195.929 MiB, 16.68% gc time, 16.60% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:33:13 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.455342 seconds (4.55 M allocations: 309.988 MiB, 2.58% gc time, 86.16% compilation time) 0.484270 seconds (2.85 M allocations: 195.424 MiB, 6.30% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 22.4s 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 2.4s 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 5.8s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:45 Progress: 0%|▏ | ETA: 0:19:24 Progress: 0%|▏ | ETA: 0:19:02 Progress: 0%|▏ | ETA: 0:19:02 Progress: 0%|▏ | ETA: 0:18:55 Progress: 1%|▎ | ETA: 0:18:46 Progress: 1%|▎ | ETA: 0:18:50 Progress: 1%|▎ | ETA: 0:18:46 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are matched 239.222690 seconds (2.19 G allocations: 143.725 GiB, 5.86% gc time, 0.33% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m00.4s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:33:17 Progress: 18%|███████▌ | ETA: 0:08:18 Progress: 37%|███████████████▏ | ETA: 0:03:09 Progress: 57%|███████████████████████▌ | ETA: 0:01:24 Progress: 77%|███████████████████████████████▊ | ETA: 0:00:33 Progress: 99%|████████████████████████████████████████▍| ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:01:54 [ Info: 833 records are matched 125.648357 seconds (1.11 G allocations: 72.816 GiB, 5.55% gc time, 0.42% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:30:22 Progress: 19%|███████▊ | ETA: 0:07:53 Progress: 38%|███████████████▋ | ETA: 0:03:01 Progress: 59%|████████████████████████▎ | ETA: 0:01:17 Progress: 80%|████████████████████████████████▊ | ETA: 0:00:28 Progress: 100%|█████████████████████████████████████████| Time: 0:01:54 [ Info: 493 records are matched 125.400028 seconds (1.11 G allocations: 72.816 GiB, 5.42% gc time, 0.42% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:25:57 Progress: 20%|████████▏ | ETA: 0:07:23 Progress: 40%|████████████████▌ | ETA: 0:02:45 Progress: 62%|█████████████████████████▎ | ETA: 0:01:10 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: 0 records are matched 124.689162 seconds (1.11 G allocations: 72.816 GiB, 5.41% gc time, 0.43% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m18.1s 1.057845 seconds (1.28 M allocations: 91.272 MiB, 1.82% gc time, 80.25% compilation time) 0.918215 seconds (1.16 M allocations: 86.630 MiB, 1.95% gc time, 75.70% compilation time) 0.900406 seconds (1.16 M allocations: 85.886 MiB, 2.12% gc time, 77.05% compilation time) 0.368930 seconds (203.63 k allocations: 11.564 MiB, 99.95% compilation time) 0.008815 seconds (6.18 k allocations: 483.492 KiB, 94.83% compilation time) 0.007815 seconds (2.65 k allocations: 247.555 KiB, 95.63% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 8.5s 0.886336 seconds (953.02 k allocations: 74.542 MiB, 3.88% gc time, 77.79% compilation time) 0.773904 seconds (860.78 k allocations: 71.566 MiB, 2.65% gc time, 72.41% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.7s Test Summary: | Pass Total Time convert_ds | 5 5 0.9s 0.118516 seconds (525.32 k allocations: 50.450 MiB, 10.50% gc time, 23.36% compilation time) 0.592882 seconds (647.62 k allocations: 57.719 MiB, 1.80% gc time, 84.67% 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 0.083288 seconds (520.43 k allocations: 51.916 MiB, 11.03% gc time) 0.479246 seconds (589.76 k allocations: 56.017 MiB, 2.24% gc time, 81.92% 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 0.127231 seconds (1.56 M allocations: 81.839 MiB, 5.92% compilation time) 0.591600 seconds (1.70 M allocations: 90.373 MiB, 69.01% 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 6.4s Test Summary: | Pass Total Time record info | 14 14 4.5s Test Summary: | Pass Total Time write VCF | 3 3 3.9s 2.208511 seconds (5.28 M allocations: 380.414 MiB, 3.02% gc time, 49.65% compilation time) 1.272480 seconds (2.86 M allocations: 194.918 MiB, 2.73% gc time, 15.58% compilation time) 1.134384 seconds (4.89 M allocations: 358.313 MiB, 4.59% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.5s 1.049533 seconds (617.53 k allocations: 54.348 MiB, 1.35% gc time, 41.44% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.8s Test Summary: | Pass Total Time filter_chr | 4 4 1.7s Progress: 0%|▏ | ETA: 0:24:16 Progress: 1%|▎ | ETA: 0:22:12 Progress: 1%|▌ | ETA: 0:21:47 Progress: 2%|▋ | ETA: 0:21:28 Progress: 2%|▊ | ETA: 0:21:11 Progress: 2%|█ | ETA: 0:21:04 Progress: 3%|█▏ | ETA: 0:20:59 Progress: 3%|█▎ | ETA: 0:20:54 Progress: 4%|█▍ | ETA: 0:20:50 Progress: 4%|█▋ | ETA: 0:20:41 Progress: 4%|█▊ | ETA: 0:20:38 Progress: 5%|█▉ | ETA: 0:20:32 Progress: 5%|██▏ | ETA: 0:20:25 Progress: 5%|██▎ | ETA: 0:20:16 Progress: 6%|██▍ | ETA: 0:20:08 Progress: 6%|██▋ | ETA: 0:20:02 Progress: 7%|██▊ | ETA: 0:19:57 Progress: 7%|██▉ | ETA: 0:19:53 Progress: 7%|███ | ETA: 0:19:49 Progress: 8%|███▎ | ETA: 0:19:45 Progress: 8%|███▍ | ETA: 0:19:37 Progress: 9%|███▌ | ETA: 0:19:29 Progress: 9%|███▊ | ETA: 0:19:22 Progress: 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99%|████████████████████████████████████████▊| ETA: 0:00:09 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 27 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: 0x731408ddcbe6) at (unknown file) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 _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/DDn3I/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: 0x7313e970a056) at (unknown file) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 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:1930 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_invoke at /source/src/gf.c:4029 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:2863 _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 _include at ./loading.jl:2923 include at ./Base.jl:309 IncludeInto at ./Base.jl:310 jfptr_IncludeInto_61059.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [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:2863 _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 _include at ./loading.jl:2923 include at ./Base.jl:309 IncludeInto at ./Base.jl:310 jfptr_IncludeInto_61059.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [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:296 _start at ./client.jl:563 jfptr__start_44596.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [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: 0x73140a15f249) 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: 99%|████████████████████████████████████████▉| ETA: 0:00:04┌ 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 0x00007313efe00010 Total snapshots: 621. Utilization: 100% ╎618 @Base/client.jl:563 _start() ╎ 618 @Base/client.jl:296 exec_options(opts::Base.JLOptions) ╎ 618 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 618 @Base/Base.jl:310 (::Base.IncludeInto)(fname::String) ╎ 618 @Base/Base.jl:309 include(mapexpr::Function, mod::Module, _path::St… ╎ 618 @Base/loading.jl:2923 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 618 @Base/loading.jl:2863 include_string(mapexpr::typeof(identity), m… ╎ ╎ 618 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 618 @Base/Base.jl:310 (::Base.IncludeInto)(fname::String) ╎ ╎ 618 @Base/Base.jl:309 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 618 @Base/loading.jl:2923 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 618 @Base/loading.jl:2863 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 618 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 618 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 618 @Test/src/Test.jl:1930 macro expansion ╎ ╎ ╎ 618 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 618 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 83 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 16 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 16 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:125 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ 10 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:387 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:383 checkbounds 4╎ ╎ ╎ ╎ ╎ 4 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 2 @Base/…ators.jl:425 > 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 3 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:387 checkbounds ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:383 checkbounds 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:11 length 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 4 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:3158 getindex 2╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:954 _getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:3158 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:954 _getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:941 _in_unit_range ╎ ╎ ╎ ╎ 56 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 56 @Base/array.jl:2465 findfirst ╎ ╎ ╎ ╎ 56 @Base/array.jl:2414 findnext 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 54 @Base/…ators.jl:1195 Fix ╎ ╎ ╎ ╎ ╎ 54 @Base/…tors.jl:1195 #_#58 ╎ ╎ ╎ ╎ ╎ 54 @Base/…tors.jl:178 isequal 54╎ ╎ ╎ ╎ ╎ 54 @Base/…ring.jl:186 == ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 2 @Base/array.jl:2465 findfirst ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:2414 findnext ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:673 isequaldata 2╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:78 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:966 getindex 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:387 checkbounds 2╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:82 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3158 getindex ╎ ╎ ╎ ╎ 1 @Base/range.jl:954 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:941 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:522 <= 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:83 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…motion.jl:637 == ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:99 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:45 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:483 next! ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:484 #next!#15 ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:465 lock_if_threading 2╎ ╎ ╎ ╎ ╎ 2 @ProgressMeter/…:453 is_threading ╎ ╎ ╎ ╎ 533 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 533 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 100 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 100 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 3╎ ╎ ╎ ╎ ╎ 100 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:156 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:2090 empty! ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1253 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:219 _unsetindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:596 memoryref ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1254 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…nge.jl:923 iterate 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ion.jl:637 == ╎ ╎ ╎ ╎ ╎ 67 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 52 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 15 @Base/array.jl:411 getindex 13╎ ╎ ╎ ╎ ╎ 15 @Base/boot.jl:649 Array 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:594 memoryref ╎ ╎ ╎ ╎ ╎ 33 @Base/array.jl:1310 push! ╎ ╎ ╎ ╎ ╎ 27 @Base/…ray.jl:1313 _push! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1176 _growend! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:87 + 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1177 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1180 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 5╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…ray.jl:1181 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1133 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ay.jl:1156 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ay.jl:1076 array_new_memory 11╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1159 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:595 memoryref 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1161 _growend_internal!(a::Vect… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1165 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 6 @Base/…ray.jl:1314 _push! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:0 __safe_setindex! 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ray.jl:1019 __safe_setindex! 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:5 Colon ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:415 UnitRange 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:426 unitrange_last ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:216 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/…ast.jl:1355 broadcasted ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ast.jl:1159 broadcasted ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:157 range ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:157 #range#29 ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:173 _range ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:218 range_start_stop ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:5 Colon ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:415 UnitRange 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:426 unitrange_last ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:463 macro expansion 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:464 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Base/…tors.jl:425 > 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 < 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:503 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:572 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…yops.jl:50 vload ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…sics.jl:470 load 2╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:479 macro expansion ╎ ╎ ╎ ╎ ╎ 6 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 6 @SIMD/…dvec.jl:481 all ╎ ╎ ╎ ╎ ╎ 6 @SIMD/…dvec.jl:476 reduce ╎ ╎ ╎ ╎ ╎ ╎ 6 @SIMD/…ics.jl:832 reduce_and 6╎ ╎ ╎ ╎ ╎ ╎ 6 @SIMD/…ics.jl:847 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:583 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @Automa/…ry.jl:56 getindex 1╎ ╎ ╎ ╎ ╎ 3 @Automa/…ry.jl:49 checkbounds 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:522 <= ╎ ╎ ╎ ╎ ╎ 27 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 27 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 27 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 27 @BufferedStreams/…:5 readbytes! 1╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/io.jl:1160 readbytes!(s::TranscodingStr… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:209 eof 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:212 eof ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @CodecZlib/…:195 process(codec::GzipDec… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/io.jl:1161 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 13 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/io.jl:359 peek ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:298 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:206 eof ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:52 buffersize 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:212 eof ╎ ╎ ╎ ╎ ╎ ╎ 11 @TranscodingStreams/…:302 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:966 getindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:387 checkbounds 10╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ls.jl:967 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:307 read ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:97 consumed! ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:98 #consumed!#1 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1163 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ors.jl:425 > 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/io.jl:1167 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ray.jl:398 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ay.jl:995 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:999 _setindex! 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:1000 _setindex! ╎ ╎ ╎ ╎ 433 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 433 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 6 @Base/array.jl:360 copy 6╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 427 @Base/…pcopy.jl:34 deepcopy 1╎ ╎ ╎ ╎ ╎ 1 @Base/…pcopy.jl:0 deepcopy_internal(x::Vector{Vec… ╎ ╎ ╎ ╎ ╎ 426 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 425 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 5╎ ╎ ╎ ╎ ╎ 425 @Base/…copy.jl:104 deepcopy_internal 58╎ ╎ ╎ ╎ ╎ 58 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 15╎ ╎ ╎ ╎ ╎ 15 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 10╎ ╎ ╎ ╎ ╎ 10 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:119 _deepcopy_memory_t(x::Memor… 14╎ ╎ ╎ ╎ ╎ 285 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ct.jl:182 in 24╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ct.jl:92 get 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 50 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:661 Array 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ot.jl:649 Array 42╎ ╎ ╎ ╎ ╎ ╎ 44 @Base/…ict.jl:86 setindex! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ler.jl:61 setproperty! 1╎ ╎ ╎ ╎ ╎ ╎ 194 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 66 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 66 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 66 @Base/…ct.jl:182 in 63╎ ╎ ╎ ╎ ╎ ╎ 66 @Base/…ct.jl:92 get 3╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 124 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:182 in 24╎ ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:92 get 6╎ ╎ ╎ ╎ ╎ ╎ 100 @Base/…py.jl:104 deepcopy_internal 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 21╎ ╎ ╎ ╎ ╎ ╎ 88 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ry.jl:175 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…ry.jl:179 copy(a::Memory{UnitRange… 17╎ ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ry.jl:180 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ry.jl:143 unsafe_copyto! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ry.jl:125 unsafe_copyto! 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…em.jl:28 memmove ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:81 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:88 * 38╎ ╎ ╎ ╎ ╎ ╎ 38 @Base/…ct.jl:86 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:87 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! 41╎ ╎ ╎ ╎ ╎ 41 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 8╎ ╎ ╎ ╎ ╎ 8 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:125 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:923 iterate ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:144 deepcopy_internal(x::MemoryRe… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tion.jl:637 == Progress: 100%|█████████████████████████████████████████| Time: 0:21:18 ====================================================================================== 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:1200 wait_forever at ./task.jl:1137 jfptr_wait_forever_51086.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Test Summary: | Pass Total Time AIM selection | 4 4 22m02.7s ============================================================== 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 0x000078266af28c40 Total snapshots: 467. Utilization: 0% ╎467 @Base/task.jl:1137 wait_forever() 466╎ 467 @Base/task.jl:1200 wait() [27] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/grm_test.jl:1 unsafe_load at ./pointer.jl:151 [inlined] getindex at /home/pkgeval/.julia/packages/Automa/EyNRt/src/memory.jl:57 [inlined] macro expansion at /home/pkgeval/.julia/packages/Automa/EyNRt/src/codegen.jl:583 [inlined] _read! at /home/pkgeval/.julia/packages/VariantCallFormat/DDn3I/src/ReaderHelper.jl:165 _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 read! at /home/pkgeval/.julia/packages/VariantCallFormat/DDn3I/src/ReaderHelper.jl:142 #copy_gt!#5 at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/convert.jl:77 copy_gt! at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/convert.jl:52 unknown function (ip: 0x7313eb51afe4) at (unknown file) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 #convert_gt#7 at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/convert.jl:0 convert_gt at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/convert.jl:262 [inlined] #grm#19 at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/grm.jl:29 grm at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/grm.jl:19 unknown function (ip: 0x7313e97399b6) at (unknown file) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_body at /source/src/interpreter.c:581 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 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:2863 _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 _include at ./loading.jl:2923 include at ./Base.jl:309 IncludeInto at ./Base.jl:310 jfptr_IncludeInto_61059.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [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:2863 _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 _include at ./loading.jl:2923 include at ./Base.jl:309 IncludeInto at ./Base.jl:310 jfptr_IncludeInto_61059.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [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:296 _start at ./client.jl:563 jfptr__start_44596.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [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: 0x73140a15f249) 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: 20555342850 (Pool: 20555327217; Big: 15633); GC: 37142 PkgEval terminated after 2726.3s: test duration exceeded the time limit