Package evaluation of VCFTools on Julia 1.13.0-DEV.943 (cce193b1aa*) started at 2025-08-02T07:59:20.140 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.48s ################################################################################ # 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 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 v4.18.0 [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 v1.7.1 [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 [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 v1.13.0 [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 v1.13.0 [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 [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 4.65s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 27.96s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_sf6cwD/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 v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_sf6cwD/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 v4.18.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 ⌅ [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 v1.7.1 [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 v1.4.3 [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 v1.13.0 [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 [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+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [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... Precompiling packages... 31977.7 ms ✓ CSV 1 dependency successfully precompiled in 32 seconds. 38 already precompiled. Test Summary: | Pass Total Time H-W test | 1 1 3.5s Test Summary: | Pass Total Time openvcf | 4 4 3.0s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.4s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.2s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:24:26 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 13.402835 seconds (10.59 M allocations: 664.093 MiB, 5.19% gc time, 95.91% compilation time: 25% of which was recompilation) 0.443916 seconds (2.86 M allocations: 195.973 MiB, 10.04% gc time, 17.89% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:23:14 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.438416 seconds (4.37 M allocations: 298.007 MiB, 2.29% gc time, 84.45% compilation time) 0.407262 seconds (2.85 M allocations: 195.340 MiB, 6.15% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 20.2s 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 1.9s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 6.1s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:43 Progress: 0%|▏ | ETA: 0:17:25 Progress: 0%|▏ | ETA: 0:17:17 Progress: 0%|▏ | ETA: 0:17:12 Progress: 0%|▎ | ETA: 0:17:06 Progress: 1%|▎ | ETA: 0:17:05 Progress: 1%|▎ | ETA: 0:16:57 Progress: 1%|▍ | ETA: 0:17:02 Progress: 1%|▍ | ETA: 0:17:01 Progress: 1%|▍ | ETA: 0:17:00 Progress: 1%|▌ | ETA: 0:17:00 Progress: 1%|▌ | ETA: 0:17:02 Progress: 1%|▌ | ETA: 0:16:58 Progress: 1%|▋ | ETA: 0:16:33 Progress: 2%|▋ | ETA: 0:16:00 Progress: 2%|▊ | ETA: 0:15:33 Progress: 2%|▊ | ETA: 0:15:11 Progress: 2%|▉ | ETA: 0:14:52 Progress: 2%|▉ | ETA: 0:14:35 Progress: 2%|█ | ETA: 0:14:24 Progress: 2%|█ | ETA: 0:14:16 Progress: 3%|█ | ETA: 0:14:20 Progress: 3%|█▏ | ETA: 0:14:21 Progress: 3%|█▏ | ETA: 0:14:23 Progress: 3%|█▏ | ETA: 0:14:27 Progress: 3%|█▎ | ETA: 0:14:30 Progress: 3%|█▎ | ETA: 0:14:33 Progress: 3%|█▎ | ETA: 0:14:36 Progress: 3%|█▍ | ETA: 0:14:37 Progress: 3%|█▍ | ETA: 0:14:40 Progress: 3%|█▍ | ETA: 0:14:41 Progress: 4%|█▌ | ETA: 0:14:39 Progress: 4%|█▌ | ETA: 0:14:40 Progress: 4%|█▌ | ETA: 0:14:42 Progress: 4%|█▋ | ETA: 0:14:44 Progress: 4%|█▋ | ETA: 0:14:45 Progress: 4%|█▋ | ETA: 0:14:47 Progress: 4%|█▊ | ETA: 0:14:48 Progress: 4%|█▊ | ETA: 0:14:49 Progress: 4%|█▊ | ETA: 0:14:51 Progress: 4%|█▉ | ETA: 0:14:51 Progress: 5%|█▉ | ETA: 0:14:51 Progress: 5%|█▉ | ETA: 0:14:52 Progress: 5%|██ | ETA: 0:14:53 Progress: 5%|██ | ETA: 0:14:53 Progress: 5%|██ | ETA: 0:14:53 Progress: 5%|██▏ | ETA: 0:14:52 Progress: 5%|██▏ | ETA: 0:14:51 Progress: 5%|██▏ | ETA: 0:14:52 Progress: 5%|██▎ | ETA: 0:14:52 Progress: 6%|██▎ | ETA: 0:14:52 Progress: 6%|██▎ | ETA: 0:14:53 Progress: 6%|██▍ | ETA: 0:14:53 Progress: 6%|██▍ | ETA: 0:14:54 Progress: 6%|██▍ | ETA: 0:14:54 Progress: 6%|██▌ | ETA: 0:14:54 Progress: 6%|██▌ | ETA: 0:14:55 Progress: 6%|██▌ | ETA: 0:14:54 Progress: 6%|██▋ | ETA: 0:14:49 Progress: 6%|██▋ | ETA: 0:14:43 Progress: 7%|██▊ | ETA: 0:14:41 Progress: 7%|██▊ | ETA: 0:14:40 Progress: 7%|██▊ | ETA: 0:14:39 Progress: 7%|██▉ | ETA: 0:14:36 Progress: 7%|██▉ | ETA: 0:14:35 Progress: 7%|███ | ETA: 0:14:35 Progress: 7%|███ | ETA: 0:14:35 Progress: 7%|███ | ETA: 0:14:35 Progress: 7%|███▏ | ETA: 0:14:35 Progress: 8%|███▏ | ETA: 0:14:35 Progress: 8%|███▏ | ETA: 0:14:35 Progress: 8%|███▎ | ETA: 0:14:34 Progress: 8%|███▎ | ETA: 0:14:33 Progress: 8%|███▎ | ETA: 0:14:32 Progress: 8%|███▍ | ETA: 0:14:32 Progress: 8%|███▍ | ETA: 0:14:31 Progress: 8%|███▍ | ETA: 0:14:30 Progress: 8%|███▌ | ETA: 0:14:29 Progress: 9%|███▌ | ETA: 0:14:28 Progress: 9%|███▌ | ETA: 0:14:27 Progress: 9%|███▋ | ETA: 0:14:25 Progress: 9%|███▋ | ETA: 0:14:24 Progress: 9%|███▋ | ETA: 0:14:24 Progress: 9%|███▊ | ETA: 0:14:24 Progress: 9%|███▊ | ETA: 0:14:23 Progress: 9%|███▊ | ETA: 0:14:23 Progress: 9%|███▉ | ETA: 0:14:23 Progress: 9%|███▉ | ETA: 0:14:22 Progress: 10%|███▉ | ETA: 0:14:21 Progress: 10%|████ | ETA: 0:14:18 Progress: 10%|████ | ETA: 0:14:18 Progress: 10%|████▏ | ETA: 0:14:17 Progress: 10%|████▏ | ETA: 0:14:16 Progress: 10%|████▏ | ETA: 0:14:16 Progress: 10%|████▎ | ETA: 0:14:15 Progress: 10%|████▎ | ETA: 0:14:14 Progress: 100%|█████████████████████████████████████████| Time: 0:01:38 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:20:08 Progress: 19%|███████▊ | ETA: 0:07:24 Progress: 39%|███████████████▉ | ETA: 0:02:45 Progress: 61%|████████████████████████▉ | ETA: 0:01:08 Progress: 83%|█████████████████████████████████▉ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 823 records are matched 217.035759 seconds (2.19 G allocations: 143.742 GiB, 6.28% gc time, 0.59% compilation time: 4% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:08 Progress: 0%|▏ | ETA: 0:17:15 Progress: 0%|▏ | ETA: 0:16:55 Progress: 0%|▏ | ETA: 0:16:46 Progress: 1%|▎ | ETA: 0:15:27 Progress: 1%|▎ | ETA: 0:15:00 Progress: 1%|▍ | ETA: 0:15:00 Progress: 1%|▍ | ETA: 0:15:05 Progress: 1%|▍ | ETA: 0:15:06 Progress: 1%|▌ | ETA: 0:15:13 Progress: 1%|▌ | ETA: 0:15:19 Progress: 1%|▌ | ETA: 0:15:25 Progress: 1%|▋ | ETA: 0:15:30 Progress: 2%|▋ | ETA: 0:15:30 Progress: 2%|▋ | ETA: 0:15:33 Progress: 2%|▊ | ETA: 0:15:38 Progress: 2%|▊ | ETA: 0:15:40 Progress: 2%|▊ | ETA: 0:15:42 Progress: 2%|▉ | ETA: 0:15:44 Progress: 2%|▉ | ETA: 0:15:45 Progress: 2%|▉ | ETA: 0:15:48 Progress: 2%|█ | ETA: 0:15:48 Progress: 2%|█ | ETA: 0:15:50 Progress: 3%|█ | ETA: 0:15:51 Progress: 3%|█▏ | ETA: 0:15:50 Progress: 3%|█▏ | ETA: 0:15:44 Progress: 3%|█▏ | ETA: 0:15:30 Progress: 3%|█▎ | ETA: 0:15:24 Progress: 3%|█▎ | ETA: 0:15:23 Progress: 3%|█▍ | ETA: 0:15:22 Progress: 3%|█▍ | ETA: 0:15:21 Progress: 3%|█▍ | ETA: 0:15:23 Progress: 4%|█▌ | ETA: 0:15:23 Progress: 4%|█▌ | ETA: 0:15:25 Progress: 4%|█▌ | ETA: 0:15:25 Progress: 4%|█▋ | ETA: 0:15:25 Progress: 4%|█▋ | ETA: 0:15:26 Progress: 4%|█▋ | ETA: 0:15:27 Progress: 4%|█▊ | ETA: 0:15:27 Progress: 4%|█▊ | ETA: 0:15:27 Progress: 4%|█▊ | ETA: 0:15:27 Progress: 4%|█▉ | ETA: 0:15:22 Progress: 5%|█▉ | ETA: 0:15:19 Progress: 5%|█▉ | ETA: 0:15:19 Progress: 5%|██ | ETA: 0:15:16 Progress: 5%|██ | ETA: 0:15:15 Progress: 5%|██▏ | ETA: 0:15:14 Progress: 5%|██▏ | ETA: 0:15:13 Progress: 5%|██▏ | ETA: 0:15:13 Progress: 5%|██▎ | ETA: 0:15:13 Progress: 5%|██▎ | ETA: 0:15:12 Progress: 6%|██▎ | ETA: 0:15:12 Progress: 6%|██▍ | ETA: 0:15:11 Progress: 6%|██▍ | ETA: 0:15:11 Progress: 6%|██▍ | ETA: 0:15:10 Progress: 6%|██▌ | ETA: 0:15:09 Progress: 6%|██▌ | ETA: 0:15:08 Progress: 6%|██▌ | ETA: 0:15:08 Progress: 6%|██▋ | ETA: 0:15:07 Progress: 6%|██▋ | ETA: 0:15:07 Progress: 6%|██▋ | ETA: 0:15:06 Progress: 7%|██▊ | ETA: 0:15:06 Progress: 7%|██▊ | ETA: 0:15:06 Progress: 7%|██▊ | ETA: 0:15:06 Progress: 7%|██▉ | ETA: 0:15:05 Progress: 7%|██▉ | ETA: 0:15:05 Progress: 7%|██▉ | ETA: 0:15:05 Progress: 7%|██▉ | ETA: 0:15:04 Progress: 7%|███ | ETA: 0:15:03 Progress: 7%|███ | ETA: 0:15:02 Progress: 7%|███ | ETA: 0:15:01 Progress: 8%|███▏ | ETA: 0:15:00 Progress: 8%|███▏ | ETA: 0:15:00 Progress: 8%|███▎ | ETA: 0:14:55 Progress: 8%|███▎ | ETA: 0:14:54 Progress: 8%|███▎ | ETA: 0:14:52 Progress: 8%|███▍ | ETA: 0:14:51 Progress: 8%|███▍ | ETA: 0:14:50 Progress: 8%|███▍ | ETA: 0:14:49 Progress: 8%|███▌ | ETA: 0:14:48 Progress: 9%|███▌ | ETA: 0:14:48 Progress: 9%|███▌ | ETA: 0:14:47 Progress: 9%|███▋ | ETA: 0:14:47 Progress: 9%|███▋ | ETA: 0:14:46 Progress: 9%|███▋ | ETA: 0:14:45 Progress: 9%|███▊ | ETA: 0:14:44 Progress: 9%|███▊ | ETA: 0:14:43 Progress: 9%|███▊ | ETA: 0:14:43 Progress: 9%|███▉ | ETA: 0:14:43 Progress: 9%|███▉ | ETA: 0:14:42 Progress: 10%|███▉ | ETA: 0:14:42 Progress: 10%|████ | ETA: 0:14:41 Progress: 10%|████ | ETA: 0:14:40 Progress: 10%|████ | ETA: 0:14:40 Progress: 10%|████▏ | ETA: 0:14:39 Progress: 10%|████▏ | ETA: 0:14:38 Progress: 10%|████▏ | ETA: 0:14:37 Progress: 10%|████▎ | ETA: 0:14:37 Progress: 100%|█████████████████████████████████████████| Time: 0:01:40 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:53:55 Progress: 20%|████████▏ | ETA: 0:06:52 Progress: 41%|████████████████▊ | ETA: 0:02:27 Progress: 64%|██████████████████████████▏ | ETA: 0:00:59 Progress: 86%|███████████████████████████████████▎ | ETA: 0:00:17 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 488 records are matched 216.530452 seconds (2.19 G allocations: 143.726 GiB, 6.36% gc time, 0.39% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:01 Progress: 0%|▏ | ETA: 0:17:34 Progress: 0%|▏ | ETA: 0:17:16 Progress: 0%|▏ | ETA: 0:17:07 Progress: 0%|▎ | ETA: 0:17:04 Progress: 1%|▎ | ETA: 0:16:59 Progress: 1%|▎ | ETA: 0:16:57 Progress: 1%|▍ | ETA: 0:16:57 Progress: 1%|▍ | ETA: 0:16:55 Progress: 1%|▍ | ETA: 0:16:54 Progress: 1%|▌ | ETA: 0:16:57 Progress: 1%|▌ | ETA: 0:16:57 Progress: 1%|▌ | ETA: 0:16:56 Progress: 1%|▌ | ETA: 0:16:54 Progress: 1%|▋ | ETA: 0:16:53 Progress: 2%|▋ | ETA: 0:16:51 Progress: 2%|▋ | ETA: 0:16:50 Progress: 2%|▊ | ETA: 0:16:48 Progress: 2%|▊ | ETA: 0:16:46 Progress: 2%|▊ | ETA: 0:16:46 Progress: 2%|▉ | ETA: 0:16:45 Progress: 2%|▉ | ETA: 0:16:43 Progress: 2%|▉ | ETA: 0:16:43 Progress: 2%|█ | ETA: 0:16:41 Progress: 2%|█ | ETA: 0:16:40 Progress: 3%|█ | ETA: 0:16:38 Progress: 3%|█▏ | ETA: 0:16:38 Progress: 3%|█▏ | ETA: 0:16:37 Progress: 3%|█▏ | ETA: 0:16:36 Progress: 3%|█▎ | ETA: 0:16:35 Progress: 3%|█▎ | ETA: 0:16:33 Progress: 3%|█▎ | ETA: 0:16:32 Progress: 3%|█▍ | ETA: 0:16:30 Progress: 3%|█▍ | ETA: 0:16:29 Progress: 3%|█▍ | ETA: 0:16:28 Progress: 4%|█▌ | ETA: 0:16:26 Progress: 4%|█▌ | ETA: 0:16:25 Progress: 4%|█▌ | ETA: 0:16:23 Progress: 4%|█▋ | ETA: 0:16:22 Progress: 4%|█▋ | ETA: 0:16:21 Progress: 4%|█▋ | ETA: 0:16:21 Progress: 4%|█▊ | ETA: 0:16:19 Progress: 4%|█▊ | ETA: 0:16:18 Progress: 4%|█▊ | ETA: 0:16:17 Progress: 4%|█▉ | ETA: 0:16:11 Progress: 5%|█▉ | ETA: 0:16:09 Progress: 5%|█▉ | ETA: 0:16:08 Progress: 5%|██ | ETA: 0:16:07 Progress: 5%|██ | ETA: 0:16:06 Progress: 5%|██ | ETA: 0:16:05 Progress: 5%|██▏ | ETA: 0:16:04 Progress: 5%|██▏ | ETA: 0:16:02 Progress: 5%|██▏ | ETA: 0:16:01 Progress: 5%|██▎ | ETA: 0:15:59 Progress: 5%|██▎ | ETA: 0:15:58 Progress: 6%|██▎ | ETA: 0:15:56 Progress: 6%|██▍ | ETA: 0:15:55 Progress: 6%|██▍ | ETA: 0:15:52 Progress: 6%|██▍ | ETA: 0:15:51 Progress: 6%|██▌ | ETA: 0:15:48 Progress: 6%|██▌ | ETA: 0:15:45 Progress: 6%|██▌ | ETA: 0:15:43 Progress: 6%|██▋ | ETA: 0:15:40 Progress: 6%|██▋ | ETA: 0:15:40 Progress: 7%|██▊ | ETA: 0:15:37 Progress: 7%|██▊ | ETA: 0:15:36 Progress: 7%|██▊ | ETA: 0:15:33 Progress: 7%|██▉ | ETA: 0:15:31 Progress: 7%|██▉ | ETA: 0:15:30 Progress: 7%|██▉ | ETA: 0:15:29 Progress: 7%|███ | ETA: 0:15:28 Progress: 7%|███ | ETA: 0:15:27 Progress: 7%|███ | ETA: 0:15:26 Progress: 8%|███▏ | ETA: 0:15:25 Progress: 8%|███▏ | ETA: 0:15:24 Progress: 8%|███▏ | ETA: 0:15:22 Progress: 8%|███▎ | ETA: 0:15:21 Progress: 8%|███▎ | ETA: 0:15:20 Progress: 8%|███▎ | ETA: 0:15:19 Progress: 8%|███▍ | ETA: 0:15:18 Progress: 8%|███▍ | ETA: 0:15:17 Progress: 8%|███▍ | ETA: 0:15:16 Progress: 8%|███▌ | ETA: 0:15:15 Progress: 9%|███▌ | ETA: 0:15:14 Progress: 9%|███▌ | ETA: 0:15:14 Progress: 9%|███▋ | ETA: 0:15:13 Progress: 9%|███▋ | ETA: 0:15:13 Progress: 9%|███▋ | ETA: 0:15:12 Progress: 9%|███▊ | ETA: 0:15:11 Progress: 9%|███▊ | ETA: 0:15:11 Progress: 9%|███▊ | ETA: 0:15:10 Progress: 9%|███▊ | ETA: 0:15:09 Progress: 9%|███▉ | ETA: 0:15:08 Progress: 10%|███▉ | ETA: 0:15:07 Progress: 10%|███▉ | ETA: 0:15:06 Progress: 10%|████ | ETA: 0:15:05 Progress: 10%|████ | ETA: 0:15:04 Progress: 10%|████ | ETA: 0:15:03 Progress: 10%|████▏ | ETA: 0:15:02 Progress: 10%|████▏ | ETA: 0:15:01 Progress: 10%|████▏ | ETA: 0:15:00 Progress: 10%|████▎ | ETA: 0:15:00 Progress: 100%|█████████████████████████████████████████| Time: 0:01:43 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:52:56 Progress: 22%|█████████ | ETA: 0:06:03 Progress: 45%|██████████████████▌ | ETA: 0:02:05 Progress: 69%|████████████████████████████▎ | ETA: 0:00:47 Progress: 93%|██████████████████████████████████████▏ | ETA: 0:00:08 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: 0 records are matched 218.626061 seconds (2.19 G allocations: 143.725 GiB, 6.39% gc time, 0.39% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m03.5s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 17:01:55 Progress: 29%|███████████▉ | ETA: 0:03:44 Progress: 60%|████████████████████████▋ | ETA: 0:01:01 Progress: 91%|█████████████████████████████████████▎ | ETA: 0:00:09 Progress: 100%|█████████████████████████████████████████| Time: 0:01:33 [ Info: 833 records are matched 103.688162 seconds (1.11 G allocations: 72.817 GiB, 6.43% gc time, 0.52% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 16:39:27 Progress: 21%|████████▋ | ETA: 0:05:34 Progress: 44%|█████████████████▉ | ETA: 0:01:58 Progress: 66%|███████████████████████████▏ | ETA: 0:00:47 Progress: 91%|█████████████████████████████████████▎ | ETA: 0:00:09 Progress: 100%|█████████████████████████████████████████| Time: 0:01:33 [ Info: 493 records are matched 100.695265 seconds (1.11 G allocations: 72.816 GiB, 6.49% gc time, 0.42% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 15:12:51 Progress: 27%|███████████ | ETA: 0:03:43 Progress: 53%|█████████████████████▉ | ETA: 0:01:12 Progress: 78%|███████████████████████████████▉ | ETA: 0:00:24 Progress: 100%|█████████████████████████████████████████| Time: 0:01:24 [ Info: 0 records are matched 94.717213 seconds (1.11 G allocations: 72.816 GiB, 6.48% gc time, 0.60% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m00.6s 0.941490 seconds (1.28 M allocations: 91.364 MiB, 2.78% gc time, 85.73% compilation time) 0.800322 seconds (1.16 M allocations: 86.627 MiB, 2.54% gc time, 81.74% compilation time) 0.781389 seconds (1.16 M allocations: 85.895 MiB, 2.13% gc time, 82.84% compilation time) 0.352663 seconds (203.65 k allocations: 11.567 MiB, 99.96% compilation time) 0.009258 seconds (6.18 k allocations: 483.492 KiB, 96.03% compilation time) 0.007579 seconds (2.65 k allocations: 247.555 KiB, 96.17% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 8.1s 0.778009 seconds (953.07 k allocations: 74.546 MiB, 3.76% gc time, 82.66% compilation time) 0.681015 seconds (860.79 k allocations: 71.564 MiB, 2.99% gc time, 81.63% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.4s Test Summary: | Pass Total Time convert_ds | 5 5 0.9s 0.103060 seconds (525.32 k allocations: 50.449 MiB, 10.73% gc time, 27.29% compilation time) 0.602885 seconds (647.55 k allocations: 57.715 MiB, 2.17% gc time, 86.17% 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 0.040833 seconds (520.43 k allocations: 51.916 MiB) 0.479127 seconds (589.78 k allocations: 56.018 MiB, 78.62% 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 convert to transpose functions: Test Failed at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 Expression: all(out[1358:var"end", :] .== 0.0) Evaluated: all(Bool[0 0 … 0 0; 0 0 … 0 0; … ; 0 0 … 0 0; 0 0 … 0 0]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:745 [inlined] [2] macro expansion @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1859 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.151253 seconds (1.56 M allocations: 81.839 MiB, 20.09% gc time, 5.38% compilation time) 0.560663 seconds (1.70 M allocations: 90.372 MiB, 80.36% 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 Fail Total Time convert to transpose functions | 12 1 13 10.5s RNG of the outermost testset: Xoshiro(0x6ad1a75ab1e02a75, 0x32ebdebad666b4b7, 0x54b080c9094d9932, 0x736d9052e8843f53, 0xd306b9bcbf3601d9) ERROR: LoadError: Some tests did not pass: 12 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:72 in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/runtests.jl:17 Testing failed after 1087.36s ERROR: LoadError: Package VCFTools errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2695 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2544 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:538 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:515 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:311 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [14] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1205.23s: package has test failures