Package evaluation to test MIToS on Julia 1.12.4 (0f21d93eaa*) started at 2026-01-27T00:55:34.421 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.16s ################################################################################ # Installation # Installing MIToS... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [51bafb47] + MIToS v3.8.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [15f4f7f2] + AutoHashEquals v2.2.0 [47718e42] + BioGenerics v0.1.5 [de9282ab] + BioStructures v4.7.0 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.5 [a0c94c4b] + FastaIO v1.1.0 [1fa38f19] + Format v1.3.7 [92fee26a] + GZip v0.6.2 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.4.0 [9c8b4983] + LightXML v0.9.3 [2ab3a3ac] + LogExpFunctions v0.3.29 [51bafb47] + MIToS v3.8.0 [e1d29d7a] + Missings v1.2.0 [86f7a689] + NamedArrays v0.10.5 [bac558e1] + OrderedCollections v1.8.1 [f9da4da7] + PairwiseListMatrices v0.11.1 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [43287f4e] + PtrArrays v1.3.0 [3cdcf5f2] + RecipesBase v1.3.4 [ae029012] + Requires v1.3.1 [a2af1166] + SortingAlgorithms v1.2.2 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [ec057cc2] + StructUtils v2.6.2 [3bb67fe8] + TranscodingStreams v0.11.3 [94ce4f54] + Libiconv_jll v1.18.0+0 [02c8fc9c] + XML2_jll v2.15.1+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching 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 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [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 v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 Installation completed after 5.64s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 47747.1 ms ✓ MIToS 27824.3 ms ✓ MIToS → MIToSBioAlignmentsExt 24881.2 ms ✓ MIToS → MIToSClusteringExt 135776.0 ms ✓ MIToS → MIToSROCAnalysisExt 4 dependencies successfully precompiled in 240 seconds. 138 already precompiled. Precompilation completed after 257.66s ################################################################################ # Testing # Testing MIToS Status `/tmp/jl_RZO63K/Project.toml` [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [00701ae9] BioAlignments v3.1.0 [de9282ab] BioStructures v4.7.0 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [8bb1440f] DelimitedFiles v1.9.1 [e30172f5] Documenter v1.16.1 [a0c94c4b] FastaIO v1.1.0 [1fa38f19] Format v1.3.7 [682c06a0] JSON v1.4.0 [9c8b4983] LightXML v0.9.3 [51bafb47] MIToS v3.8.0 [86f7a689] NamedArrays v0.10.5 [bac558e1] OrderedCollections v1.8.1 [f9da4da7] PairwiseListMatrices v0.11.1 [f535d66d] ROCAnalysis v0.3.6 [3cdcf5f2] RecipesBase v1.3.4 [90137ffa] StaticArrays v1.9.16 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.10 [3bb67fe8] TranscodingStreams v0.11.3 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [9a3f8284] Random v1.11.0 [9e88b42a] Serialization v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_RZO63K/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [15f4f7f2] AutoHashEquals v2.2.0 [00701ae9] BioAlignments v3.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.1 [de9282ab] BioStructures v4.7.0 [3c28c6f8] BioSymbols v5.2.0 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [34da2185] Compat v4.18.1 [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 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.16.1 [a0c94c4b] FastaIO v1.1.0 [1a297f60] FillArrays v1.16.0 [1fa38f19] Format v1.3.7 [92fee26a] GZip v0.6.2 [d7ba0133] Git v1.5.0 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v1.0.0 [842dd82b] InlineStrings v1.4.5 [524e6230] IntervalTrees v1.1.0 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.4.0 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [9c8b4983] LightXML v0.9.3 [2ab3a3ac] LogExpFunctions v0.3.29 [51bafb47] MIToS v3.8.0 [d0879d2d] MarkdownAST v0.1.2 [e1d29d7a] Missings v1.2.0 [86f7a689] NamedArrays v0.10.5 [b8a86587] NearestNeighbors v0.4.26 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [f9da4da7] PairwiseListMatrices v0.11.1 [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 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [f535d66d] ROCAnalysis v0.3.6 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [ec057cc2] StructUtils v2.6.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [2e619515] Expat_jll v2.7.3+0 [020c3dae] Git_LFS_jll v3.7.0+0 [f8c6e375] Git_jll v2.52.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.2.1+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [02c8fc9c] XML2_jll v2.15.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates 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 [76f85450] LibGit2 v1.11.0 [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 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [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 v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [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 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Testing Running tests... Precompiling packages... 4328.8 ms ✓ BioGenerics 1567.1 ms ✓ XML2_jll 18425.7 ms ✓ BioStructures 1150.8 ms ✓ LightXML 45204.1 ms ✓ MIToS 5 dependencies successfully precompiled in 72 seconds. 62 already precompiled. Precompiling packages... 146127.2 ms ✓ DataFrames 35443.2 ms ✓ ROCAnalysis 2 dependencies successfully precompiled in 184 seconds. 67 already precompiled. Precompiling packages... 1030.8 ms ✓ StructUtils → StructUtilsTablesExt 1 dependency successfully precompiled in 1 seconds. 11 already precompiled. Precompiling packages... 8015.9 ms ✓ BioStructures → BioStructuresDataFramesExt 1 dependency successfully precompiled in 9 seconds. 53 already precompiled. Precompiling packages... 4593.6 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 7 seconds. 48 already precompiled. Precompiling packages... 12029.1 ms ✓ MIToS → MIToSROCAnalysisExt 1 dependency successfully precompiled in 14 seconds. 107 already precompiled. Precompiling packages... 4293.9 ms ✓ Clustering 1 dependency successfully precompiled in 5 seconds. 30 already precompiled. Precompiling packages... 5364.9 ms ✓ MIToS → MIToSClusteringExt 1 dependency successfully precompiled in 6 seconds. 72 already precompiled. Test Summary: | Pass Total Time Aqua | 10 10 1m04.2s Unbound type parameters | 1 1 0.2s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 8.0s Compat bounds | 4 4 0.7s Piracy | 1 1 0.1s Persistent tasks | 1 1 30.5s ┌ Warning: No occupancy values found. Using 1.0 for all atoms. └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/PDBParser.jl:27 Test Summary: | Pass Total Time Deprecated | 45 45 1m02.7s Deprecated | 45 45 1m00.8s Test Summary: | Pass Total Time Utils | 49 49 4.0s get_n_words! | 18 18 0.2s hascoordinates | 2 2 0.0s select_element | 2 2 0.5s Matrices to and from lists | 6 6 0.7s General IO | 17 17 2.3s check_pdbcode | 4 4 0.0s ┌ Warning: Sequence identifier seq is taken; using seq(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier seq is taken; using seq(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier seq is taken; using seq(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier seq is taken; using seq(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier a is taken; using a(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier b is taken; using b(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier b is taken; using b(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier a is taken; using a(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier b is taken; using b(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier b is taken; using b(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier item(1) is taken; using item(1)(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier item(1) is taken; using item(1)(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier x is taken; using x(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier x is taken; using x(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier x(1) is taken; using x(1)(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier x(1) is taken; using x(1)(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier x is taken; using x(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier x is taken; using x(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier x(1) is taken; using x(1)(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier x(1) is taken; using x(1)(2) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: indexing is deprecated for OrderedSet, please rewrite your code to use iteration │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: Sequence identifier SEQUENCE is taken; using SEQUENCE(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier dupl is taken; using dupl(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: Sequence identifier SEQUENCE is taken; using SEQUENCE(1) instead. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/GeneralParserMethods.jl:201 ┌ Warning: The second argument should be a feature name, not the sequence identifier: AZBR. │ Possible sequence features: Type and Title └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/MultipleSequenceAlignment.jl:661 ┌ Warning: The second argument should be a feature name, not the sequence identifier: AZBR. │ Possible sequence features: Type and Title └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/MultipleSequenceAlignment.jl:661 Precompiling packages... 13796.0 ms ✓ BioSequences 3667.6 ms ✓ BioAlignments 2 dependencies successfully precompiled in 18 seconds. 11 already precompiled. Precompiling packages... 1650.7 ms ✓ BioStructures → BioStructuresBioSequencesExt 1 dependency successfully precompiled in 2 seconds. 26 already precompiled. Precompiling packages... 1965.8 ms ✓ BioStructures → BioStructuresBioAlignmentsExt 6065.6 ms ✓ MIToS → MIToSBioAlignmentsExt 2 dependencies successfully precompiled in 9 seconds. 72 already precompiled. ┌ Warning: There was no possible to match the ColMap annotations. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:73 ┌ Warning: There was no possible to match the ColMap annotations. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:73 ┌ Warning: Sequence order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1026 ┌ Warning: Column order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1039 ┌ Warning: Sequence order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1026 ┌ Warning: Sequence order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1026 ┌ Warning: Column order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1039 ┌ Warning: Column order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1039 ┌ Warning: Sequence order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1026 ┌ Warning: Sequence order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1026 ┌ Warning: Joining MSAs by sequences name found no matches. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:778 ┌ Warning: Joining MSAs by sequences name found no matches. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:778 ┌ Warning: Joining MSAs by sequences name found no matches. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:778 ┌ Warning: Joining MSAs by sequences name found no matches. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:778 ┌ Warning: Column order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1039 ┌ Warning: Column order may not be preserved due to unsorted matching positions. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:1039 ┌ Warning: Joining MSAs by columns name found no matches. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:778 ┌ Warning: Joining MSAs by columns name found no matches. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:778 ┌ Warning: Joining MSAs by columns name found no matches. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:778 ┌ Warning: Joining MSAs by columns name found no matches. └ @ MIToS.MSA ~/.julia/packages/MIToS/UFW9m/src/MSA/Concatenation.jl:778 Test Summary: | Pass Total Time MSA | 27444 27444 4m39.0s Residue | 20679 20679 3.4s Alphabet | 69 69 1.1s Three letters name | 11 11 0.2s Annotations | 92 92 2.9s MultipleSequenceAlignment | 445 445 21.0s GeneralParserMethods | 50 50 3.4s IO | 236 236 22.0s Test using MSA files | 220 220 7.5s MSAEditing.jl | 90 90 41.3s MSA Stats | 44 44 1.2s n_effective | 3 3 1.0s MSAQuality | 10 10 1.6s AnnotatedSequence | 125 125 4.5s Shuffle | 117 117 25.4s Identity | 4244 4244 7.3s ResidueSubstitutionMatrices | 13 13 2.1s BioAlignmentsExt | 2 2 1.0s Clusters | 100 100 0.0s Hobohm I | 11 11 2.3s MSA Annotations | 20 20 1.9s getindex | 233 233 8.8s hcat | 113 113 3.1s vcat | 48 48 1.0s _find_gaps | 1 1 0.8s join MSAs | 461 461 13.8s MSA Plots recipe | 7 7 0.5s ┌ Warning: GaussDCA.jl not gaussdca_installed: ArgumentError("Package Pkg not found in current path.") └ @ Main ~/.julia/packages/MIToS/UFW9m/test/Information/Externals.jl:38 Test Summary: | Pass Total Time Information | 862 862 1m02.4s ContingencyTables | 514 514 17.3s Counters | 201 201 14.8s Information Measures | 52 52 6.7s Iterations | 26 26 9.5s CorrectedMutualInformation | 55 55 10.9s Pairwise Gap Percentage | 10 10 1.1s _create_script | 4 4 0.2s ┌ Warning: There is no alpha carbon in residue │ PDBResidueIdentifier(PDB_number="", number="115", name="ASN", group="ATOM", model="1", chain="E") └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/Kabsch.jl:85 ┌ Warning: There is no alpha carbon in residue │ PDBResidueIdentifier(PDB_number="97", number="115", name="ASN", group="ATOM", model="1", chain="A") └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/Kabsch.jl:85 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE FUL is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE NDG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE BMA is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE MAN is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE GAL is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE MAN is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE FUC is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE NDG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE BMA is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE MAN is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE GAL is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE MAN is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: RESIDUE NAG is unknown to MIToS.PDB (AtomsData.jl) └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AtomsData.jl:846 ┌ Warning: Using 2 residues for RMSD calculation because there are 1 residues without CA: [2] └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/Kabsch.jl:247 ┌ Error: Error fetching UniProt Accession INVALID_ACCESSION from AlphaFoldDB. └ @ MIToS.PDB ~/.julia/packages/MIToS/UFW9m/src/PDB/AlphaFoldDB.jl:16 Test Summary: | Pass Total Time PDB | 13975 13975 2m40.1s Parse PDB and PDBML | 143 143 22.0s RESTful PDB Interface | 10 10 6.6s Write PDB files | 29 29 13.4s Helper functions | 5 5 0.0s MMCIFDict conversions | 72 72 0.7s MolecularStructure from residues | 8 8 15.4s Vector{PDBResidue} from MolecularStructure | 6 6 1.7s Contacts | 13304 13304 13.2s Kabsch algorithm | 70 70 52.6s AtomsData internals | 187 187 1.1s Check amino acid residues | 8 8 0.0s Extract protein sequences from PDB | 44 44 1.7s AlphaFoldDB Tests | 8 8 24.5s Read PDB with short atom lines | 18 18 0.0s Show constructors | 3 3 0.8s Copy and deepcopy | 16 16 0.3s PDBResidues | 16 16 0.6s cross PDBAtom | 3 3 0.0s change_b_factor | 10 10 0.9s MMCIF parse_file filters | 8 8 0.0s Parsing AlphaFold 3 output mmCIF file | 4 4 0.1s Plot recipe | 3 3 0.5s ┌ Warning: 22 is already in the mapping with the value 22. The value is replaced by 22 └ @ MIToS.SIFTS ~/.julia/packages/MIToS/UFW9m/src/SIFTS/ResidueMapping.jl:406 ┌ Warning: 25 is already in the mapping with the value 25. The value is replaced by 25 └ @ MIToS.SIFTS ~/.julia/packages/MIToS/UFW9m/src/SIFTS/ResidueMapping.jl:406 Test Summary: | Pass Total Time SIFTS | 831 831 1m26.2s SIFTS Mappings | 687 687 20.0s 1NSA | 3 3 2.8s find & filter | 2 2 0.6s MIToS 1.0 error | 1 1 0.0s download | 5 5 1.0s Ensembl | 9 9 0.1s SCOP2B | 5 5 0.2s SCOP2 | 10 10 0.2s SIFTSResidue show | 2 2 1.7s _name methods | 11 11 0.1s get methods | 11 11 1.0s parse_file error | 2 2 0.0s SIFTS Summary | 83 83 57.9s ┌ Warning: The MSA lacks DR PDB annotations (common in recent Pfam). └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:67 [ Info: Downloading SIFTS file: pdb_chain_pfam.csv.gz [ Info: Downloading SIFTS file: pdb_chain_uniprot.csv.gz [ Info: Reusing existing SIFTS file: pdb_chain_pfam.csv.gz ┌ Warning: The MSA lacks DR PDB annotations (common in recent Pfam). └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:67 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 2 (T) != SIFTS residue (UniProt/Pfam: S, PDB: 4) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 3 (L) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 4 (N) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 5 (S) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 6 (Y) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 7 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 8 (M) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 9 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 10 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 11 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 12 (M) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 13 (Y) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 14 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 15 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 16 (L) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 17 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 18 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 19 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 20 (G) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 21 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 22 (L) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 23 (T) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 24 (L) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 25 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 26 (D) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 27 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 28 (L) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 29 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 30 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 31 (F) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 32 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 33 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 34 (S) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 35 (V) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 36 (P) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 37 (S) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 38 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 39 (Y) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 40 (N) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 41 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 42 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 43 (R) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 44 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 45 (L) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 46 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 47 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 48 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 49 (C) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 50 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 51 (R) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 52 (H) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 53 (P) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 54 (D) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 55 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 56 (C) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 57 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 58 (V) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 59 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 60 (Y) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 61 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 62 (N) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 63 (R) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 64 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 65 (T) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 66 (T) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 67 (F) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 68 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 69 (W) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 70 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 71 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 72 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 73 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 74 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 75 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 76 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 77 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 78 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 79 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 80 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 81 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 82 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 83 (T) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 84 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 85 (D) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 86 (N) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 87 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 88 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 89 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 90 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 91 (F) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 92 (D) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 93 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 94 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 95 (P) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 96 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 97 (N) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 98 (F) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 99 (E) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 100 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 101 (T) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 102 (D) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 103 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 104 (G) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 105 (F) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 106 (I) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 107 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 108 (A) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 109 (K) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 110 (Q) != SIFTS residue (UniProt/Pfam: , PDB: ) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 ┌ Warning: PF09645 F112_SSV1/3-112 2VQC A : MSA sequence residue at 2 (T) != SIFTS residue (UniProt/Pfam: S, PDB: 4) └ @ MIToS.Pfam ~/.julia/packages/MIToS/UFW9m/src/Pfam/PDB.jl:320 Test Summary: | Pass Total Time Pfam | 2487 2487 53.1s Download | 1 1 0.6s PDB code | 2 2 15.6s Pfam SIFTS helpers | 21 21 3.9s Mapping PDB/Pfam | 2453 2453 18.2s AUC | 3 3 11.5s PDB mapping branches | 7 7 1.0s ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ @ Documenter ~/.julia/packages/Documenter/xvqbW/src/utilities/utilities.jl:680 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. [ Info: Skipped ExpandTemplates step (doctest only). [ Info: Skipped CrossReferences step (doctest only). [ Info: Skipped CheckDocument step (doctest only). [ Info: Skipped Populate step (doctest only). [ Info: Skipped RenderDocument step (doctest only). Test Summary: | Pass Total Time Doctests: MIToS | 1 1 56.2s ----- =D ----- Testing MIToS tests passed Testing completed after 1131.02s PkgEval succeeded after 1446.09s