Package evaluation of BiobakeryUtils on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T20:03:50.003 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.12s ################################################################################ # Installation # Installing BiobakeryUtils... Resolving package versions... Installed Conda ─ v1.10.2 Updating `~/.julia/environments/v1.12/Project.toml` [fa5322f5] + BiobakeryUtils v0.7.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [7d9fca2a] + Arpack v0.5.4 [fa5322f5] + BiobakeryUtils v0.7.0 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.17.0 [8f4d0f93] + Conda v1.10.2 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 ⌅ [85a47980] + Dictionaries v0.3.29 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [a58aae7d] + EcoBase v0.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [313cdc1a] + Indexing v1.1.1 [842dd82b] + InlineStrings v1.4.4 [bd334432] + InlineTest v0.2.0 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [3bd8f0ae] + Microbiome v0.10.1 [e1d29d7a] + Missings v1.2.0 [6f286f6a] + MultivariateStats v0.10.3 [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 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [e0db7c4e] + ReTest v0.3.4 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [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 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [81def892] + VersionParsing v1.3.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 ⌅ [68821587] + Arpack_jll v3.5.1+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 v1.6.0 [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 v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [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 v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Building Conda → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Installation completed after 7.15s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 160.1s ################################################################################ # Testing # Testing BiobakeryUtils Status `/tmp/jl_0jk2nx/Project.toml` [fa5322f5] BiobakeryUtils v0.7.0 [336ed68f] CSV v0.10.15 [8bb1440f] DelimitedFiles v1.9.1 [3bd8f0ae] Microbiome v0.10.1 [e0db7c4e] ReTest v0.3.4 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_0jk2nx/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [7d9fca2a] Arpack v0.5.4 [fa5322f5] BiobakeryUtils v0.7.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.17.0 [8f4d0f93] Conda v1.10.2 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 ⌅ [85a47980] Dictionaries v0.3.29 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [a58aae7d] EcoBase v0.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [313cdc1a] Indexing v1.1.1 [842dd82b] InlineStrings v1.4.4 [bd334432] InlineTest v0.2.0 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [2ab3a3ac] LogExpFunctions v0.3.29 [3bd8f0ae] Microbiome v0.10.1 [e1d29d7a] Missings v1.2.0 [6f286f6a] MultivariateStats v0.10.3 [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 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [e0db7c4e] ReTest v0.3.4 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [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 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [81def892] VersionParsing v1.3.0 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 ⌅ [68821587] Arpack_jll v3.5.1+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 v1.6.0 [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 v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [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 v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ Info: Downloading miniconda installer ... [ Info: Installing miniconda ... PREFIX=/home/pkgeval/.julia/conda/3/x86_64 Unpacking payload ... Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2 Extracting ca-certificates-2025.4.26-hbd8a1cb_0.conda Extracting ld_impl_linux-64-2.43-h712a8e2_4.conda Extracting libgomp-15.1.0-h767d61c_2.conda Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2 Extracting python_abi-3.12-7_cp312.conda Extracting tzdata-2025b-h78e105d_0.conda Extracting _openmp_mutex-4.5-2_gnu.tar.bz2 Extracting libgcc-15.1.0-h767d61c_2.conda Extracting c-ares-1.34.5-hb9d3cd8_0.conda Extracting libexpat-2.7.0-h5888daf_0.conda Extracting libffi-3.4.6-h2dba641_1.conda Extracting libgcc-ng-15.1.0-h69a702a_2.conda Extracting libiconv-1.18-h4ce23a2_1.conda Extracting liblzma-5.8.1-hb9d3cd8_1.conda Extracting libstdcxx-15.1.0-h8f9b012_2.conda Extracting libzlib-1.3.1-hb9d3cd8_2.conda Extracting ncurses-6.5-h2d0b736_3.conda Extracting openssl-3.5.0-h7b32b05_1.conda Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda Extracting bzip2-1.0.8-h4bc722e_7.conda Extracting cpp-expected-1.1.0-hff21bea_1.conda Extracting fmt-11.1.4-h07f6e7f_1.conda Extracting keyutils-1.6.1-h166bdaf_0.tar.bz2 Extracting libedit-3.1.20250104-pl5321h7949ede_0.conda Extracting libev-4.33-hd590300_2.conda Extracting libnsl-2.0.1-hd590300_0.conda Extracting libsolv-0.7.32-h7955e40_2.conda Extracting libsqlite-3.49.2-hee588c1_0.conda Extracting libssh2-1.11.1-hcf80075_0.conda Extracting libstdcxx-ng-15.1.0-h4852527_2.conda Extracting libuuid-2.38.1-h0b41bf4_0.conda Extracting libxcrypt-4.4.36-hd590300_1.conda Extracting lz4-c-1.10.0-h5888daf_1.conda Extracting lzo-2.10-hd590300_1001.conda Extracting readline-8.2-h8c095d6_2.conda Extracting reproc-cpp-14.2.5.post0-h5888daf_0.conda Extracting simdjson-3.12.3-h84d6215_0.conda Extracting tk-8.6.13-noxft_h4845f30_101.conda Extracting yaml-cpp-0.8.0-h3f2d84a_0.conda Extracting zstd-1.5.7-hb8e6e7a_2.conda Extracting icu-75.1-he02047a_0.conda Extracting krb5-1.21.3-h659f571_0.conda Extracting libnghttp2-1.64.0-h161d5f1_0.conda Extracting nlohmann_json-3.11.3-he02047a_1.conda Extracting python-3.12.10-h9e4cc4f_0_cpython.conda Extracting libcurl-8.13.0-h332b0f4_0.conda Extracting libxml2-2.13.8-h4bc477f_0.conda Extracting menuinst-2.2.0-py312h7900ff3_0.conda Extracting archspec-0.2.5-pyhd8ed1ab_0.conda Extracting boltons-24.0.0-pyhd8ed1ab_1.conda Extracting brotli-python-1.1.0-py312h2ec8cdc_2.conda Extracting certifi-2025.4.26-pyhd8ed1ab_0.conda Extracting charset-normalizer-3.4.2-pyhd8ed1ab_0.conda Extracting colorama-0.4.6-pyhd8ed1ab_1.conda Extracting distro-1.9.0-pyhd8ed1ab_1.conda Extracting frozendict-2.4.6-py312h66e93f0_0.conda Extracting hpack-4.1.0-pyhd8ed1ab_0.conda Extracting hyperframe-6.1.0-pyhd8ed1ab_0.conda Extracting idna-3.10-pyhd8ed1ab_1.conda Extracting jsonpointer-3.0.0-py312h7900ff3_1.conda Extracting libarchive-3.7.7-h75ea233_4.conda Extracting packaging-25.0-pyh29332c3_1.conda Extracting platformdirs-4.3.8-pyhe01879c_0.conda Extracting pluggy-1.5.0-pyhd8ed1ab_1.conda Extracting pycosat-0.6.6-py312h66e93f0_2.conda Extracting pycparser-2.22-pyh29332c3_1.conda Extracting pysocks-1.7.1-pyha55dd90_7.conda Extracting ruamel.yaml.clib-0.2.8-py312h66e93f0_1.conda Extracting setuptools-80.1.0-pyhff2d567_0.conda Extracting truststore-0.10.1-pyh29332c3_0.conda Extracting wheel-0.45.1-pyhd8ed1ab_1.conda Extracting cffi-1.17.1-py312h06ac9bb_0.conda Extracting h2-4.2.0-pyhd8ed1ab_0.conda Extracting jsonpatch-1.33-pyhd8ed1ab_1.conda Extracting libmamba-2.1.1-h430c389_0.conda Extracting pip-25.1.1-pyh8b19718_0.conda Extracting ruamel.yaml-0.18.10-py312h66e93f0_0.conda Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda Extracting libmambapy-2.1.1-py312h07448e0_0.conda Extracting mamba-2.1.1-had4a41a_0.conda Extracting zstandard-0.23.0-py312h66e93f0_2.conda Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_1.conda Extracting urllib3-2.4.0-pyhd8ed1ab_0.conda Extracting requests-2.32.3-pyhd8ed1ab_1.conda Extracting conda-package-handling-2.4.0-pyh7900ff3_2.conda Extracting conda-25.3.0-py312h7900ff3_0.conda Extracting conda-libmamba-solver-25.3.0-pyhd8ed1ab_0.conda Installing base environment... Transaction Prefix: /home/pkgeval/.julia/conda/3/x86_64 Updating specs: - _libgcc_mutex==0.1=conda_forge - ca-certificates==2025.4.26=hbd8a1cb_0 - ld_impl_linux-64==2.43=h712a8e2_4 - libgomp==15.1.0=h767d61c_2 - pybind11-abi==4=hd8ed1ab_3 - python_abi==3.12=7_cp312 - tzdata==2025b=h78e105d_0 - _openmp_mutex==4.5=2_gnu - libgcc==15.1.0=h767d61c_2 - c-ares==1.34.5=hb9d3cd8_0 - libexpat==2.7.0=h5888daf_0 - libffi==3.4.6=h2dba641_1 - libgcc-ng==15.1.0=h69a702a_2 - libiconv==1.18=h4ce23a2_1 - liblzma==5.8.1=hb9d3cd8_1 - libstdcxx==15.1.0=h8f9b012_2 - libzlib==1.3.1=hb9d3cd8_2 - ncurses==6.5=h2d0b736_3 - openssl==3.5.0=h7b32b05_1 - reproc==14.2.5.0post0=hb9d3cd8_0 - bzip2==1.0.8=h4bc722e_7 - cpp-expected==1.1.0=hff21bea_1 - fmt==11.1.4=h07f6e7f_1 - keyutils==1.6.1=h166bdaf_0 - libedit==3.1.20250104=pl5321h7949ede_0 - libev==4.33=hd590300_2 - libnsl==2.0.1=hd590300_0 - libsolv==0.7.32=h7955e40_2 - libsqlite==3.49.2=hee588c1_0 - libssh2==1.11.1=hcf80075_0 - libstdcxx-ng==15.1.0=h4852527_2 - libuuid==2.38.1=h0b41bf4_0 - libxcrypt==4.4.36=hd590300_1 - lz4-c==1.10.0=h5888daf_1 - lzo==2.10=hd590300_1001 - readline==8.2=h8c095d6_2 - reproc-cpp==14.2.5.0post0=h5888daf_0 - simdjson==3.12.3=h84d6215_0 - tk==8.6.13=noxft_h4845f30_101 - yaml-cpp==0.8.0=h3f2d84a_0 - zstd==1.5.7=hb8e6e7a_2 - icu==75.1=he02047a_0 - krb5==1.21.3=h659f571_0 - libnghttp2==1.64.0=h161d5f1_0 - nlohmann_json==3.11.3=he02047a_1 - python==3.12.10=h9e4cc4f_0_cpython - libcurl==8.13.0=h332b0f4_0 - libxml2==2.13.8=h4bc477f_0 - menuinst==2.2.0=py312h7900ff3_0 - archspec==0.2.5=pyhd8ed1ab_0 - boltons==24.0.0=pyhd8ed1ab_1 - brotli-python==1.1.0=py312h2ec8cdc_2 - certifi==2025.4.26=pyhd8ed1ab_0 - charset-normalizer==3.4.2=pyhd8ed1ab_0 - colorama==0.4.6=pyhd8ed1ab_1 - distro==1.9.0=pyhd8ed1ab_1 - frozendict==2.4.6=py312h66e93f0_0 - hpack==4.1.0=pyhd8ed1ab_0 - hyperframe==6.1.0=pyhd8ed1ab_0 - idna==3.10=pyhd8ed1ab_1 - jsonpointer==3.0.0=py312h7900ff3_1 - libarchive==3.7.7=h75ea233_4 - packaging==25.0=pyh29332c3_1 - platformdirs==4.3.8=pyhe01879c_0 - pluggy==1.5.0=pyhd8ed1ab_1 - pycosat==0.6.6=py312h66e93f0_2 - pycparser==2.22=pyh29332c3_1 - pysocks==1.7.1=pyha55dd90_7 - ruamel.yaml.clib==0.2.8=py312h66e93f0_1 - setuptools==80.1.0=pyhff2d567_0 - truststore==0.10.1=pyh29332c3_0 - wheel==0.45.1=pyhd8ed1ab_1 - cffi==1.17.1=py312h06ac9bb_0 - h2==4.2.0=pyhd8ed1ab_0 - jsonpatch==1.33=pyhd8ed1ab_1 - libmamba==2.1.1=h430c389_0 - pip==25.1.1=pyh8b19718_0 - ruamel.yaml==0.18.10=py312h66e93f0_0 - tqdm==4.67.1=pyhd8ed1ab_1 - libmambapy==2.1.1=py312h07448e0_0 - mamba==2.1.1=had4a41a_0 - zstandard==0.23.0=py312h66e93f0_2 - conda-package-streaming==0.11.0=pyhd8ed1ab_1 - urllib3==2.4.0=pyhd8ed1ab_0 - requests==2.32.3=pyhd8ed1ab_1 - conda-package-handling==2.4.0=pyh7900ff3_2 - conda==25.3.0=py312h7900ff3_0 - conda-libmamba-solver==25.3.0=pyhd8ed1ab_0 Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────────────── + _libgcc_mutex 0.1 conda_forge conda-forge + _openmp_mutex 4.5 2_gnu conda-forge + archspec 0.2.5 pyhd8ed1ab_0 conda-forge + boltons 24.0.0 pyhd8ed1ab_1 conda-forge + brotli-python 1.1.0 py312h2ec8cdc_2 conda-forge + bzip2 1.0.8 h4bc722e_7 conda-forge + c-ares 1.34.5 hb9d3cd8_0 conda-forge + ca-certificates 2025.4.26 hbd8a1cb_0 conda-forge + certifi 2025.4.26 pyhd8ed1ab_0 conda-forge + cffi 1.17.1 py312h06ac9bb_0 conda-forge + charset-normalizer 3.4.2 pyhd8ed1ab_0 conda-forge + colorama 0.4.6 pyhd8ed1ab_1 conda-forge + conda 25.3.0 py312h7900ff3_0 conda-forge + conda-libmamba-solver 25.3.0 pyhd8ed1ab_0 conda-forge + conda-package-handling 2.4.0 pyh7900ff3_2 conda-forge + conda-package-streaming 0.11.0 pyhd8ed1ab_1 conda-forge + cpp-expected 1.1.0 hff21bea_1 conda-forge + distro 1.9.0 pyhd8ed1ab_1 conda-forge + fmt 11.1.4 h07f6e7f_1 conda-forge + frozendict 2.4.6 py312h66e93f0_0 conda-forge + h2 4.2.0 pyhd8ed1ab_0 conda-forge + hpack 4.1.0 pyhd8ed1ab_0 conda-forge + hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge + icu 75.1 he02047a_0 conda-forge + idna 3.10 pyhd8ed1ab_1 conda-forge + jsonpatch 1.33 pyhd8ed1ab_1 conda-forge + jsonpointer 3.0.0 py312h7900ff3_1 conda-forge + keyutils 1.6.1 h166bdaf_0 conda-forge + krb5 1.21.3 h659f571_0 conda-forge + ld_impl_linux-64 2.43 h712a8e2_4 conda-forge + libarchive 3.7.7 h75ea233_4 conda-forge + libcurl 8.13.0 h332b0f4_0 conda-forge + libedit 3.1.20250104 pl5321h7949ede_0 conda-forge + libev 4.33 hd590300_2 conda-forge + libexpat 2.7.0 h5888daf_0 conda-forge + libffi 3.4.6 h2dba641_1 conda-forge + libgcc 15.1.0 h767d61c_2 conda-forge + libgcc-ng 15.1.0 h69a702a_2 conda-forge + libgomp 15.1.0 h767d61c_2 conda-forge + libiconv 1.18 h4ce23a2_1 conda-forge + liblzma 5.8.1 hb9d3cd8_1 conda-forge + libmamba 2.1.1 h430c389_0 conda-forge + libmambapy 2.1.1 py312h07448e0_0 conda-forge + libnghttp2 1.64.0 h161d5f1_0 conda-forge + libnsl 2.0.1 hd590300_0 conda-forge + libsolv 0.7.32 h7955e40_2 conda-forge + libsqlite 3.49.2 hee588c1_0 conda-forge + libssh2 1.11.1 hcf80075_0 conda-forge + libstdcxx 15.1.0 h8f9b012_2 conda-forge + libstdcxx-ng 15.1.0 h4852527_2 conda-forge + libuuid 2.38.1 h0b41bf4_0 conda-forge + libxcrypt 4.4.36 hd590300_1 conda-forge + libxml2 2.13.8 h4bc477f_0 conda-forge + libzlib 1.3.1 hb9d3cd8_2 conda-forge + lz4-c 1.10.0 h5888daf_1 conda-forge + lzo 2.10 hd590300_1001 conda-forge + mamba 2.1.1 had4a41a_0 conda-forge + menuinst 2.2.0 py312h7900ff3_0 conda-forge + ncurses 6.5 h2d0b736_3 conda-forge + nlohmann_json 3.11.3 he02047a_1 conda-forge + openssl 3.5.0 h7b32b05_1 conda-forge + packaging 25.0 pyh29332c3_1 conda-forge + pip 25.1.1 pyh8b19718_0 conda-forge + platformdirs 4.3.8 pyhe01879c_0 conda-forge + pluggy 1.5.0 pyhd8ed1ab_1 conda-forge + pybind11-abi 4 hd8ed1ab_3 conda-forge + pycosat 0.6.6 py312h66e93f0_2 conda-forge + pycparser 2.22 pyh29332c3_1 conda-forge + pysocks 1.7.1 pyha55dd90_7 conda-forge + python 3.12.10 h9e4cc4f_0_cpython conda-forge + python_abi 3.12 7_cp312 conda-forge + readline 8.2 h8c095d6_2 conda-forge + reproc 14.2.5.post0 hb9d3cd8_0 conda-forge + reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge + requests 2.32.3 pyhd8ed1ab_1 conda-forge + ruamel.yaml 0.18.10 py312h66e93f0_0 conda-forge + ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge + setuptools 80.1.0 pyhff2d567_0 conda-forge + simdjson 3.12.3 h84d6215_0 conda-forge + tk 8.6.13 noxft_h4845f30_101 conda-forge + tqdm 4.67.1 pyhd8ed1ab_1 conda-forge + truststore 0.10.1 pyh29332c3_0 conda-forge + tzdata 2025b h78e105d_0 conda-forge + urllib3 2.4.0 pyhd8ed1ab_0 conda-forge + wheel 0.45.1 pyhd8ed1ab_1 conda-forge + yaml-cpp 0.8.0 h3f2d84a_0 conda-forge + zstandard 0.23.0 py312h66e93f0_2 conda-forge + zstd 1.5.7 hb8e6e7a_2 conda-forge Summary: Install: 88 packages Total download: 0 B ───────────────────────────────────────────────────────────────────────────────────── Transaction starting Linking _libgcc_mutex-0.1-conda_forge Linking ca-certificates-2025.4.26-hbd8a1cb_0 Linking ld_impl_linux-64-2.43-h712a8e2_4 Linking libgomp-15.1.0-h767d61c_2 Linking pybind11-abi-4-hd8ed1ab_3 Linking python_abi-3.12-7_cp312 Linking tzdata-2025b-h78e105d_0 Linking _openmp_mutex-4.5-2_gnu Linking libgcc-15.1.0-h767d61c_2 Linking c-ares-1.34.5-hb9d3cd8_0 Linking libexpat-2.7.0-h5888daf_0 Linking libffi-3.4.6-h2dba641_1 Linking libgcc-ng-15.1.0-h69a702a_2 Linking libiconv-1.18-h4ce23a2_1 Linking liblzma-5.8.1-hb9d3cd8_1 Linking libstdcxx-15.1.0-h8f9b012_2 Linking libzlib-1.3.1-hb9d3cd8_2 Linking ncurses-6.5-h2d0b736_3 Linking openssl-3.5.0-h7b32b05_1 Linking reproc-14.2.5.post0-hb9d3cd8_0 Linking bzip2-1.0.8-h4bc722e_7 Linking cpp-expected-1.1.0-hff21bea_1 Linking fmt-11.1.4-h07f6e7f_1 Linking keyutils-1.6.1-h166bdaf_0 Linking libedit-3.1.20250104-pl5321h7949ede_0 Linking libev-4.33-hd590300_2 Linking libnsl-2.0.1-hd590300_0 Linking libsolv-0.7.32-h7955e40_2 Linking libsqlite-3.49.2-hee588c1_0 Linking libssh2-1.11.1-hcf80075_0 Linking libstdcxx-ng-15.1.0-h4852527_2 Linking libuuid-2.38.1-h0b41bf4_0 Linking libxcrypt-4.4.36-hd590300_1 Linking lz4-c-1.10.0-h5888daf_1 Linking lzo-2.10-hd590300_1001 Linking readline-8.2-h8c095d6_2 Linking reproc-cpp-14.2.5.post0-h5888daf_0 Linking simdjson-3.12.3-h84d6215_0 Linking tk-8.6.13-noxft_h4845f30_101 Linking yaml-cpp-0.8.0-h3f2d84a_0 Linking zstd-1.5.7-hb8e6e7a_2 Linking icu-75.1-he02047a_0 Linking krb5-1.21.3-h659f571_0 Linking libnghttp2-1.64.0-h161d5f1_0 Linking nlohmann_json-3.11.3-he02047a_1 Linking python-3.12.10-h9e4cc4f_0_cpython Linking libcurl-8.13.0-h332b0f4_0 Linking libxml2-2.13.8-h4bc477f_0 Linking menuinst-2.2.0-py312h7900ff3_0 Linking archspec-0.2.5-pyhd8ed1ab_0 Linking boltons-24.0.0-pyhd8ed1ab_1 Linking brotli-python-1.1.0-py312h2ec8cdc_2 Linking certifi-2025.4.26-pyhd8ed1ab_0 Linking charset-normalizer-3.4.2-pyhd8ed1ab_0 Linking colorama-0.4.6-pyhd8ed1ab_1 Linking distro-1.9.0-pyhd8ed1ab_1 Linking frozendict-2.4.6-py312h66e93f0_0 Linking hpack-4.1.0-pyhd8ed1ab_0 Linking hyperframe-6.1.0-pyhd8ed1ab_0 Linking idna-3.10-pyhd8ed1ab_1 Linking jsonpointer-3.0.0-py312h7900ff3_1 Linking libarchive-3.7.7-h75ea233_4 Linking packaging-25.0-pyh29332c3_1 Linking platformdirs-4.3.8-pyhe01879c_0 Linking pluggy-1.5.0-pyhd8ed1ab_1 Linking pycosat-0.6.6-py312h66e93f0_2 Linking pycparser-2.22-pyh29332c3_1 Linking pysocks-1.7.1-pyha55dd90_7 Linking ruamel.yaml.clib-0.2.8-py312h66e93f0_1 Linking setuptools-80.1.0-pyhff2d567_0 Linking truststore-0.10.1-pyh29332c3_0 Linking wheel-0.45.1-pyhd8ed1ab_1 Linking cffi-1.17.1-py312h06ac9bb_0 Linking h2-4.2.0-pyhd8ed1ab_0 Linking jsonpatch-1.33-pyhd8ed1ab_1 Linking libmamba-2.1.1-h430c389_0 Linking pip-25.1.1-pyh8b19718_0 Linking ruamel.yaml-0.18.10-py312h66e93f0_0 Linking tqdm-4.67.1-pyhd8ed1ab_1 Linking libmambapy-2.1.1-py312h07448e0_0 Linking mamba-2.1.1-had4a41a_0 Linking zstandard-0.23.0-py312h66e93f0_2 Linking conda-package-streaming-0.11.0-pyhd8ed1ab_1 Linking urllib3-2.4.0-pyhd8ed1ab_0 Linking requests-2.32.3-pyhd8ed1ab_1 Linking conda-package-handling-2.4.0-pyh7900ff3_2 Linking conda-25.3.0-py312h7900ff3_0 Linking conda-libmamba-solver-25.3.0-pyhd8ed1ab_0 Transaction finished installation finished. [ Info: Running `conda create -q -y -p /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils` in root environment Channels: - conda-forge Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ Info: Running `conda config --add channels bioconda --file /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/condarc-julia.yml --force` in BiobakeryUtils environment [ Info: Running `conda config --add channels conda-forge --file /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/condarc-julia.yml --force` in BiobakeryUtils environment Warning: 'conda-forge' already in 'channels' list, moving to the top [ Info: Running `conda config --add channels biobakery --file /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/condarc-julia.yml --force` in BiobakeryUtils environment [ Info: Running `conda install -q -y humann` in BiobakeryUtils environment Channels: - biobakery - conda-forge - bioconda Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils added / updated specs: - humann The following packages will be downloaded: package | build ---------------------------|----------------- _r-mutex-1.0.1 | anacondar_1 3 KB conda-forge anyio-4.9.0 | pyh29332c3_0 123 KB conda-forge argcomplete-3.6.2 | pyhd8ed1ab_0 41 KB conda-forge argon2-cffi-25.1.0 | pyhd8ed1ab_0 18 KB conda-forge argon2-cffi-bindings-21.2.0| py312h66e93f0_5 34 KB conda-forge arrow-1.3.0 | pyhd8ed1ab_1 98 KB conda-forge asttokens-3.0.0 | pyhd8ed1ab_1 28 KB conda-forge async-lru-2.0.5 | pyh29332c3_0 17 KB conda-forge attrs-25.3.0 | pyh71513ae_0 56 KB conda-forge babel-2.17.0 | pyhd8ed1ab_0 6.6 MB conda-forge bcbio-gff-0.7.1 | pyh7e72e81_2 21 KB bioconda beautifulsoup4-4.13.4 | pyha770c72_0 143 KB conda-forge binutils_impl_linux-64-2.44| h4bf12b8_1 3.6 MB conda-forge bioconductor-biobase-2.66.0| r44h3df3fcb_0 2.6 MB bioconda bioconductor-biocgenerics-0.52.0| r44hdfd78af_3 678 KB bioconda bioconductor-biomformat-1.34.0| r44hdfd78af_0 598 KB bioconda bioconductor-biostrings-2.74.0| r44h3df3fcb_1 13.8 MB bioconda bioconductor-data-packages-20250625| hdfd78af_0 250 KB bioconda bioconductor-genomeinfodb-1.42.0| r44hdfd78af_2 4.2 MB bioconda bioconductor-genomeinfodbdata-1.2.13| r44hdfd78af_0 8 KB bioconda bioconductor-iranges-2.40.0| r44h3df3fcb_2 2.5 MB bioconda bioconductor-microbiome-1.28.0| r44hdfd78af_0 1.0 MB bioconda bioconductor-multtest-2.62.0| r44h3df3fcb_1 893 KB bioconda bioconductor-phyloseq-1.50.0| r44hdfd78af_0 6.6 MB bioconda bioconductor-rhdf5-2.50.0 | r44h77050f0_1 3.1 MB bioconda bioconductor-rhdf5filters-1.18.0| r44h77050f0_1 554 KB bioconda bioconductor-rhdf5lib-1.28.0| r44h15a9599_0 3.9 MB bioconda bioconductor-s4vectors-0.44.0| r44h3df3fcb_2 2.7 MB bioconda bioconductor-ucsc.utils-1.2.0| r44h9ee0642_1 308 KB bioconda bioconductor-xvector-0.46.0| r44h15a9599_2 726 KB bioconda bioconductor-zlibbioc-1.52.0| r44h3df3fcb_2 249 KB bioconda biom-format-2.1.16 | py312h66e93f0_2 8.6 MB conda-forge biopython-1.85 | py312h66e93f0_1 3.3 MB conda-forge blast-2.16.0 | h66d330f_5 141.4 MB bioconda bleach-6.2.0 | pyh29332c3_4 138 KB conda-forge bleach-with-css-6.2.0 | h82add2a_4 4 KB conda-forge bowtie2-2.5.4 | he96a11b_6 14.3 MB bioconda brotli-1.1.0 | hb9d3cd8_3 19 KB conda-forge brotli-bin-1.1.0 | hb9d3cd8_3 19 KB conda-forge brotli-python-1.1.0 | py312h2ec8cdc_3 343 KB conda-forge bwidget-1.10.1 | ha770c72_1 127 KB conda-forge bx-python-0.13.0 | py312h5e9d817_1 1.1 MB bioconda ca-certificates-2025.7.14 | hbd8a1cb_0 152 KB conda-forge cached-property-1.5.2 | hd8ed1ab_1 4 KB conda-forge cached_property-1.5.2 | pyha770c72_1 11 KB conda-forge cairo-1.18.4 | h3394656_0 955 KB conda-forge capnproto-1.0.2 | h766bdaa_3 3.9 MB conda-forge certifi-2025.7.14 | pyhd8ed1ab_0 156 KB conda-forge click-8.2.1 | pyh707e725_0 86 KB conda-forge cmseq-1.0.4 | pyhb7b1952_0 25 KB bioconda comm-0.2.2 | pyhd8ed1ab_1 12 KB conda-forge contourpy-1.3.2 | py312h68727a3_0 270 KB conda-forge curl-8.14.1 | h332b0f4_0 176 KB conda-forge cycler-0.12.1 | pyhd8ed1ab_1 13 KB conda-forge debugpy-1.8.14 | py312h2ec8cdc_0 2.5 MB conda-forge decorator-5.2.1 | pyhd8ed1ab_0 14 KB conda-forge defusedxml-0.7.1 | pyhd8ed1ab_0 23 KB conda-forge dendropy-5.0.8 | pyhdfd78af_1 327 KB bioconda diamond-2.1.12 | h13889ed_2 19.5 MB bioconda entrez-direct-22.4 | he881be0_0 14.0 MB bioconda exceptiongroup-1.3.0 | pyhd8ed1ab_0 21 KB conda-forge executing-2.2.0 | pyhd8ed1ab_0 29 KB conda-forge fasttree-2.1.11 | h7b50bb2_5 269 KB bioconda font-ttf-dejavu-sans-mono-2.37| hab24e00_0 388 KB conda-forge font-ttf-inconsolata-3.000 | h77eed37_0 94 KB conda-forge font-ttf-source-code-pro-2.038| h77eed37_0 684 KB conda-forge font-ttf-ubuntu-0.83 | h77eed37_3 1.5 MB conda-forge fontconfig-2.15.0 | h7e30c49_1 259 KB conda-forge fonts-conda-ecosystem-1 | 0 4 KB conda-forge fonts-conda-forge-1 | 0 4 KB conda-forge fonttools-4.58.5 | py312h178313f_0 2.7 MB conda-forge fqdn-1.5.1 | pyhd8ed1ab_1 16 KB conda-forge freetype-2.13.3 | ha770c72_1 168 KB conda-forge fribidi-1.0.10 | h36c2ea0_0 112 KB conda-forge gawk-5.3.1 | hcd3d067_0 1.1 MB conda-forge gcc_impl_linux-64-15.1.0 | h4393ad2_3 72.6 MB conda-forge gfortran_impl_linux-64-15.1.0| h3b9cdf2_3 17.8 MB conda-forge glpk-5.0 | h445213a_0 1023 KB conda-forge gmp-6.3.0 | hac33072_2 449 KB conda-forge graphite2-1.3.14 | h5888daf_0 96 KB conda-forge gsl-2.7 | he838d99_0 3.2 MB conda-forge gxx_impl_linux-64-15.1.0 | h6a1bac1_3 14.8 MB conda-forge h11-0.16.0 | pyhd8ed1ab_0 37 KB conda-forge h5py-3.14.0 |nompi_py312h3faca00_100 1.3 MB conda-forge harfbuzz-11.2.1 | h3beb420_0 1.7 MB conda-forge hclust2-1.0.0 | pyh864c0ab_1 15 KB bioconda hdf5-1.14.6 |nompi_h6e4c0c1_102 3.5 MB conda-forge htslib-1.22 | h566b1c6_0 3.1 MB bioconda httpcore-1.0.9 | pyh29332c3_0 48 KB conda-forge httpx-0.28.1 | pyhd8ed1ab_0 62 KB conda-forge humann-4.0.0a1 | py312_0 81.6 MB biobakery importlib-metadata-8.7.0 | pyhe01879c_1 34 KB conda-forge importlib_resources-6.5.2 | pyhd8ed1ab_0 33 KB conda-forge ipykernel-6.29.5 | pyh3099207_0 116 KB conda-forge ipython-9.4.0 | pyhfa0c392_0 614 KB conda-forge ipython_pygments_lexers-1.1.1| pyhd8ed1ab_0 14 KB conda-forge iqtree-3.0.1 | h503566f_0 4.2 MB bioconda isoduration-20.11.0 | pyhd8ed1ab_1 19 KB conda-forge jedi-0.19.2 | pyhd8ed1ab_1 824 KB conda-forge jinja2-3.1.6 | pyhd8ed1ab_0 110 KB conda-forge jq-1.8.1 | h73b1eb8_0 306 KB conda-forge json5-0.12.0 | pyhd8ed1ab_0 33 KB conda-forge jsonschema-4.24.0 | pyhd8ed1ab_0 73 KB conda-forge jsonschema-specifications-2025.4.1| pyh29332c3_0 19 KB conda-forge jsonschema-with-format-nongpl-4.24.0| hd8ed1ab_0 8 KB conda-forge jupyter-lsp-2.2.5 | pyhe01879c_2 56 KB conda-forge jupyter_client-8.6.3 | pyhd8ed1ab_1 104 KB conda-forge jupyter_core-5.8.1 | pyh31011fe_0 58 KB conda-forge jupyter_events-0.12.0 | pyh29332c3_0 23 KB conda-forge jupyter_server-2.16.0 | pyhe01879c_0 336 KB conda-forge jupyter_server_terminals-0.5.3| pyhd8ed1ab_1 19 KB conda-forge jupyterlab-4.4.4 | pyhd8ed1ab_0 7.9 MB conda-forge jupyterlab_pygments-0.3.0 | pyhd8ed1ab_2 18 KB conda-forge jupyterlab_server-2.27.3 | pyhd8ed1ab_1 48 KB conda-forge k8-1.2 | he8db53b_6 7.2 MB bioconda kernel-headers_linux-64-3.10.0| he073ed8_18 921 KB conda-forge kiwisolver-1.4.8 | py312h68727a3_1 70 KB conda-forge lcms2-2.17 | h717163a_0 242 KB conda-forge ld_impl_linux-64-2.44 | h1423503_1 660 KB conda-forge lerc-4.0.0 | h0aef613_1 258 KB conda-forge libaec-1.1.4 | h3f801dc_0 36 KB conda-forge libasprintf-0.25.1 | h8e693c7_0 52 KB conda-forge libblas-3.9.0 |32_h59b9bed_openblas 17 KB 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pyhd8ed1ab_1 26 KB conda-forge statsmodels-0.14.5 | py312h8b63200_0 11.5 MB conda-forge sysroot_linux-64-2.17 | h0157908_18 14.5 MB conda-forge terminado-0.18.1 | pyh0d859eb_0 22 KB conda-forge tinycss2-1.4.0 | pyhd8ed1ab_0 28 KB conda-forge tk-8.6.13 |noxft_hd72426e_102 3.1 MB conda-forge tktable-2.10 | h8d826fa_7 90 KB conda-forge toml-0.10.2 | pyhd8ed1ab_1 22 KB conda-forge tomli-2.2.1 | pyhd8ed1ab_1 19 KB conda-forge tomlkit-0.13.3 | pyha770c72_0 38 KB conda-forge tornado-6.5.1 | py312h66e93f0_0 831 KB conda-forge traitlets-5.14.3 | pyhd8ed1ab_1 107 KB conda-forge trimal-1.5.0 | h9948957_2 211 KB bioconda types-python-dateutil-2.9.0.20250708| pyhd8ed1ab_0 24 KB conda-forge typing-extensions-4.14.1 | h4440ef1_0 88 KB conda-forge typing_extensions-4.14.1 | pyhe01879c_0 50 KB conda-forge typing_utils-0.1.0 | pyhd8ed1ab_1 15 KB conda-forge unicodedata2-16.0.0 | py312h66e93f0_0 395 KB conda-forge uri-template-1.3.0 | pyhd8ed1ab_1 23 KB conda-forge urllib3-2.5.0 | pyhd8ed1ab_0 99 KB conda-forge wcwidth-0.2.13 | pyhd8ed1ab_1 32 KB conda-forge webcolors-24.11.1 | pyhd8ed1ab_0 18 KB conda-forge webencodings-0.5.1 | pyhd8ed1ab_3 15 KB conda-forge websocket-client-1.8.0 | pyhd8ed1ab_1 46 KB conda-forge wget-1.21.4 | hda4d442_0 752 KB conda-forge xmltodict-0.14.2 | pyhd8ed1ab_1 15 KB conda-forge xorg-libice-1.1.2 | hb9d3cd8_0 57 KB conda-forge xorg-libsm-1.2.6 | he73a12e_0 27 KB conda-forge xorg-libx11-1.8.12 | h4f16b4b_0 816 KB conda-forge xorg-libxau-1.0.12 | hb9d3cd8_0 14 KB conda-forge xorg-libxdmcp-1.1.5 | hb9d3cd8_0 19 KB conda-forge xorg-libxext-1.3.6 | hb9d3cd8_0 49 KB conda-forge xorg-libxrender-0.9.12 | hb9d3cd8_0 32 KB conda-forge xorg-libxt-1.3.1 | hb9d3cd8_0 371 KB conda-forge yaml-0.2.5 | h7f98852_2 87 KB conda-forge yq-3.4.3 | pyhe01879c_2 29 KB conda-forge zeromq-4.3.5 | h3b0a872_7 328 KB conda-forge zipp-3.23.0 | pyhd8ed1ab_0 22 KB conda-forge zlib-1.3.1 | hb9d3cd8_2 90 KB conda-forge ------------------------------------------------------------ Total: 990.7 MB The following NEW packages will be INSTALLED: _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu _r-mutex conda-forge/noarch::_r-mutex-1.0.1-anacondar_1 anyio conda-forge/noarch::anyio-4.9.0-pyh29332c3_0 argcomplete conda-forge/noarch::argcomplete-3.6.2-pyhd8ed1ab_0 argon2-cffi conda-forge/noarch::argon2-cffi-25.1.0-pyhd8ed1ab_0 argon2-cffi-bindi~ conda-forge/linux-64::argon2-cffi-bindings-21.2.0-py312h66e93f0_5 arrow conda-forge/noarch::arrow-1.3.0-pyhd8ed1ab_1 asttokens conda-forge/noarch::asttokens-3.0.0-pyhd8ed1ab_1 async-lru conda-forge/noarch::async-lru-2.0.5-pyh29332c3_0 attrs conda-forge/noarch::attrs-25.3.0-pyh71513ae_0 babel conda-forge/noarch::babel-2.17.0-pyhd8ed1ab_0 bcbio-gff bioconda/noarch::bcbio-gff-0.7.1-pyh7e72e81_2 beautifulsoup4 conda-forge/noarch::beautifulsoup4-4.13.4-pyha770c72_0 binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.44-h4bf12b8_1 bioconductor-biob~ 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matplotlib-base conda-forge/linux-64::matplotlib-base-3.10.3-py312hd3ec401_0 matplotlib-inline conda-forge/noarch::matplotlib-inline-0.1.7-pyhd8ed1ab_1 metaphlan bioconda/noarch::metaphlan-4.2.2-pyhdfd78af_0 minimap2 bioconda/linux-64::minimap2-2.30-h577a1d6_0 mistune conda-forge/noarch::mistune-3.1.3-pyh29332c3_0 mpfr conda-forge/linux-64::mpfr-4.2.1-h90cbb55_3 munkres conda-forge/noarch::munkres-1.1.4-pyhd8ed1ab_1 muscle bioconda/linux-64::muscle-5.3-h9948957_2 nbclient conda-forge/noarch::nbclient-0.10.2-pyhd8ed1ab_0 nbconvert-core conda-forge/noarch::nbconvert-core-7.16.6-pyh29332c3_0 nbformat conda-forge/noarch::nbformat-5.10.4-pyhd8ed1ab_1 ncbi-vdb bioconda/linux-64::ncbi-vdb-3.2.1-h9948957_0 ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3 nest-asyncio conda-forge/noarch::nest-asyncio-1.6.0-pyhd8ed1ab_1 notebook conda-forge/noarch::notebook-7.4.4-pyhd8ed1ab_0 notebook-shim conda-forge/noarch::notebook-shim-0.2.4-pyhd8ed1ab_1 numpy 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perl-compress-raw~ conda-forge/linux-64::perl-compress-raw-bzip2-2.201-pl5321hbf60520_1 perl-compress-raw~ conda-forge/linux-64::perl-compress-raw-zlib-2.202-pl5321hadc24fc_0 perl-encode conda-forge/linux-64::perl-encode-3.21-pl5321hb9d3cd8_1 perl-exporter conda-forge/noarch::perl-exporter-5.74-pl5321hd8ed1ab_0 perl-exporter-tiny conda-forge/noarch::perl-exporter-tiny-1.002002-pl5321hd8ed1ab_0 perl-extutils-mak~ conda-forge/noarch::perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0 perl-io-compress bioconda/linux-64::perl-io-compress-2.201-pl5321h503566f_5 perl-io-zlib bioconda/noarch::perl-io-zlib-1.15-pl5321hdfd78af_1 perl-json bioconda/noarch::perl-json-4.10-pl5321hdfd78af_1 perl-json-xs bioconda/linux-64::perl-json-xs-4.03-pl5321h9948957_4 perl-list-moreuti~ bioconda/noarch::perl-list-moreutils-0.430-pl5321hdfd78af_0 perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.430-pl5321h7b50bb2_5 perl-parent conda-forge/noarch::perl-parent-0.243-pl5321hd8ed1ab_0 perl-pathtools 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conda-forge/linux-64::r-haven-2.5.4-r44h0d4f4ea_1 r-hexbin conda-forge/linux-64::r-hexbin-1.28.5-r44hb67ce94_0 r-highr conda-forge/noarch::r-highr-0.11-r44hc72bb7e_1 r-hms conda-forge/noarch::r-hms-1.1.3-r44hc72bb7e_2 r-htmltools conda-forge/linux-64::r-htmltools-0.5.8.1-r44ha18555a_1 r-htmlwidgets conda-forge/noarch::r-htmlwidgets-1.6.4-r44h785f33e_3 r-httpcode conda-forge/linux-64::r-httpcode-0.3.0-r44ha770c72_4 r-httpuv conda-forge/linux-64::r-httpuv-1.6.15-r44ha18555a_1 r-httr conda-forge/noarch::r-httr-1.4.7-r44hc72bb7e_1 r-ids conda-forge/noarch::r-ids-1.0.1-r44hc72bb7e_4 r-igraph conda-forge/linux-64::r-igraph-2.0.3-r44h510f1ce_1 r-ipred conda-forge/linux-64::r-ipred-0.9_15-r44hdb488b9_1 r-irdisplay conda-forge/noarch::r-irdisplay-1.1-r44hd8ed1ab_3 r-irkernel conda-forge/noarch::r-irkernel-1.3.2-r44h785f33e_2 r-isoband conda-forge/linux-64::r-isoband-0.2.7-r44ha18555a_3 r-iterators conda-forge/noarch::r-iterators-1.0.14-r44hc72bb7e_3 r-jpeg conda-forge/linux-64::r-jpeg-0.1_11-r44hc5f1ce6_0 r-jquerylib conda-forge/noarch::r-jquerylib-0.1.4-r44hc72bb7e_3 r-jsonlite conda-forge/linux-64::r-jsonlite-2.0.0-r44h2b5f3a1_0 r-kernsmooth conda-forge/linux-64::r-kernsmooth-2.23_26-r44h8461fee_0 r-knitr conda-forge/noarch::r-knitr-1.50-r44hc72bb7e_0 r-labeling conda-forge/noarch::r-labeling-0.4.3-r44hc72bb7e_1 r-later conda-forge/linux-64::r-later-1.4.2-r44h93ab643_0 r-lattice conda-forge/linux-64::r-lattice-0.22_7-r44h2b5f3a1_0 r-lava conda-forge/noarch::r-lava-1.8.1-r44hc72bb7e_0 r-lazyeval conda-forge/linux-64::r-lazyeval-0.2.2-r44hb1dbf0f_5 r-lifecycle conda-forge/noarch::r-lifecycle-1.0.4-r44hc72bb7e_1 r-listenv conda-forge/noarch::r-listenv-0.9.1-r44hc72bb7e_1 r-litedown conda-forge/noarch::r-litedown-0.7-r44hc72bb7e_0 r-lobstr conda-forge/linux-64::r-lobstr-1.1.2-r44ha18555a_4 r-lubridate conda-forge/linux-64::r-lubridate-1.9.4-r44h2b5f3a1_0 r-magrittr conda-forge/linux-64::r-magrittr-2.0.3-r44hb1dbf0f_3 r-maps conda-forge/linux-64::r-maps-3.4.3-r44h2b5f3a1_0 r-markdown conda-forge/noarch::r-markdown-2.0-r44hc72bb7e_0 r-mass conda-forge/linux-64::r-mass-7.3_64-r44h2b5f3a1_0 r-matrix conda-forge/linux-64::r-matrix-1.7_3-r44h2ae2be5_0 r-memoise conda-forge/noarch::r-memoise-2.0.1-r44hc72bb7e_3 r-mgcv conda-forge/linux-64::r-mgcv-1.9_3-r44h2ae2be5_0 r-mime conda-forge/linux-64::r-mime-0.13-r44h2b5f3a1_0 r-modelmetrics conda-forge/linux-64::r-modelmetrics-1.2.2.2-r44h0d4f4ea_4 r-modelr conda-forge/noarch::r-modelr-0.1.11-r44hc72bb7e_2 r-munsell conda-forge/noarch::r-munsell-0.5.1-r44hc72bb7e_1 r-mvtnorm conda-forge/linux-64::r-mvtnorm-1.3_3-r44h9ad1c49_0 r-nlme conda-forge/linux-64::r-nlme-3.1_168-r44hb67ce94_0 r-nnet conda-forge/linux-64::r-nnet-7.3_20-r44h2b5f3a1_0 r-numderiv conda-forge/noarch::r-numderiv-2016.8_1.1-r44hc72bb7e_6 r-openssl conda-forge/linux-64::r-openssl-2.3.3-r44he8289e2_0 r-openxlsx conda-forge/linux-64::r-openxlsx-4.2.8-r44h93ab643_0 r-optparse conda-forge/noarch::r-optparse-1.7.5-r44hc72bb7e_1 r-parallelly conda-forge/linux-64::r-parallelly-1.45.0-r44h2b5f3a1_0 r-patchwork conda-forge/noarch::r-patchwork-1.3.1-r44hc72bb7e_0 r-pbdzmq conda-forge/linux-64::r-pbdzmq-0.3_14-r44h549f438_0 r-permute conda-forge/noarch::r-permute-0.9_8-r44hc72bb7e_0 r-pillar conda-forge/noarch::r-pillar-1.11.0-r44hc72bb7e_0 r-pixmap conda-forge/noarch::r-pixmap-0.4_13-r44hc72bb7e_1 r-pkgconfig conda-forge/noarch::r-pkgconfig-2.0.3-r44hc72bb7e_4 r-plyr conda-forge/linux-64::r-plyr-1.8.9-r44ha18555a_1 r-png conda-forge/linux-64::r-png-0.1_8-r44h21f035c_2 r-prettyunits conda-forge/noarch::r-prettyunits-1.2.0-r44hc72bb7e_1 r-proc conda-forge/linux-64::r-proc-1.18.5-r44ha18555a_1 r-processx conda-forge/linux-64::r-processx-3.8.6-r44h2b5f3a1_0 r-prodlim conda-forge/linux-64::r-prodlim-2025.04.28-r44h93ab643_0 r-progress conda-forge/noarch::r-progress-1.2.3-r44hc72bb7e_1 r-progressr conda-forge/noarch::r-progressr-0.15.1-r44hc72bb7e_0 r-promises conda-forge/linux-64::r-promises-1.3.2-r44h93ab643_0 r-proxy conda-forge/linux-64::r-proxy-0.4_27-r44hb1dbf0f_3 r-pryr conda-forge/linux-64::r-pryr-0.1.6-r44h0d4f4ea_2 r-ps conda-forge/linux-64::r-ps-1.9.1-r44h2b5f3a1_0 r-purrr conda-forge/linux-64::r-purrr-1.1.0-r44h54b55ab_0 r-quantmod conda-forge/noarch::r-quantmod-0.4.28-r44hc72bb7e_0 r-r.methodss3 conda-forge/noarch::r-r.methodss3-1.8.2-r44hc72bb7e_3 r-r.oo conda-forge/noarch::r-r.oo-1.27.1-r44hc72bb7e_0 r-r.utils conda-forge/noarch::r-r.utils-2.13.0-r44hc72bb7e_0 r-r6 conda-forge/noarch::r-r6-2.6.1-r44hc72bb7e_0 r-ragg conda-forge/linux-64::r-ragg-1.4.0-r44hdcc764c_0 r-randomforest conda-forge/linux-64::r-randomforest-4.7_1.2-r44hb67ce94_0 r-rappdirs conda-forge/linux-64::r-rappdirs-0.3.3-r44hb1dbf0f_3 r-rbiom conda-forge/linux-64::r-rbiom-2.2.1-r44h93ab643_0 r-rbokeh conda-forge/noarch::r-rbokeh-0.5.2-r44hc72bb7e_4 r-rcolorbrewer conda-forge/noarch::r-rcolorbrewer-1.1_3-r44h785f33e_3 r-rcpp conda-forge/linux-64::r-rcpp-1.1.0-r44h93ab643_0 r-rcpparmadillo conda-forge/linux-64::r-rcpparmadillo-14.4.2_1-r44hc2d650c_0 r-rcppeigen conda-forge/linux-64::r-rcppeigen-0.3.4.0.2-r44hb79369c_0 r-readr conda-forge/linux-64::r-readr-2.1.5-r44h0d4f4ea_1 r-readxl conda-forge/linux-64::r-readxl-1.4.5-r44h328fee5_0 r-recipes conda-forge/noarch::r-recipes-1.3.1-r44hc72bb7e_0 r-recommended conda-forge/noarch::r-recommended-4.4-r44hd8ed1ab_1007 r-rematch conda-forge/noarch::r-rematch-2.0.0-r44hc72bb7e_1 r-rematch2 conda-forge/noarch::r-rematch2-2.1.2-r44hc72bb7e_4 r-repr conda-forge/noarch::r-repr-1.1.7-r44h785f33e_1 r-reprex conda-forge/noarch::r-reprex-2.1.1-r44hc72bb7e_1 r-reshape2 conda-forge/linux-64::r-reshape2-1.4.4-r44h0d4f4ea_4 r-rjson conda-forge/linux-64::r-rjson-0.2.23-r44h93ab643_0 r-rlang conda-forge/linux-64::r-rlang-1.1.6-r44h93ab643_0 r-rmarkdown conda-forge/noarch::r-rmarkdown-2.29-r44hc72bb7e_0 r-robustbase conda-forge/linux-64::r-robustbase-0.99_4_1-r44h9ad1c49_0 r-rpart conda-forge/linux-64::r-rpart-4.1.24-r44h2b5f3a1_0 r-rstudioapi conda-forge/noarch::r-rstudioapi-0.17.1-r44hc72bb7e_0 r-rtsne conda-forge/linux-64::r-rtsne-0.17-r44h4387864_1 r-rvest conda-forge/noarch::r-rvest-1.0.4-r44hc72bb7e_1 r-sass conda-forge/linux-64::r-sass-0.4.10-r44h93ab643_0 r-scales conda-forge/noarch::r-scales-1.4.0-r44hc72bb7e_0 r-selectr conda-forge/noarch::r-selectr-0.4_2-r44hc72bb7e_4 r-shape conda-forge/noarch::r-shape-1.4.6.1-r44ha770c72_1 r-shiny conda-forge/noarch::r-shiny-1.11.1-r44h785f33e_0 r-slam conda-forge/linux-64::r-slam-0.1_55-r44h0444075_0 r-sourcetools conda-forge/linux-64::r-sourcetools-0.1.7_1-r44ha18555a_2 r-sp conda-forge/linux-64::r-sp-2.2_0-r44h2b5f3a1_0 r-sparsevctrs conda-forge/linux-64::r-sparsevctrs-0.3.4-r44h2b5f3a1_0 r-spatial conda-forge/linux-64::r-spatial-7.3_18-r44h2b5f3a1_0 r-squarem conda-forge/noarch::r-squarem-2021.1-r44hc72bb7e_3 r-stringi conda-forge/linux-64::r-stringi-1.8.7-r44h3c328a7_0 r-stringr conda-forge/noarch::r-stringr-1.5.1-r44h785f33e_1 r-survival conda-forge/linux-64::r-survival-3.8_3-r44h2b5f3a1_0 r-sys conda-forge/linux-64::r-sys-3.4.3-r44h2b5f3a1_0 r-systemfonts conda-forge/linux-64::r-systemfonts-1.2.3-r44h5c043a3_0 r-tensora conda-forge/linux-64::r-tensora-0.36.2.1-r44hb1dbf0f_1 r-textshaping conda-forge/linux-64::r-textshaping-1.0.1-r44h16f7c1a_0 r-tibble conda-forge/linux-64::r-tibble-3.3.0-r44h2b5f3a1_0 r-tidyr conda-forge/linux-64::r-tidyr-1.3.1-r44h0d4f4ea_1 r-tidyselect conda-forge/noarch::r-tidyselect-1.2.1-r44hc72bb7e_1 r-tidyverse conda-forge/noarch::r-tidyverse-2.0.0-r44h785f33e_2 r-timechange conda-forge/linux-64::r-timechange-0.3.0-r44ha18555a_1 r-timedate conda-forge/noarch::r-timedate-4041.110-r44hc72bb7e_0 r-tinytex conda-forge/noarch::r-tinytex-0.57-r44hc72bb7e_0 r-triebeard conda-forge/linux-64::r-triebeard-0.4.1-r44ha18555a_2 r-ttr conda-forge/linux-64::r-ttr-0.24.4-r44hdb488b9_1 r-tzdb conda-forge/linux-64::r-tzdb-0.5.0-r44h93ab643_0 r-urltools conda-forge/linux-64::r-urltools-1.7.3-r44ha18555a_5 r-utf8 conda-forge/linux-64::r-utf8-1.2.6-r44h2b5f3a1_0 r-uuid conda-forge/linux-64::r-uuid-1.2_1-r44hdb488b9_0 r-vctrs conda-forge/linux-64::r-vctrs-0.6.5-r44h0d4f4ea_1 r-vegan conda-forge/linux-64::r-vegan-2.7_1-r44h012206f_0 r-vipor conda-forge/noarch::r-vipor-0.4.7-r44hc72bb7e_1 r-viridislite conda-forge/noarch::r-viridislite-0.4.2-r44hc72bb7e_2 r-vroom conda-forge/linux-64::r-vroom-1.6.5-r44h0d4f4ea_1 r-withr conda-forge/noarch::r-withr-3.0.2-r44hc72bb7e_0 r-xfun conda-forge/linux-64::r-xfun-0.52-r44h93ab643_0 r-xml2 conda-forge/linux-64::r-xml2-1.3.8-r44h1bb2df6_0 r-xtable conda-forge/noarch::r-xtable-1.8_4-r44hc72bb7e_6 r-xts conda-forge/linux-64::r-xts-0.14.1-r44h2b5f3a1_0 r-yaml conda-forge/linux-64::r-yaml-2.3.10-r44hdb488b9_0 r-zip conda-forge/linux-64::r-zip-2.3.3-r44h2b5f3a1_0 r-zoo conda-forge/linux-64::r-zoo-1.8_14-r44h2b5f3a1_0 raxml bioconda/linux-64::raxml-8.2.13-h7b50bb2_3 readline conda-forge/linux-64::readline-8.2-h8c095d6_2 referencing conda-forge/noarch::referencing-0.36.2-pyh29332c3_0 requests conda-forge/noarch::requests-2.32.4-pyhd8ed1ab_0 rfc3339-validator conda-forge/noarch::rfc3339-validator-0.1.4-pyhd8ed1ab_1 rfc3986-validator conda-forge/noarch::rfc3986-validator-0.1.1-pyh9f0ad1d_0 rpds-py conda-forge/linux-64::rpds-py-0.26.0-py312h680f630_0 rpsbproc bioconda/linux-64::rpsbproc-0.5.0-hd6d6fdc_3 samtools bioconda/linux-64::samtools-1.22-h96c455f_0 scipy conda-forge/linux-64::scipy-1.16.0-py312hf734454_0 seaborn conda-forge/noarch::seaborn-0.13.2-hd8ed1ab_3 seaborn-base conda-forge/noarch::seaborn-base-0.13.2-pyhd8ed1ab_3 sed conda-forge/linux-64::sed-4.9-h6688a6e_0 send2trash conda-forge/noarch::send2trash-1.8.3-pyh0d859eb_1 setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0 six conda-forge/noarch::six-1.17.0-pyhd8ed1ab_0 sniffio conda-forge/noarch::sniffio-1.3.1-pyhd8ed1ab_1 soupsieve conda-forge/noarch::soupsieve-2.7-pyhd8ed1ab_0 stack_data conda-forge/noarch::stack_data-0.6.3-pyhd8ed1ab_1 statsmodels conda-forge/linux-64::statsmodels-0.14.5-py312h8b63200_0 sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.17-h0157908_18 terminado conda-forge/noarch::terminado-0.18.1-pyh0d859eb_0 tinycss2 conda-forge/noarch::tinycss2-1.4.0-pyhd8ed1ab_0 tk conda-forge/linux-64::tk-8.6.13-noxft_hd72426e_102 tktable conda-forge/linux-64::tktable-2.10-h8d826fa_7 toml conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_1 tomli conda-forge/noarch::tomli-2.2.1-pyhd8ed1ab_1 tomlkit conda-forge/noarch::tomlkit-0.13.3-pyha770c72_0 tornado conda-forge/linux-64::tornado-6.5.1-py312h66e93f0_0 traitlets conda-forge/noarch::traitlets-5.14.3-pyhd8ed1ab_1 trimal bioconda/linux-64::trimal-1.5.0-h9948957_2 types-python-date~ conda-forge/noarch::types-python-dateutil-2.9.0.20250708-pyhd8ed1ab_0 typing-extensions conda-forge/noarch::typing-extensions-4.14.1-h4440ef1_0 typing_extensions conda-forge/noarch::typing_extensions-4.14.1-pyhe01879c_0 typing_utils conda-forge/noarch::typing_utils-0.1.0-pyhd8ed1ab_1 tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0 unicodedata2 conda-forge/linux-64::unicodedata2-16.0.0-py312h66e93f0_0 uri-template conda-forge/noarch::uri-template-1.3.0-pyhd8ed1ab_1 urllib3 conda-forge/noarch::urllib3-2.5.0-pyhd8ed1ab_0 wcwidth conda-forge/noarch::wcwidth-0.2.13-pyhd8ed1ab_1 webcolors conda-forge/noarch::webcolors-24.11.1-pyhd8ed1ab_0 webencodings conda-forge/noarch::webencodings-0.5.1-pyhd8ed1ab_3 websocket-client conda-forge/noarch::websocket-client-1.8.0-pyhd8ed1ab_1 wget conda-forge/linux-64::wget-1.21.4-hda4d442_0 wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1 xmltodict conda-forge/noarch::xmltodict-0.14.2-pyhd8ed1ab_1 xorg-libice conda-forge/linux-64::xorg-libice-1.1.2-hb9d3cd8_0 xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.6-he73a12e_0 xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.12-h4f16b4b_0 xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.12-hb9d3cd8_0 xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb9d3cd8_0 xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.12-hb9d3cd8_0 xorg-libxt conda-forge/linux-64::xorg-libxt-1.3.1-hb9d3cd8_0 yaml conda-forge/linux-64::yaml-0.2.5-h7f98852_2 yq conda-forge/noarch::yq-3.4.3-pyhe01879c_2 zeromq conda-forge/linux-64::zeromq-4.3.5-h3b0a872_7 zipp conda-forge/noarch::zipp-3.23.0-pyhd8ed1ab_0 zlib conda-forge/linux-64::zlib-1.3.1-hb9d3cd8_2 zstandard conda-forge/linux-64::zstandard-0.23.0-py312h66e93f0_2 zstd conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ Info: Running `conda install -q -y tbb=2020.2` in BiobakeryUtils environment Channels: - biobakery - conda-forge - bioconda Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils added / updated specs: - tbb=2020.2 The following packages will be downloaded: package | build ---------------------------|----------------- tbb-2020.2 | h4bd325d_4 1.5 MB conda-forge ------------------------------------------------------------ Total: 1.5 MB The following NEW packages will be INSTALLED: tbb conda-forge/linux-64::tbb-2020.2-h4bd325d_4 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done [ Info: Running `conda install -q -y kneaddata` in BiobakeryUtils environment Channels: - biobakery - conda-forge - bioconda Platform: linux-64 Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils added / updated specs: - kneaddata The following packages will be downloaded: package | build ---------------------------|----------------- alsa-lib-1.2.14 | hb9d3cd8_0 553 KB conda-forge bmtool-3.101 | h503566f_6 73 KB bioconda fastqc-0.12.1 | hdfd78af_0 11.1 MB bioconda giflib-5.2.2 | hd590300_0 75 KB conda-forge kneaddata-0.12.3 | pyhdfd78af_0 402 KB bioconda libcups-2.3.3 | hb8b1518_5 4.3 MB conda-forge openjdk-23.0.2 | h53dfc1b_2 181.4 MB conda-forge srprism-2.4.24 | hd6d6fdc_6 557 KB bioconda trf-4.10.0rc2 | h7b50bb2_0 67 KB bioconda trimmomatic-0.39 | hdfd78af_2 144 KB bioconda xorg-libxfixes-6.0.1 | hb9d3cd8_0 19 KB conda-forge xorg-libxi-1.8.2 | hb9d3cd8_0 46 KB conda-forge xorg-libxrandr-1.5.4 | hb9d3cd8_0 29 KB conda-forge xorg-libxtst-1.2.5 | hb9d3cd8_3 32 KB conda-forge ------------------------------------------------------------ Total: 198.8 MB The following NEW packages will be INSTALLED: alsa-lib conda-forge/linux-64::alsa-lib-1.2.14-hb9d3cd8_0 bmtool bioconda/linux-64::bmtool-3.101-h503566f_6 fastqc bioconda/noarch::fastqc-0.12.1-hdfd78af_0 giflib conda-forge/linux-64::giflib-5.2.2-hd590300_0 kneaddata bioconda/noarch::kneaddata-0.12.3-pyhdfd78af_0 libcups conda-forge/linux-64::libcups-2.3.3-hb8b1518_5 openjdk conda-forge/linux-64::openjdk-23.0.2-h53dfc1b_2 srprism bioconda/linux-64::srprism-2.4.24-hd6d6fdc_6 trf bioconda/linux-64::trf-4.10.0rc2-h7b50bb2_0 trimmomatic bioconda/noarch::trimmomatic-0.39-hdfd78af_2 xorg-libxfixes conda-forge/linux-64::xorg-libxfixes-6.0.1-hb9d3cd8_0 xorg-libxi conda-forge/linux-64::xorg-libxi-1.8.2-hb9d3cd8_0 xorg-libxrandr conda-forge/linux-64::xorg-libxrandr-1.5.4-hb9d3cd8_0 xorg-libxtst conda-forge/linux-64::xorg-libxtst-1.2.5-hb9d3cd8_3 Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done ┌ Warning: Don't forget to add /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/bin to your PATH! │ │ This can be done in a julia session with: │ │ `ENV["PATH"] = ENV["PATH"] * ":" * "/home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/bin"`, │ or you can set it in your shell environment. └ @ BiobakeryUtils ~/.julia/packages/BiobakeryUtils/ypFMk/src/utils.jl:29 [ Info: Running command: `metaphlan --help` usage: metaphlan --input_type {fastq,fasta,mapout,sam} [--force] [--db_dir METAPHLAN_DB] [-x INDEX] [--mapout FILE_NAME] [--min_mapq_val MIN_MAPQ_VAL] [--no_map] [--tmp_dir] [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE] [--bowtie2_build BOWTIE2_BUILD] [--tax_lev TAXONOMIC_LEVEL] [--min_alignment_len] [--ignore_eukaryotes] [--ignore_bacteria] [--ignore_archaea] [--ignore_ksgbs] [--ignore_usgbs] [--stat_q] [--perc_nonzero] [--ignore_markers IGNORE_MARKERS] [--avoid_disqm] [--stat] [-t ANALYSIS TYPE] [--nreads NUMBER_OF_READS] [--pres_th PRESENCE_THRESHOLD] [-o output file] [--sample_id_key name] [--use_group_representative] [--sample_id value] [-s sam_output_file] [--CAMI_format_output] [--skip_unclassified_estimation] [--biom_format_output] [--biom_mdelim mdelim] [--profile_vsc] [--vsc_out VSC_OUT] [--vsc_breadth VSC_BREADTH] [--long_reads] [--max_gcsd MAX_GCSD] [--minimap2_exe MINIMAP2_EXE] [--minimap2_ps minimap2 presets] [--nbases NUMBER_OF_BASES] [--split_reads] [--split_readlen SPLIT_READLEN] [--nproc N] [--subsampling SUBSAMPLING] [--mapping_subsampling] [--subsampling_seed SUBSAMPLING_SEED] [--subsampling_output SUBSAMPLING_OUTPUT] [--subsampling_paired SUBSAMPLING_PAIRED] [-1 FORWARD_READS] [-2 REVERSE_READS] [--install] [--offline] [--force_download] [--read_min_len READ_MIN_LEN] [--verbose] [-v] [-h] [INPUT_FILE] MetaPhlAn version 4.2.2 (4 Jun 2025): METAgenomic PHyLogenetic ANalysis for metagenomic taxonomic profiling. AUTHORS: Aitor Blanco-Miguez (aitor.blancomiguez@unitn.it), Francesco Beghini (francesco.beghini@unitn.it), Nicola Segata (nicola.segata@unitn.it), Duy Tin Truong, Francesco Asnicar (f.asnicar@unitn.it), Claudia Mengoni (claudia.mengoni@unitn.it), Linda Cova (linda.cova@unitn.it) positional arguments: INPUT_FILE the input file can be: * a fastq file containing metagenomic reads OR * a BowTie2 produced SAM file. OR * a minimap2 produced SAM file (for long reads). OR * an intermediary mapping file of the metagenome generated by a previous MetaPhlAn run (mapout) If the input file is missing, the script assumes that the input is provided using the standard input, or named pipes. IMPORTANT: the type of input needs to be specified with --input_type Required arguments: --input_type {fastq,fasta,mapout,sam} set whether the input is the FASTA file of metagenomic reads or the SAM file of the mapping of the reads against the MetaPhlAn db. Mapping arguments: --force Force profiling of the input file by removing the mapout file --db_dir METAPHLAN_DB Folder containing the MetaPhlAn database. You can specify the location by exporting the DEFAULT_DB_FOLDER variable in the shell (old --bowtie2db option).[default /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/lib/python3.12/site-packages/metaphlan/metaphlan_databases] -x INDEX, --index INDEX Specify the id of the database version to use. If "latest", MetaPhlAn will get the latest version. If an index name is provided, MetaPhlAn will try to use it, if available, and skip the online check. If the database files are not found on the local MetaPhlAn installation they will be automatically downloaded [default latest] --mapout FILE_NAME The file for saving the mapping output (old --bowtie2out option) --min_mapq_val MIN_MAPQ_VAL Minimum mapping quality value (MAPQ) [default 5 for short reads, 50 for long reads] --no_map Avoid storing the --mapout map file --tmp_dir The folder used to store temporary files [default is the OS dependent tmp dir] Bowtie2 arguments: --bt2_ps BowTie2 presets Presets options for BowTie2 (applied only when a FASTA file is provided) The choices enabled in MetaPhlAn are: * sensitive * very-sensitive * sensitive-local * very-sensitive-local [default very-sensitive] --bowtie2_exe BOWTIE2_EXE Full path and name of the BowTie2 executable. This option allowsMetaPhlAn to reach the executable even when it is not in the system PATH or the system PATH is unreachable --bowtie2_build BOWTIE2_BUILD Full path to the bowtie2-build command to use, deafult assumes that 'bowtie2-build is present in the system path Post-mapping arguments: --tax_lev TAXONOMIC_LEVEL The taxonomic level for the relative abundance output: 'a' : all taxonomic levels 'k' : kingdoms 'p' : phyla only 'c' : classes only 'o' : orders only 'f' : families only 'g' : genera only 's' : species only 't' : SGBs only [default 'a'] --min_alignment_len The sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded. [default None] --ignore_eukaryotes Do not profile eukaryotic organisms --ignore_bacteria Do not profile bacterial organisms --ignore_archaea Do not profile archeal organisms --ignore_ksgbs Do not profile known SGBs (together with --sgb option) --ignore_usgbs Do not profile unknown SGBs (together with --sgb option) --stat_q Quantile value for the robust average [default 0.2] --perc_nonzero Percentage of markers with a non zero relative abundance for misidentify a species [default 0.33] --ignore_markers IGNORE_MARKERS File containing a list of markers to ignore. --avoid_disqm Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample. It is generally recommended to keep the disambiguation procedure in order to minimize false positives --stat Statistical approach for converting marker abundances into clade abundances 'avg_g' : clade global (i.e. normalizing all markers together) average 'avg_l' : average of length-normalized marker counts 'tavg_g' : truncated clade global average at --stat_q quantile 'tavg_l' : truncated average of length-normalized marker counts (at --stat_q) 'wavg_g' : winsorized clade global average (at --stat_q) 'wavg_l' : winsorized average of length-normalized marker counts (at --stat_q) 'med' : median of length-normalized marker counts [default tavg_g] Additional analysis types and arguments: -t ANALYSIS TYPE Type of analysis to perform: * rel_ab: profiling a metagenomes in terms of relative abundances * rel_ab_w_read_stats: profiling a metagenomes in terms of relative abundances and estimate the number of reads coming from each clade. * clade_profiles: normalized marker counts for clades with at least a non-null marker * marker_ab_table: normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified) * marker_pres_table: list of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th [default 'rel_ab'] --nreads NUMBER_OF_READS The total number of reads in the original metagenome. It is mandatory when the --input_type is a SAM file. --pres_th PRESENCE_THRESHOLD Threshold for calling a marker present by the -t marker_pres_table option Output arguments: -o output file, --output_file output file The output file (if not specified stdout) --sample_id_key name Specify the sample ID key for this analysis. Defaults to 'SampleID'. --use_group_representative Use a species as representative for species groups. --sample_id value Specify the sample ID for this analysis. Defaults to 'Metaphlan_Analysis'. -s sam_output_file, --samout sam_output_file The sam output file --CAMI_format_output Report the profiling using the CAMI output format --skip_unclassified_estimation Do not scale relative abundances to the estimate unclassified taxa --biom_format_output Report the profiling using the biom output format --biom_mdelim mdelim Delimiter for metadata in the biom output format [default '|'] Viral Sequence Clusters Analisys: --profile_vsc Add this parameter to profile Viruses with VSCs approach. --vsc_out VSC_OUT Path to the VSCs breadth-of-coverage output file --vsc_breadth VSC_BREADTH Minimum Breadth of Coverage for a Viral Group to be reported. Default is 0.75 (at least 75 percent breadth to report), 0.5 for long reads Long reads arguments: --long_reads Add this parameter to profile long reads. --max_gcsd MAX_GCSD Specify the max gap-compressed sequence divergence (minimap2) allowed between marker and read, default value is 0.10 --minimap2_exe MINIMAP2_EXE Full path and name of the Minimap2 executable. This option allowsMetaPhlAn to reach the executable even when it is not in the system PATH or the system PATH is unreachable --minimap2_ps minimap2 presets Presets options for Minimap2 (applied only when a FASTA/Q file is provided) Please refer to the minimap2 documentation and provide the options in a string such as: '-x asm20 -B 3 -O 3,12' [default '-x asm20 -B 3 -O 3,12'] --nbases NUMBER_OF_BASES The total number of bases in the original metagenome. It is mandatory when the --input_type is a SAM file from long reads mapping (--long_reads is selected) --split_reads Add this parameter to profile long reads by splitting into short reads. --split_readlen SPLIT_READLEN Specify length of the reads to be split into when using --split_reads, default value is 150 Other arguments: --nproc N The number of CPUs to use for parallelizing the mapping [default 4] --subsampling SUBSAMPLING Specify the number of reads to be considered from the input metagenomes (number of bases if --long_reads) [default None] --mapping_subsampling If used, the subsamping will be done on the mapping results instead of on the reads. --subsampling_seed SUBSAMPLING_SEED Random seed to use in the selection of the subsampled reads. Choose "random for a random behaviour --subsampling_output SUBSAMPLING_OUTPUT The output file for the subsampled reads. If not specified the subsampled reads will not be saved. --subsampling_paired SUBSAMPLING_PAIRED Specify the number of paired reads to be considered from the input metagenomes [default None] -1 FORWARD_READS Specify the fastq file with forward reads of the input metagenomes. Reads are assumed to be in the same order in the forward and reverse files! [default None] -2 REVERSE_READS Specify the fastq file with reverse reads of the input metagenomes. Reads are assumed to be in the same order in the forward and reverse files! [default None] --install Only checks if the MetaPhlAn DB is installed and installs it if not. All other parameters are ignored. --offline If used, MetaPhlAn will not check for new database updates. --force_download Force the re-download of the latest MetaPhlAn database. --read_min_len READ_MIN_LEN Specify the minimum length of the reads to be considered when parsing the input file with 'read_fastx.py' script, default value is 70 --verbose Makes MetaPhlAn verbose -v, --version Prints the current MetaPhlAn version and exit -h, --help show this help message and exit [ Info: Running command: `humann -i '' -o '' --help` usage: humann [-h] -i -o [--threads <1>] [--version] [-r] [--bypass-nucleotide-index] [--bypass-nucleotide-search] [--bypass-prescreen] [--bypass-translated-search] [--taxonomic-profile ] [--memory-use {minimum,maximum}] [--input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom}] [-v] [--metaphlan ] [--metaphlan-options ] [--prescreen-threshold <0.5>] [--average-read-length <150.0>] [--bowtie2 ] [--bowtie-options ] [--nucleotide-database ] [--nucleotide-identity-threshold <0.0>] [--nucleotide-query-coverage-threshold <90.0>] [--nucleotide-subject-coverage-threshold <50.0>] [--diamond ] [--diamond-options ] [--evalue <1.0>] [--protein-database ] [--translated-alignment {diamond}] [--translated-identity-threshold <50.0>] [--translated-query-coverage-threshold <90.0>] [--translated-subject-coverage-threshold <50.0>] [--count-normalization {Adjusted CPMs,Adjusted RPKs,RPKs,Counts}] [--utility-database ] [--gap-fill {on,off}] [--minpath {on,off}] [--pathways {metacyc,unipathway}] [--pathways-database ] [--xipe {on,off}] [--annotation-gene-index <2>] [--id-mapping ] [--remove-temp-output] [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--o-log ] [--output-basename ] [--output-format {tsv,biom}] [--output-max-decimals <10>] [--remove-column-description-output] [--remove-stratified-output] HUMAnN : HMP Unified Metabolic Analysis Network 3 options: -h, --help show this help message and exit [0] Common settings: -i , --input input file of type {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom} [REQUIRED] -o , --output directory to write output files [REQUIRED] --threads <1> number of threads/processes [DEFAULT: 1] --version show program's version number and exit [1] Workflow refinement: -r, --resume bypass commands if the output files exist --bypass-nucleotide-index bypass the nucleotide index step and run on the indexed ChocoPhlAn database --bypass-nucleotide-search bypass the nucleotide search steps --bypass-prescreen bypass the prescreen step and run on the full ChocoPhlAn database --bypass-translated-search bypass the translated search step --taxonomic-profile a taxonomic profile (the output file created by metaphlan) [DEFAULT: file will be created] --memory-use {minimum,maximum} the amount of memory to use [DEFAULT: minimum] --input-format {fastq,fastq.gz,fasta,fasta.gz,sam,bam,blastm8,genetable,biom} the format of the input file [DEFAULT: format identified by software] -v, --verbose additional output is printed [2] Configure tier 1: prescreen: --metaphlan directory containing the MetaPhlAn software [DEFAULT: $PATH] --metaphlan-options options to be provided to the MetaPhlAn software [DEFAULT: "-t rel_ab_w_read_stats"] --prescreen-threshold <0.5> minimum estimated genome coverage for inclusion in pangenome search [DEFAULT: 0.5] --average-read-length <150.0> average read length for input file [DEFAULT: 150.0] [3] Configure tier 2: nucleotide search: --bowtie2 directory containing the bowtie2 executable [DEFAULT: $PATH] --bowtie-options options to be provided to the bowtie software [DEFAULT: "--very-sensitive --no-hd --no-sq"] --nucleotide-database directory containing the nucleotide database [DEFAULT: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/lib/python3.12/site-packages/humann/data/chocophlan_DEMO] --nucleotide-identity-threshold <0.0> identity threshold for nucleotide alignments [DEFAULT: 0.0] --nucleotide-query-coverage-threshold <90.0> query coverage threshold for nucleotide alignments [DEFAULT: 90.0] --nucleotide-subject-coverage-threshold <50.0> subject coverage threshold for nucleotide alignments [DEFAULT: 50.0] [3] Configure tier 2: translated search: --diamond directory containing the diamond executable [DEFAULT: $PATH] --diamond-options options to be provided to the diamond software [DEFAULT: "--top 1 --sensitive --outfmt 6"] --evalue <1.0> the evalue threshold to use with the translated search [DEFAULT: 1.0] --protein-database directory containing the protein database [DEFAULT: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/lib/python3.12/site-packages/humann/data/uniref_DEMO] --translated-alignment {diamond} software to use for translated alignment [DEFAULT: diamond] --translated-identity-threshold <50.0> identity threshold for translated alignments [DEFAULT: 50.0] --translated-query-coverage-threshold <90.0> query coverage threshold for translated alignments [DEFAULT: 90.0] --translated-subject-coverage-threshold <50.0> subject coverage threshold for translated alignments [DEFAULT: 50.0] [5] Gene and pathway quantification: --count-normalization {Adjusted CPMs,Adjusted RPKs,RPKs,Counts} normalization mode for results from both nucleotide and translated search [DEFAULT: Adjusted CPMs] --utility-database directory containing the utility database [DEFAULT: /home/pkgeval/.julia/conda/3/x86_64/envs/BiobakeryUtils/lib/python3.12/site-packages/humann/data/utility_DEMO] --gap-fill {on,off} turn on/off the gap fill computation [DEFAULT: on] --minpath {on,off} turn on/off the minpath computation [DEFAULT: on] --pathways {metacyc,unipathway} the database to use for pathway computations [DEFAULT: metacyc] --pathways-database mapping file (or files, at most two in a comma-delimited list) to use for pathway computations [DEFAULT: metacyc database ] --xipe {on,off} turn on/off the xipe computation [DEFAULT: off] --annotation-gene-index <2> the index of the gene in the sequence annotation [DEFAULT: 2] --id-mapping id mapping file for alignments [DEFAULT: alignment reference used] [6] More output configuration: --remove-temp-output remove temp output files [DEFAULT: temp files are not removed] --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} level of messages to display in log [DEFAULT: DEBUG] --o-log log file [DEFAULT: sample_0.log] --output-basename the basename for the output files [DEFAULT: input file basename] --output-format {tsv,biom} the format of the output files [DEFAULT: tsv] --output-max-decimals <10> the number of decimals to output [DEFAULT: 10] --remove-column-description-output remove the description in the output column [DEFAULT: output column includes description] --remove-stratified-output remove stratification from output [DEFAULT: output is stratified] Pass CLI | 12 Metaphlan | 27 HUMAnN | 14 Main.BiobakeryUtilsTests | 53 Testing BiobakeryUtils tests passed Testing completed after 498.59s PkgEval succeeded after 722.56s