Package evaluation to test VCFTools on Julia 1.14.0-DEV.1441 (812f3beb0a*) started at 2025-12-30T17:25:52.645 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.01s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [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 v1.1.0 [38540f10] + CommonSolve v0.2.6 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [4c63d2b9] + StatsFuns v1.5.2 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 5.05s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 Precompilation failed after 13.55s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_2JE78p/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.9 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [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_2JE78p/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [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 v1.1.0 [38540f10] CommonSolve v0.2.6 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [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 v1.13.0 [b27032c2] LibCURL v1.0.0 [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 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.4s Test Summary: | Pass Total Time openvcf | 4 4 2.3s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 1.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.1s ┌ 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: 0:19:53 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 10.987353 seconds (9.78 M allocations: 552.473 MiB, 6.65% gc time, 94.98% compilation time: 16% of which was recompilation) 0.393501 seconds (2.37 M allocations: 141.305 MiB, 10.69% gc time, 13.88% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:20:56 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.246600 seconds (4.01 M allocations: 236.786 MiB, 3.38% gc time, 82.54% compilation time) 0.405771 seconds (2.37 M allocations: 141.299 MiB, 6.36% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 16.9s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.3s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.3s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.7s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 1.5s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:27 Progress: 0%|▏ | ETA: 0:22:07 Progress: 0%|▏ | ETA: 0:19:55 Progress: 0%|▏ | ETA: 0:20:54 Progress: 0%|▎ | ETA: 0:19:56 Progress: 1%|▎ | ETA: 0:19:07 Progress: 1%|▎ | ETA: 0:19:44 Progress: 1%|▍ | ETA: 0:19:13 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19%|███████▉ | ETA: 0:07:53 Progress: 38%|███████████████▋ | ETA: 0:03:04 Progress: 62%|█████████████████████████▎ | ETA: 0:01:12 Progress: 85%|██████████████████████████████████▊ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:56 [ Info: 823 records are matched 240.891843 seconds (2.01 G allocations: 106.140 GiB, 17.93% gc time, 0.37% compilation time: 9% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:11:24 Progress: 0%|▏ | ETA: 0:13:48 Progress: 0%|▏ | ETA: 0:14:22 Progress: 1%|▎ | ETA: 0:16:00 Progress: 1%|▎ | ETA: 0:15:48 Progress: 1%|▎ | ETA: 0:15:48 Progress: 1%|▍ | ETA: 0:16:40 Progress: 1%|▍ | ETA: 0:16:35 Progress: 1%|▍ | ETA: 0:17:11 Progress: 1%|▌ | ETA: 0:17:01 Progress: 1%|▌ | ETA: 0:16:54 Progress: 1%|▌ | ETA: 0:17:08 Progress: 1%|▋ | ETA: 0:16:48 Progress: 2%|▋ | ETA: 0:16:30 Progress: 2%|▊ | ETA: 0:16:49 Progress: 2%|▊ | ETA: 0:16:45 Progress: 2%|▊ | ETA: 0:16:40 Progress: 2%|▉ | ETA: 0:16:58 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[ Info: 488 records are matched 248.329447 seconds (2.01 G allocations: 106.121 GiB, 19.19% gc time, 0.17% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:22 Progress: 0%|▏ | ETA: 0:23:13 Progress: 0%|▏ | ETA: 0:21:19 Progress: 0%|▏ | ETA: 0:20:30 Progress: 0%|▎ | ETA: 0:21:57 Progress: 1%|▎ | ETA: 0:21:00 Progress: 1%|▎ | ETA: 0:20:26 Progress: 1%|▎ | ETA: 0:21:06 Progress: 1%|▍ | ETA: 0:20:43 Progress: 1%|▍ | ETA: 0:20:21 Progress: 1%|▍ | ETA: 0:20:10 Progress: 1%|▌ | ETA: 0:20:44 Progress: 1%|▌ | ETA: 0:20:28 Progress: 1%|▌ | ETA: 0:20:13 Progress: 1%|▋ | ETA: 0:20:38 Progress: 2%|▋ | ETA: 0:20:28 Progress: 2%|▋ | ETA: 0:20:19 Progress: 2%|▊ | ETA: 0:20:43 Progress: 2%|▊ | ETA: 0:20:33 Progress: 2%|▊ | ETA: 0:20:24 Progress: 2%|▊ | ETA: 0:20:18 Progress: 2%|▉ | ETA: 0:20:41 Progress: 2%|▉ | ETA: 0:20:33 Progress: 2%|▉ | ETA: 0:20:24 Progress: 2%|█ | ETA: 0:20:38 Progress: 2%|█ | ETA: 0:20:27 Progress: 3%|█ | ETA: 0:20:18 Progress: 3%|█▏ | ETA: 0:20:30 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100%|█████████████████████████████████████████| Time: 0:02:14 [ Info: 0 records are matched 273.224579 seconds (2.01 G allocations: 106.120 GiB, 19.54% gc time, 0.26% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m48.1s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:56:30 Progress: 10%|████ | ETA: 0:18:11 Progress: 30%|████████████▍ | ETA: 0:04:33 Progress: 51%|████████████████████▊ | ETA: 0:01:57 Progress: 71%|█████████████████████████████▎ | ETA: 0:00:49 Progress: 91%|█████████████████████████████████████▌ | ETA: 0:00:11 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: 833 records are matched 132.982561 seconds (1.02 G allocations: 53.885 GiB, 16.60% gc time, 0.32% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:49:20 Progress: 17%|███████▏ | ETA: 0:09:46 Progress: 37%|███████████████▏ | ETA: 0:03:31 Progress: 56%|███████████████████████▏ | ETA: 0:01:37 Progress: 75%|██████████████████████████████▋ | ETA: 0:00:43 Progress: 98%|████████████████████████████████████████▏| ETA: 0:00:03 Progress: 100%|█████████████████████████████████████████| Time: 0:02:08 [ Info: 493 records are matched 137.832091 seconds (1.02 G allocations: 53.885 GiB, 17.32% gc time, 0.31% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:21:26 Progress: 18%|███████▎ | ETA: 0:09:25 Progress: 35%|██████████████▌ | ETA: 0:03:41 Progress: 55%|██████████████████████▋ | ETA: 0:01:40 Progress: 75%|██████████████████████████████▋ | ETA: 0:00:42 Progress: 99%|████████████████████████████████████████▌| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:02:05 [ Info: 0 records are matched 135.442677 seconds (1.02 G allocations: 53.885 GiB, 17.35% gc time, 0.34% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m48.8s 0.938745 seconds (1.26 M allocations: 68.021 MiB, 83.11% compilation time) 0.846629 seconds (1.15 M allocations: 64.052 MiB, 4.22% gc time, 82.35% compilation time) 0.747706 seconds (1.15 M allocations: 63.097 MiB, 81.53% compilation time) 0.335115 seconds (206.06 k allocations: 10.756 MiB, 99.96% compilation time) 0.010625 seconds (6.46 k allocations: 394.180 KiB, 95.74% compilation time) 0.007843 seconds (2.65 k allocations: 165.414 KiB, 96.36% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 6.8s 0.685447 seconds (1.04 M allocations: 57.780 MiB, 79.42% compilation time) 0.663332 seconds (876.85 k allocations: 51.591 MiB, 5.12% gc time, 73.65% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 4.1s Test Summary: | Pass Total Time convert_ds | 5 5 0.8s 0.111513 seconds (525.74 k allocations: 30.690 MiB, 18.28% gc time, 31.01% compilation time) 0.471908 seconds (643.87 k allocations: 37.247 MiB, 87.65% 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 0.096679 seconds (520.58 k allocations: 32.160 MiB, 48.30% gc time) 0.337151 seconds (595.44 k allocations: 36.387 MiB, 83.70% 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 0.130370 seconds (1.56 M allocations: 62.080 MiB, 7.18% compilation time) 0.367631 seconds (1.71 M allocations: 70.269 MiB, 7.01% gc time, 74.32% 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 4.5s Test Summary: | Pass Total Time record info | 14 14 3.3s Test Summary: | Pass Total Time write VCF | 3 3 2.6s 2.259270 seconds (4.80 M allocations: 296.462 MiB, 24.46% gc time, 39.13% compilation time) 0.940653 seconds (2.39 M allocations: 142.635 MiB, 2.55% gc time, 22.12% compilation time) 0.840376 seconds (4.42 M allocations: 276.459 MiB, 5.67% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.4s 0.848699 seconds (604.82 k allocations: 33.379 MiB, 3.56% gc time, 37.59% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 2.8s Test Summary: | Pass Total Time filter_chr | 4 4 1.5s Progress: 0%|▏ | ETA: 0:20:18 Progress: 1%|▍ | ETA: 0:18:58 Progress: 1%|▋ | ETA: 0:16:49 Progress: 2%|▉ | ETA: 0:15:44 Progress: 3%|█▏ | ETA: 0:15:18 Progress: 3%|█▍ | ETA: 0:15:01 Progress: 4%|█▋ | ETA: 0:14:31 Progress: 5%|█▉ | ETA: 0:14:25 Progress: 5%|██▏ | ETA: 0:14:38 Progress: 6%|██▎ | ETA: 0:14:40 Progress: 6%|██▌ | ETA: 0:14:57 Progress: 7%|██▋ | ETA: 0:15:11 Progress: 7%|██▉ | ETA: 0:15:34 Progress: 7%|███ | ETA: 0:15:41 Progress: 8%|███▏ | ETA: 0:15:49 Progress: 8%|███▍ | ETA: 0:15:59 Progress: 9%|███▌ | ETA: 0:16:05 Progress: 9%|███▋ | ETA: 0:16:18 Progress: 9%|███▉ | ETA: 0:16:23 Progress: 10%|████ | ETA: 0:16:31 Progress: 10%|████▏ | ETA: 0:16:36 Progress: 11%|████▎ | ETA: 0:16:33 Progress: 11%|████▌ 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