Package evaluation of BiobakeryUtils on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T16:29:02.702 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.38s ################################################################################ # Installation # Installing BiobakeryUtils... Resolving package versions... Installed Conda ─ v1.10.2 Updating `~/.julia/environments/v1.11/Project.toml` [fa5322f5] + BiobakeryUtils v0.7.0 Updating `~/.julia/environments/v1.11/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 v4.16.0 [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 v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 [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 v1.4.3 [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 v1.8.0 [90014a1f] + PDMats v0.11.33 [69de0a69] + Parsers v2.8.1 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [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 v2.5.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.4.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [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 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [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 v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+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 9.57s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 37.78s ################################################################################ # Testing # Testing BiobakeryUtils Status `/tmp/jl_Hzoayw/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 v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Hzoayw/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 v4.16.0 [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 v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [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 v1.4.3 [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 v1.8.0 [90014a1f] PDMats v0.11.33 [69de0a69] Parsers v2.8.1 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [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 v2.5.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.4.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [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 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.11.0 [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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+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-2025.1.31-hbcca054_0.conda Extracting ld_impl_linux-64-2.43-h712a8e2_4.conda Extracting libgomp-14.2.0-h767d61c_2.conda Extracting pybind11-abi-4-hd8ed1ab_3.tar.bz2 Extracting python_abi-3.12-5_cp312.conda Extracting tzdata-2025a-h78e105d_0.conda Extracting _openmp_mutex-4.5-2_gnu.tar.bz2 Extracting libgcc-14.2.0-h767d61c_2.conda Extracting c-ares-1.34.4-hb9d3cd8_0.conda Extracting libexpat-2.6.4-h5888daf_0.conda Extracting libffi-3.4.6-h2dba641_0.conda Extracting libgcc-ng-14.2.0-h69a702a_2.conda Extracting libiconv-1.18-h4ce23a2_1.conda Extracting liblzma-5.6.4-hb9d3cd8_0.conda Extracting libstdcxx-14.2.0-h8f9b012_2.conda Extracting libzlib-1.3.1-hb9d3cd8_2.conda Extracting ncurses-6.5-h2d0b736_3.conda Extracting openssl-3.4.1-h7b32b05_0.conda Extracting reproc-14.2.5.post0-hb9d3cd8_0.conda Extracting bzip2-1.0.8-h4bc722e_7.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 libsqlite-3.49.1-hee588c1_1.conda Extracting libssh2-1.11.1-hf672d98_0.conda Extracting libstdcxx-ng-14.2.0-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 tk-8.6.13-noxft_h4845f30_101.conda Extracting fmt-11.0.2-h434a139_0.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 libsolv-0.7.30-h3509ff9_0.conda Extracting python-3.12.9-h9e4cc4f_1_cpython.conda Extracting yaml-cpp-0.8.0-h59595ed_0.conda Extracting zstd-1.5.6-ha6fb4c9_0.conda Extracting libcurl-8.12.1-h332b0f4_0.conda Extracting libxml2-2.13.6-h8d12d68_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-2025.1.31-pyhd8ed1ab_0.conda Extracting charset-normalizer-3.4.1-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-h4585015_3.conda Extracting packaging-24.2-pyhd8ed1ab_2.conda Extracting platformdirs-4.3.6-pyhd8ed1ab_1.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-75.8.2-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-1.5.12-h49b8a8d_0.conda Extracting pip-25.0.1-pyh8b19718_0.conda Extracting ruamel.yaml-0.18.10-py312h66e93f0_0.conda Extracting tqdm-4.67.1-pyhd8ed1ab_1.conda Extracting libmambapy-1.5.12-py312hbaee817_0.conda Extracting zstandard-0.23.0-py312hef9b889_1.conda Extracting conda-package-streaming-0.11.0-pyhd8ed1ab_1.conda Extracting urllib3-2.3.0-pyhd8ed1ab_0.conda Extracting requests-2.32.3-pyhd8ed1ab_1.conda Extracting conda-package-handling-2.4.0-pyh7900ff3_2.conda Extracting conda-24.11.3-py312h7900ff3_0.conda Extracting conda-libmamba-solver-24.9.0-pyhd8ed1ab_0.conda Extracting mamba-1.5.12-py312h9460a1c_0.conda Installing base environment... Transaction Prefix: /home/pkgeval/.julia/conda/3/x86_64 Updating specs: - conda-forge/linux-64::_libgcc_mutex==0.1=conda_forge[md5=d7c89558ba9fa0495403155b64376d81] - conda-forge/linux-64::ca-certificates==2025.1.31=hbcca054_0[md5=19f3a56f68d2fd06c516076bff482c52] - conda-forge/linux-64::ld_impl_linux-64==2.43=h712a8e2_4[md5=01f8d123c96816249efd255a31ad7712] - conda-forge/linux-64::libgomp==14.2.0=h767d61c_2[md5=06d02030237f4d5b3d9a7e7d348fe3c6] - conda-forge/noarch::pybind11-abi==4=hd8ed1ab_3[md5=878f923dd6acc8aeb47a75da6c4098be] - conda-forge/linux-64::python_abi==3.12=5_cp312[md5=0424ae29b104430108f5218a66db7260] - conda-forge/noarch::tzdata==2025a=h78e105d_0[md5=dbcace4706afdfb7eb891f7b37d07c04] - conda-forge/linux-64::_openmp_mutex==4.5=2_gnu[md5=73aaf86a425cc6e73fcf236a5a46396d] - conda-forge/linux-64::libgcc==14.2.0=h767d61c_2[md5=ef504d1acbd74b7cc6849ef8af47dd03] - conda-forge/linux-64::c-ares==1.34.4=hb9d3cd8_0[md5=e2775acf57efd5af15b8e3d1d74d72d3] - conda-forge/linux-64::libexpat==2.6.4=h5888daf_0[md5=db833e03127376d461e1e13e76f09b6c] - conda-forge/linux-64::libffi==3.4.6=h2dba641_0[md5=e3eb7806380bc8bcecba6d749ad5f026] - conda-forge/linux-64::libgcc-ng==14.2.0=h69a702a_2[md5=a2222a6ada71fb478682efe483ce0f92] - conda-forge/linux-64::libiconv==1.18=h4ce23a2_1[md5=e796ff8ddc598affdf7c173d6145f087] - conda-forge/linux-64::liblzma==5.6.4=hb9d3cd8_0[md5=42d5b6a0f30d3c10cd88cb8584fda1cb] - conda-forge/linux-64::libstdcxx==14.2.0=h8f9b012_2[md5=a78c856b6dc6bf4ea8daeb9beaaa3fb0] - conda-forge/linux-64::libzlib==1.3.1=hb9d3cd8_2[md5=edb0dca6bc32e4f4789199455a1dbeb8] - conda-forge/linux-64::ncurses==6.5=h2d0b736_3[md5=47e340acb35de30501a76c7c799c41d7] - conda-forge/linux-64::openssl==3.4.1=h7b32b05_0[md5=41adf927e746dc75ecf0ef841c454e48] - conda-forge/linux-64::reproc==14.2.5.post0=hb9d3cd8_0[md5=69fbc0a9e42eb5fe6733d2d60d818822] - conda-forge/linux-64::bzip2==1.0.8=h4bc722e_7[md5=62ee74e96c5ebb0af99386de58cf9553] - conda-forge/linux-64::keyutils==1.6.1=h166bdaf_0[md5=30186d27e2c9fa62b45fb1476b7200e3] - conda-forge/linux-64::libedit==3.1.20250104=pl5321h7949ede_0[md5=c277e0a4d549b03ac1e9d6cbbe3d017b] - conda-forge/linux-64::libev==4.33=hd590300_2[md5=172bf1cd1ff8629f2b1179945ed45055] - conda-forge/linux-64::libnsl==2.0.1=hd590300_0[md5=30fd6e37fe21f86f4bd26d6ee73eeec7] - conda-forge/linux-64::libsqlite==3.49.1=hee588c1_1[md5=73cea06049cc4174578b432320a003b8] - conda-forge/linux-64::libssh2==1.11.1=hf672d98_0[md5=be2de152d8073ef1c01b7728475f2fe7] - conda-forge/linux-64::libstdcxx-ng==14.2.0=h4852527_2[md5=c75da67f045c2627f59e6fcb5f4e3a9b] - conda-forge/linux-64::libuuid==2.38.1=h0b41bf4_0[md5=40b61aab5c7ba9ff276c41cfffe6b80b] - conda-forge/linux-64::libxcrypt==4.4.36=hd590300_1[md5=5aa797f8787fe7a17d1b0821485b5adc] - conda-forge/linux-64::lz4-c==1.10.0=h5888daf_1[md5=9de5350a85c4a20c685259b889aa6393] - conda-forge/linux-64::lzo==2.10=hd590300_1001[md5=ec7398d21e2651e0dcb0044d03b9a339] - conda-forge/linux-64::readline==8.2=h8c095d6_2[md5=283b96675859b20a825f8fa30f311446] - conda-forge/linux-64::reproc-cpp==14.2.5.post0=h5888daf_0[md5=828302fca535f9cfeb598d5f7c204323] - conda-forge/linux-64::tk==8.6.13=noxft_h4845f30_101[md5=d453b98d9c83e71da0741bb0ff4d76bc] - conda-forge/linux-64::fmt==11.0.2=h434a139_0[md5=995f7e13598497691c1dc476d889bc04] - conda-forge/linux-64::icu==75.1=he02047a_0[md5=8b189310083baabfb622af68fd9d3ae3] - conda-forge/linux-64::krb5==1.21.3=h659f571_0[md5=3f43953b7d3fb3aaa1d0d0723d91e368] - conda-forge/linux-64::libnghttp2==1.64.0=h161d5f1_0[md5=19e57602824042dfd0446292ef90488b] - conda-forge/linux-64::libsolv==0.7.30=h3509ff9_0[md5=02539b77d25aa4f65b20246549e256c3] - conda-forge/linux-64::python==3.12.9=h9e4cc4f_1_cpython[md5=d82342192dfc9145185190e651065aa9] - conda-forge/linux-64::yaml-cpp==0.8.0=h59595ed_0[md5=965eaacd7c18eb8361fd12bb9e7a57d7] - conda-forge/linux-64::zstd==1.5.6=ha6fb4c9_0[md5=4d056880988120e29d75bfff282e0f45] - conda-forge/linux-64::libcurl==8.12.1=h332b0f4_0[md5=45e9dc4e7b25e2841deb392be085500e] - conda-forge/linux-64::libxml2==2.13.6=h8d12d68_0[md5=328382c0e0ca648e5c189d5ec336c604] - conda-forge/linux-64::menuinst==2.2.0=py312h7900ff3_0[md5=f22f8e77b36e67297feffe03eefd5375] - conda-forge/noarch::archspec==0.2.5=pyhd8ed1ab_0[md5=845b38297fca2f2d18a29748e2ece7fa] - conda-forge/noarch::boltons==24.0.0=pyhd8ed1ab_1[md5=d88c38e66d85ecc9c7e2c4110676bbf4] - conda-forge/linux-64::brotli-python==1.1.0=py312h2ec8cdc_2[md5=b0b867af6fc74b2a0aa206da29c0f3cf] - conda-forge/noarch::certifi==2025.1.31=pyhd8ed1ab_0[md5=c207fa5ac7ea99b149344385a9c0880d] - conda-forge/noarch::charset-normalizer==3.4.1=pyhd8ed1ab_0[md5=e83a31202d1c0a000fce3e9cf3825875] - conda-forge/noarch::colorama==0.4.6=pyhd8ed1ab_1[md5=962b9857ee8e7018c22f2776ffa0b2d7] - conda-forge/noarch::distro==1.9.0=pyhd8ed1ab_1[md5=0a2014fd9860f8b1eaa0b1f3d3771a08] - conda-forge/linux-64::frozendict==2.4.6=py312h66e93f0_0[md5=9fa8408745a0621314b7751d11fecc18] - conda-forge/noarch::hpack==4.1.0=pyhd8ed1ab_0[md5=0a802cb9888dd14eeefc611f05c40b6e] - conda-forge/noarch::hyperframe==6.1.0=pyhd8ed1ab_0[md5=8e6923fc12f1fe8f8c4e5c9f343256ac] - conda-forge/noarch::idna==3.10=pyhd8ed1ab_1[md5=39a4f67be3286c86d696df570b1201b7] - conda-forge/linux-64::jsonpointer==3.0.0=py312h7900ff3_1[md5=6b51f7459ea4073eeb5057207e2e1e3d] - conda-forge/linux-64::libarchive==3.7.7=h4585015_3[md5=a28808eae584c7f519943719b2a2b386] - conda-forge/noarch::packaging==24.2=pyhd8ed1ab_2[md5=3bfed7e6228ebf2f7b9eaa47f1b4e2aa] - conda-forge/noarch::platformdirs==4.3.6=pyhd8ed1ab_1[md5=577852c7e53901ddccc7e6a9959ddebe] - conda-forge/noarch::pluggy==1.5.0=pyhd8ed1ab_1[md5=e9dcbce5f45f9ee500e728ae58b605b6] - conda-forge/linux-64::pycosat==0.6.6=py312h66e93f0_2[md5=08223e6a73e0bca5ade16ec4cebebf23] - conda-forge/noarch::pycparser==2.22=pyh29332c3_1[md5=12c566707c80111f9799308d9e265aef] - conda-forge/noarch::pysocks==1.7.1=pyha55dd90_7[md5=461219d1a5bd61342293efa2c0c90eac] - conda-forge/linux-64::ruamel.yaml.clib==0.2.8=py312h66e93f0_1[md5=532c3e5d0280be4fea52396ec1fa7d5d] - conda-forge/noarch::setuptools==75.8.2=pyhff2d567_0[md5=9bddfdbf4e061821a1a443f93223be61] - conda-forge/noarch::truststore==0.10.1=pyh29332c3_0[md5=373a72aeffd8a5d93652ef1235062252] - conda-forge/noarch::wheel==0.45.1=pyhd8ed1ab_1[md5=75cb7132eb58d97896e173ef12ac9986] - conda-forge/linux-64::cffi==1.17.1=py312h06ac9bb_0[md5=a861504bbea4161a9170b85d4d2be840] - conda-forge/noarch::h2==4.2.0=pyhd8ed1ab_0[md5=b4754fb1bdcb70c8fd54f918301582c6] - conda-forge/noarch::jsonpatch==1.33=pyhd8ed1ab_1[md5=cb60ae9cf02b9fcb8004dec4089e5691] - conda-forge/linux-64::libmamba==1.5.12=h49b8a8d_0[md5=d6aec145c4f2473c09c2699d74f6dfc0] - conda-forge/noarch::pip==25.0.1=pyh8b19718_0[md5=79b5c1440aedc5010f687048d9103628] - conda-forge/linux-64::ruamel.yaml==0.18.10=py312h66e93f0_0[md5=5260b7fb19694ee5bc4ed0ee7a2a769f] - conda-forge/noarch::tqdm==4.67.1=pyhd8ed1ab_1[md5=9efbfdc37242619130ea42b1cc4ed861] - conda-forge/linux-64::libmambapy==1.5.12=py312hbaee817_0[md5=88dd983e44c86cdde2817ecfa7d84d5a] - conda-forge/linux-64::zstandard==0.23.0=py312hef9b889_1[md5=8b7069e9792ee4e5b4919a7a306d2e67] - conda-forge/noarch::conda-package-streaming==0.11.0=pyhd8ed1ab_1[md5=027138b89fbe94c3870eee49bb2e1da6] - conda-forge/noarch::urllib3==2.3.0=pyhd8ed1ab_0[md5=32674f8dbfb7b26410ed580dd3c10a29] - conda-forge/noarch::requests==2.32.3=pyhd8ed1ab_1[md5=a9b9368f3701a417eac9edbcae7cb737] - conda-forge/noarch::conda-package-handling==2.4.0=pyh7900ff3_2[md5=32c158f481b4fd7630c565030f7bc482] - conda-forge/linux-64::conda==24.11.3=py312h7900ff3_0[md5=bdaca5d82db98d8b5639f058a818ff03] - conda-forge/noarch::conda-libmamba-solver==24.9.0=pyhd8ed1ab_0[md5=45378d089c5f72c9c0d63d58414c645d] - conda-forge/linux-64::mamba==1.5.12=py312h9460a1c_0[md5=59a9360536caad98732fdfdc320e41dc] Package Version Build Channel Size ───────────────────────────────────────────────────────────────────────────────────── Install: ───────────────────────────────────────────────────────────────────────────────────── + _libgcc_mutex 0.1 conda_forge conda-forge + ca-certificates 2025.1.31 hbcca054_0 conda-forge + ld_impl_linux-64 2.43 h712a8e2_4 conda-forge + libgomp 14.2.0 h767d61c_2 conda-forge + pybind11-abi 4 hd8ed1ab_3 conda-forge + python_abi 3.12 5_cp312 conda-forge + tzdata 2025a h78e105d_0 conda-forge + _openmp_mutex 4.5 2_gnu conda-forge + libgcc 14.2.0 h767d61c_2 conda-forge + c-ares 1.34.4 hb9d3cd8_0 conda-forge + libexpat 2.6.4 h5888daf_0 conda-forge + libffi 3.4.6 h2dba641_0 conda-forge + libgcc-ng 14.2.0 h69a702a_2 conda-forge + libiconv 1.18 h4ce23a2_1 conda-forge + liblzma 5.6.4 hb9d3cd8_0 conda-forge + libstdcxx 14.2.0 h8f9b012_2 conda-forge + libzlib 1.3.1 hb9d3cd8_2 conda-forge + ncurses 6.5 h2d0b736_3 conda-forge + openssl 3.4.1 h7b32b05_0 conda-forge + reproc 14.2.5.post0 hb9d3cd8_0 conda-forge + bzip2 1.0.8 h4bc722e_7 conda-forge + keyutils 1.6.1 h166bdaf_0 conda-forge + libedit 3.1.20250104 pl5321h7949ede_0 conda-forge + libev 4.33 hd590300_2 conda-forge + libnsl 2.0.1 hd590300_0 conda-forge + libsqlite 3.49.1 hee588c1_1 conda-forge + libssh2 1.11.1 hf672d98_0 conda-forge + libstdcxx-ng 14.2.0 h4852527_2 conda-forge + libuuid 2.38.1 h0b41bf4_0 conda-forge + libxcrypt 4.4.36 hd590300_1 conda-forge + lz4-c 1.10.0 h5888daf_1 conda-forge + lzo 2.10 hd590300_1001 conda-forge + readline 8.2 h8c095d6_2 conda-forge + reproc-cpp 14.2.5.post0 h5888daf_0 conda-forge + tk 8.6.13 noxft_h4845f30_101 conda-forge + fmt 11.0.2 h434a139_0 conda-forge + icu 75.1 he02047a_0 conda-forge + krb5 1.21.3 h659f571_0 conda-forge + libnghttp2 1.64.0 h161d5f1_0 conda-forge + libsolv 0.7.30 h3509ff9_0 conda-forge + python 3.12.9 h9e4cc4f_1_cpython conda-forge + yaml-cpp 0.8.0 h59595ed_0 conda-forge + zstd 1.5.6 ha6fb4c9_0 conda-forge + libcurl 8.12.1 h332b0f4_0 conda-forge + libxml2 2.13.6 h8d12d68_0 conda-forge + menuinst 2.2.0 py312h7900ff3_0 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 + certifi 2025.1.31 pyhd8ed1ab_0 conda-forge + charset-normalizer 3.4.1 pyhd8ed1ab_0 conda-forge + colorama 0.4.6 pyhd8ed1ab_1 conda-forge + distro 1.9.0 pyhd8ed1ab_1 conda-forge + frozendict 2.4.6 py312h66e93f0_0 conda-forge + hpack 4.1.0 pyhd8ed1ab_0 conda-forge + hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge + idna 3.10 pyhd8ed1ab_1 conda-forge + jsonpointer 3.0.0 py312h7900ff3_1 conda-forge + libarchive 3.7.7 h4585015_3 conda-forge + packaging 24.2 pyhd8ed1ab_2 conda-forge + platformdirs 4.3.6 pyhd8ed1ab_1 conda-forge + pluggy 1.5.0 pyhd8ed1ab_1 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 + ruamel.yaml.clib 0.2.8 py312h66e93f0_1 conda-forge + setuptools 75.8.2 pyhff2d567_0 conda-forge + truststore 0.10.1 pyh29332c3_0 conda-forge + wheel 0.45.1 pyhd8ed1ab_1 conda-forge + cffi 1.17.1 py312h06ac9bb_0 conda-forge + h2 4.2.0 pyhd8ed1ab_0 conda-forge + jsonpatch 1.33 pyhd8ed1ab_1 conda-forge + libmamba 1.5.12 h49b8a8d_0 conda-forge + pip 25.0.1 pyh8b19718_0 conda-forge + ruamel.yaml 0.18.10 py312h66e93f0_0 conda-forge + tqdm 4.67.1 pyhd8ed1ab_1 conda-forge + libmambapy 1.5.12 py312hbaee817_0 conda-forge + zstandard 0.23.0 py312hef9b889_1 conda-forge + conda-package-streaming 0.11.0 pyhd8ed1ab_1 conda-forge + urllib3 2.3.0 pyhd8ed1ab_0 conda-forge + requests 2.32.3 pyhd8ed1ab_1 conda-forge + conda-package-handling 2.4.0 pyh7900ff3_2 conda-forge + conda 24.11.3 py312h7900ff3_0 conda-forge + conda-libmamba-solver 24.9.0 pyhd8ed1ab_0 conda-forge + mamba 1.5.12 py312h9460a1c_0 conda-forge Summary: Install: 85 packages Total download: 0 B ───────────────────────────────────────────────────────────────────────────────────── Transaction starting Transaction finished To activate this environment, use: micromamba activate /home/pkgeval/.julia/conda/3/x86_64 Or to execute a single command in this environment, use: micromamba run -p /home/pkgeval/.julia/conda/3/x86_64 mycommand 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-23.1.0 | pyhd8ed1ab_1 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 beautifulsoup4-4.13.3 | pyha770c72_0 142 KB conda-forge binutils_impl_linux-64-2.43| h4bf12b8_4 5.8 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-20250401| 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_0 3.0 MB bioconda bioconductor-rhdf5filters-1.18.0| r44h77050f0_0 564 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_5 14.3 MB bioconda brotli-1.1.0 | hb9d3cd8_2 19 KB conda-forge brotli-bin-1.1.0 | hb9d3cd8_2 18 KB conda-forge bwidget-1.10.1 | ha770c72_0 126 KB conda-forge c-ares-1.34.5 | hb9d3cd8_0 202 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 click-8.1.8 | pyh707e725_0 83 KB conda-forge comm-0.2.2 | pyhd8ed1ab_1 12 KB conda-forge contourpy-1.3.1 | py312h68727a3_0 270 KB conda-forge curl-8.13.0 | h332b0f4_0 178 KB conda-forge cycler-0.12.1 | pyhd8ed1ab_1 13 KB conda-forge debugpy-1.8.13 | 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-5.0.6 | pyhdfd78af_0 326 KB bioconda diamond-2.1.11 | h5ca1c30_1 3.5 MB bioconda entrez-direct-22.4 | he881be0_0 14.0 MB bioconda exceptiongroup-1.2.2 | pyhd8ed1ab_1 20 KB conda-forge executing-2.1.0 | pyhd8ed1ab_1 28 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 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conda-forge setuptools-78.1.0 | pyhff2d567_0 768 KB conda-forge six-1.17.0 | pyhd8ed1ab_0 16 KB conda-forge sniffio-1.3.1 | pyhd8ed1ab_1 15 KB conda-forge soupsieve-2.5 | pyhd8ed1ab_1 36 KB conda-forge stack_data-0.6.3 | pyhd8ed1ab_1 26 KB conda-forge statsmodels-0.14.4 | py312hc0a28a1_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 tktable-2.10 | h8bc8fbc_6 89 KB conda-forge toml-0.10.2 | pyhd8ed1ab_1 22 KB conda-forge tomli-2.2.1 | pyhd8ed1ab_1 19 KB conda-forge tomlkit-0.13.2 | pyha770c72_1 36 KB conda-forge tornado-6.4.2 | py312h66e93f0_0 821 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-2.9.0.20241206| pyhd8ed1ab_0 22 KB conda-forge typing-extensions-4.13.1 | hf5ce1d7_0 88 KB conda-forge typing_extensions-4.13.1 | pyh29332c3_0 51 KB conda-forge typing_utils-0.1.0 | pyhd8ed1ab_1 15 KB conda-forge tzdata-2025b | h78e105d_0 120 KB conda-forge unicodedata2-16.0.0 | py312h66e93f0_0 395 KB conda-forge uri-template-1.3.0 | pyhd8ed1ab_1 23 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 | pyhd8ed1ab_1 23 KB conda-forge zeromq-4.3.5 | h3b0a872_7 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conda-forge/noarch::babel-2.17.0-pyhd8ed1ab_0 beautifulsoup4 conda-forge/noarch::beautifulsoup4-4.13.3-pyha770c72_0 binutils_impl_lin~ conda-forge/linux-64::binutils_impl_linux-64-2.43-h4bf12b8_4 bioconductor-biob~ bioconda/linux-64::bioconductor-biobase-2.66.0-r44h3df3fcb_0 bioconductor-bioc~ bioconda/noarch::bioconductor-biocgenerics-0.52.0-r44hdfd78af_3 bioconductor-biom~ bioconda/noarch::bioconductor-biomformat-1.34.0-r44hdfd78af_0 bioconductor-bios~ bioconda/linux-64::bioconductor-biostrings-2.74.0-r44h3df3fcb_1 bioconductor-data~ bioconda/noarch::bioconductor-data-packages-20250401-hdfd78af_0 bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodb-1.42.0-r44hdfd78af_2 bioconductor-geno~ bioconda/noarch::bioconductor-genomeinfodbdata-1.2.13-r44hdfd78af_0 bioconductor-iran~ bioconda/linux-64::bioconductor-iranges-2.40.0-r44h3df3fcb_2 bioconductor-micr~ bioconda/noarch::bioconductor-microbiome-1.28.0-r44hdfd78af_0 bioconductor-mult~ 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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-1.14-pl5321hdfd78af_0 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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statsmodels conda-forge/linux-64::statsmodels-0.14.4-py312hc0a28a1_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_h4845f30_101 tktable conda-forge/linux-64::tktable-2.10-h8bc8fbc_6 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-0.13.2-pyha770c72_1 tornado conda-forge/linux-64::tornado-6.4.2-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-2.9.0.20241206-pyhd8ed1ab_0 typing-extensions conda-forge/noarch::typing-extensions-4.13.1-hf5ce1d7_0 typing_extensions conda-forge/noarch::typing_extensions-4.13.1-pyh29332c3_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::urllib3-2.3.0-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-pyhd8ed1ab_1 zeromq conda-forge/linux-64::zeromq-4.3.5-h3b0a872_7 zipp conda-forge/noarch::zipp-3.21.0-pyhd8ed1ab_1 zlib conda-forge/linux-64::zlib-1.3.1-hb9d3cd8_2 zstandard conda-forge/linux-64::zstandard-0.23.0-py312h66e93f0_1 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-1.2.13 | hb9d3cd8_0 547 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-0.12.2 | pyhdfd78af_0 406 KB bioconda libcups-2.3.3 | h4637d8d_4 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-4.09.1 | h7b50bb2_7 68 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-1.2.13-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-0.12.2-pyhdfd78af_0 libcups conda-forge/linux-64::libcups-2.3.3-h4637d8d_4 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-4.09.1-h7b50bb2_7 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,bowtie2out,sam} [--force] [--bowtie2db METAPHLAN_BOWTIE2_DB] [-x INDEX] [--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE] [--bowtie2_build BOWTIE2_BUILD] [--bowtie2out FILE_NAME] [--min_mapq_val MIN_MAPQ_VAL] [--no_map] [--tmp_dir] [--tax_lev TAXONOMIC_LEVEL] [--min_cu_len] [--min_alignment_len] [--add_viruses] [--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] [--clade] [--min_ab] [--profile_vsc] [--vsc_out VSC_OUT] [--vsc_breadth VSC_BREADTH] [-o output file] [--sample_id_key name] [--use_group_representative] [--sample_id value] [-s sam_output_file] [--legacy-output] [--CAMI_format_output] [--unclassified_estimation] [--mpa3] [--biom biom_output] [--mdelim mdelim] [--nproc N] [--subsampling SUBSAMPLING] [--subsampling_output SUBSAMPLING_OUTPUT] [--subsampling_paired SUBSAMPLING_PAIRED] [-1 FORWARD_READS] [-2 REVERSE_READS] [--mapping_subsampling] [--subsampling_seed SUBSAMPLING_SEED] [--install] [--offline] [--force_download] [--read_min_len READ_MIN_LEN] [-v] [-h] [INPUT_FILE] [OUTPUT_FILE] DESCRIPTION MetaPhlAn version 4.1.1 (11 Mar 2024): METAgenomic PHyLogenetic ANalysis for metagenomic taxonomic profiling. AUTHORS: Aitor Blanco-Miguez (aitor.blancomiguez@unitn.it), Francesco Beghini (francesco.beghini@unitn.it), Moreno Zolfo (moreno.zolfo@unitn.it), Nicola Segata (nicola.segata@unitn.it), Duy Tin Truong, Francesco Asnicar (f.asnicar@unitn.it), Claudia Mengoni (claudia.mengoni@unitn.it) COMMON COMMANDS We assume here that MetaPhlAn is installed using the several options available (pip, conda, PyPi) Also BowTie2 should be in the system path with execution and read permissions, and Perl should be installed) ========== MetaPhlAn clade-abundance estimation ================= The basic usage of MetaPhlAn consists in the identification of the clades (from phyla to species ) present in the metagenome obtained from a microbiome sample and their relative abundance. This correspond to the default analysis type (-t rel_ab). * Profiling a metagenome from raw reads: $ metaphlan metagenome.fastq --input_type fastq -o profiled_metagenome.txt * You can take advantage of multiple CPUs and save the intermediate BowTie2 output for re-running MetaPhlAn extremely quickly: $ metaphlan metagenome.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq -o profiled_metagenome.txt * If you already mapped your metagenome against the marker DB (using a previous MetaPhlAn run), you can obtain the results in few seconds by using the previously saved --bowtie2out file and specifying the input (--input_type bowtie2out): $ metaphlan metagenome.bowtie2.bz2 --nproc 5 --input_type bowtie2out -o profiled_metagenome.txt * bowtie2out files generated with MetaPhlAn versions below 3 are not compatibile. Starting from MetaPhlAn 3.0, the BowTie2 ouput now includes the size of the profiled metagenome and the average read length. If you want to re-run MetaPhlAn using these file you should provide the metagenome size via --nreads: $ metaphlan metagenome.bowtie2.bz2 --nproc 5 --input_type bowtie2out --nreads 520000 -o profiled_metagenome.txt * You can also provide an externally BowTie2-mapped SAM if you specify this format with --input_type. Two steps: first apply BowTie2 and then feed MetaPhlAn with the obtained sam: $ bowtie2 --sam-no-hd --sam-no-sq --no-unal --very-sensitive -S metagenome.sam -x ${mpa_dir}/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 -U metagenome.fastq $ metaphlan metagenome.sam --input_type sam -o profiled_metagenome.txt * We can also natively handle paired-end metagenomes, and, more generally, metagenomes stored in multiple files (but you need to specify the --bowtie2out parameter): $ metaphlan metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 --input_type fastq ------------------------------------------------------------------- ========== Marker level analysis ============================ MetaPhlAn introduces the capability of characterizing organisms at the strain level using non aggregated marker information. Such capability comes with several slightly different flavours and are a way to perform strain tracking and comparison across multiple samples. Usually, MetaPhlAn is first ran with the default -t to profile the species present in the community, and then a strain-level profiling can be performed to zoom-in into specific species of interest. This operation can be performed quickly as it exploits the --bowtie2out intermediate file saved during the execution of the default analysis type. * The following command will output the abundance of each marker with a RPK (reads per kilo-base) higher 0.0. (we are assuming that metagenome_outfmt.bz2 has been generated before as shown above). $ metaphlan -t marker_ab_table metagenome_outfmt.bz2 --input_type bowtie2out -o marker_abundance_table.txt The obtained RPK can be optionally normalized by the total number of reads in the metagenome to guarantee fair comparisons of abundances across samples. The number of reads in the metagenome needs to be passed with the '--nreads' argument * The list of markers present in the sample can be obtained with '-t marker_pres_table' $ metaphlan -t marker_pres_table metagenome_outfmt.bz2 --input_type bowtie2out -o marker_abundance_table.txt The --pres_th argument (default 1.0) set the minimum RPK value to consider a marker present * The list '-t clade_profiles' analysis type reports the same information of '-t marker_ab_table' but the markers are reported on a clade-by-clade basis. $ metaphlan -t clade_profiles metagenome_outfmt.bz2 --input_type bowtie2out -o marker_abundance_table.txt * Finally, to obtain all markers present for a specific clade and all its subclades, the '-t clade_specific_strain_tracker' should be used. For example, the following command is reporting the presence/absence of the markers for the B. fragilis species and its strains the optional argument --min_ab specifies the minimum clade abundance for reporting the markers $ metaphlan -t clade_specific_strain_tracker --clade s__Bacteroides_fragilis metagenome_outfmt.bz2 --input_type bowtie2out -o marker_abundance_table.txt ------------------------------------------------------------------- positional arguments: INPUT_FILE the input file can be: * a fastq file containing metagenomic reads OR * a BowTie2 produced SAM file. OR * an intermediary mapping file of the metagenome generated by a previous MetaPhlAn run 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 OUTPUT_FILE the tab-separated output file of the predicted taxon relative abundances [stdout if not present] Required arguments: --input_type {fastq,fasta,bowtie2out,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 bowtie2out file --bowtie2db METAPHLAN_BOWTIE2_DB Folder containing the MetaPhlAn database. You can specify the location by exporting the DEFAULT_DB_FOLDER variable in the shell.[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] --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 --bowtie2out FILE_NAME The file for saving the output of BowTie2 --min_mapq_val MIN_MAPQ_VAL Minimum mapping quality value (MAPQ) [default 5] --no_map Avoid storing the --bowtie2out map file --tmp_dir The folder used to store temporary files [default is the OS dependent tmp dir] 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_cu_len minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances [default 2000] --min_alignment_len The sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded. [default None] --add_viruses Together with --mpa3, allow the profiling of viral organisms --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. * reads_map: mapping from reads to clades (only reads hitting a marker) * 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_counts: non-normalized marker counts [use with extreme caution] * marker_pres_table: list of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th * clade_specific_strain_tracker: list of markers present for a specific clade, specified with --clade, and all its subclades [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 --clade The clade for clade_specific_strain_tracker analysis --min_ab The minimum percentage abundance for the clade in the clade_specific_strain_tracker analysis 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) Output arguments: -o output file, --output_file output file The output file (if not specified as positional argument) --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 --legacy-output Old MetaPhlAn2 two columns output --CAMI_format_output Report the profiling using the CAMI output format --unclassified_estimation Scale relative abundances to the number of reads mapping to identified clades in order to estimate unclassified taxa --mpa3 Perform the analysis using the MetaPhlAn 3 algorithm --biom biom_output, --biom_output_file biom_output If requesting biom file output: The name of the output file in biom format --mdelim mdelim, --metadata_delimiter_char mdelim Delimiter for bug metadata: - defaults to pipe. e.g. the pipe in k__Bacteria|p__Proteobacteria 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 [default None] --subsampling_output SUBSAMPLING_OUTPUT The output file for the subsampled reads. If --subsampling_paired is specified two files are created with suffixes R1 and R2. 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] --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 --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 -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 431.86s PkgEval succeeded after 515.4s