diff --git a/run_pharokka_and_phold_and_phynteny.ipynb b/run_pharokka_and_phold_and_phynteny.ipynb index 031b832..8b0da22 100644 --- a/run_pharokka_and_phold_and_phynteny.ipynb +++ b/run_pharokka_and_phold_and_phynteny.ipynb @@ -49,7 +49,7 @@ "colab": { "base_uri": "https://localhost:8080/" }, - "outputId": "e6c390ad-965b-43f6-9dae-8e8ea0be75da" + "outputId": "d4efb860-d6d4-4f44-b903-f2404361780f" }, "outputs": [ { @@ -72,7 +72,7 @@ " environment location: /usr/local\n", "\n", " added / updated specs:\n", - " - pharokka==1.7.3\n", + " - pharokka==1.7.4\n", " - phold==0.2.0\n", " - pip\n", " - python=3.10\n", @@ -86,639 +86,581 @@ " _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge\n", " _openmp_mutex-4.5 | 2_kmp_llvm 6 KB conda-forge\n", " about-time-4.2.1 | pyhd8ed1ab_0 16 KB conda-forge\n", - " aiohttp-3.9.5 | py310h2372a71_0 682 KB conda-forge\n", + " aiohappyeyeballs-2.4.3 | pyhd8ed1ab_0 19 KB conda-forge\n", + " aiohttp-3.11.7 | py310h89163eb_0 780 KB conda-forge\n", " aiosignal-1.3.1 | pyhd8ed1ab_0 12 KB conda-forge\n", " alive-progress-3.1.5 | pyhd8ed1ab_0 65 KB conda-forge\n", " alsa-lib-1.2.6.1 | h7f98852_0 578 KB conda-forge\n", - " anaconda-anon-usage-0.4.4 |py310hfc0e8ea_100 25 KB\n", + " anaconda-anon-usage-0.5.0 |py310hfc0e8ea_100 27 KB\n", " aragorn-1.2.41 | h031d066_3 143 KB bioconda\n", - " aria2-1.36.0 | h1e4e653_3 1.8 MB conda-forge\n", - " async-timeout-4.0.3 | pyhd8ed1ab_0 11 KB conda-forge\n", - " attrs-23.2.0 | pyh71513ae_0 53 KB conda-forge\n", - " aws-c-auth-0.7.20 | h5f1c8d9_0 103 KB conda-forge\n", - " aws-c-cal-0.6.12 | h2ba76a8_0 45 KB conda-forge\n", - " aws-c-common-0.9.17 | h4ab18f5_0 222 KB conda-forge\n", - " aws-c-compression-0.2.18 | h36a0aea_4 19 KB conda-forge\n", - " aws-c-event-stream-0.4.2 | h161de36_10 53 KB conda-forge\n", - " aws-c-http-0.8.1 | h63f54a0_13 191 KB conda-forge\n", - " aws-c-io-0.14.8 | h96d4d28_0 154 KB conda-forge\n", - " aws-c-mqtt-0.10.4 | hcc7299c_2 160 KB conda-forge\n", - " aws-c-s3-0.5.9 | h10bd90f_0 107 KB conda-forge\n", - " aws-c-sdkutils-0.1.16 | h36a0aea_0 54 KB conda-forge\n", - " aws-checksums-0.1.18 | h36a0aea_4 49 KB conda-forge\n", - " aws-crt-cpp-0.26.8 | h4f3a3cc_11 332 KB conda-forge\n", - 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" unicodedata2-15.1.0 | py310h2372a71_0 365 KB conda-forge\n", - " urllib3-2.2.2 | pyhd8ed1ab_1 93 KB conda-forge\n", + " unicodedata2-15.1.0 | py310ha75aee5_1 359 KB conda-forge\n", + " urllib3-2.2.3 | pyhd8ed1ab_0 96 KB conda-forge\n", " wget-1.21.4 | hda4d442_0 752 KB conda-forge\n", - " wheel-0.43.0 | pyhd8ed1ab_1 57 KB conda-forge\n", - " xorg-fixesproto-5.0 | h7f98852_1002 9 KB conda-forge\n", - " xorg-inputproto-2.3.2 | h7f98852_1002 19 KB conda-forge\n", - " xorg-kbproto-1.0.7 | h7f98852_1002 27 KB conda-forge\n", - " xorg-libx11-1.8.9 | hb711507_1 813 KB conda-forge\n", - " xorg-libxau-1.0.11 | hd590300_0 14 KB conda-forge\n", - " xorg-libxdmcp-1.1.3 | h7f98852_0 19 KB conda-forge\n", - " xorg-libxext-1.3.4 | h0b41bf4_2 49 KB conda-forge\n", - " xorg-libxfixes-5.0.3 | h7f98852_1004 18 KB conda-forge\n", - " xorg-libxi-1.7.10 | h7f98852_0 46 KB conda-forge\n", - " xorg-libxrender-0.9.11 | hd590300_0 37 KB conda-forge\n", - " xorg-libxtst-1.2.3 | h7f98852_1002 31 KB conda-forge\n", - " xorg-recordproto-1.14.2 | h7f98852_1002 8 KB conda-forge\n", - " xorg-renderproto-0.11.1 | h7f98852_1002 9 KB conda-forge\n", - " xorg-xextproto-7.3.0 | h0b41bf4_1003 30 KB conda-forge\n", - " xorg-xproto-7.0.31 | h7f98852_1007 73 KB conda-forge\n", + " wheel-0.45.1 | pyhd8ed1ab_0 62 KB conda-forge\n", + " xorg-libx11-1.8.10 | h4f16b4b_0 819 KB conda-forge\n", + " xorg-libxau-1.0.11 | hb9d3cd8_1 14 KB conda-forge\n", + " xorg-libxdmcp-1.1.5 | hb9d3cd8_0 19 KB conda-forge\n", + " xorg-libxext-1.3.6 | hb9d3cd8_0 49 KB conda-forge\n", + " xorg-libxfixes-6.0.1 | hb9d3cd8_0 19 KB conda-forge\n", + " xorg-libxi-1.8.2 | hb9d3cd8_0 46 KB conda-forge\n", + " xorg-libxrender-0.9.11 | hb9d3cd8_1 37 KB conda-forge\n", + " xorg-libxtst-1.2.5 | hb9d3cd8_3 32 KB conda-forge\n", + " xorg-xorgproto-2024.1 | hb9d3cd8_1 552 KB conda-forge\n", " xxhash-0.8.2 | hd590300_0 95 KB conda-forge\n", " yaml-0.2.5 | h7f98852_2 87 KB conda-forge\n", - " yarl-1.9.4 | py310h2372a71_0 111 KB conda-forge\n", + " yarl-1.18.0 | py310ha75aee5_0 136 KB conda-forge\n", " zlib-1.2.13 | h4ab18f5_6 91 KB conda-forge\n", - " zstandard-0.23.0 | py310h64cae3c_0 398 KB conda-forge\n", - " zstd-1.5.6 | ha6fb4c9_0 542 KB conda-forge\n", + " zstandard-0.23.0 | py310ha39cb0e_1 399 KB conda-forge\n", " ------------------------------------------------------------\n", - " Total: 2.73 GB\n", + " Total: 2.58 GB\n", "\n", "The following NEW packages will be INSTALLED:\n", "\n", " about-time conda-forge/noarch::about-time-4.2.1-pyhd8ed1ab_0 \n", - " aiohttp conda-forge/linux-64::aiohttp-3.9.5-py310h2372a71_0 \n", + " aiohappyeyeballs conda-forge/noarch::aiohappyeyeballs-2.4.3-pyhd8ed1ab_0 \n", + " aiohttp conda-forge/linux-64::aiohttp-3.11.7-py310h89163eb_0 \n", " aiosignal conda-forge/noarch::aiosignal-1.3.1-pyhd8ed1ab_0 \n", " alive-progress conda-forge/noarch::alive-progress-3.1.5-pyhd8ed1ab_0 \n", " alsa-lib conda-forge/linux-64::alsa-lib-1.2.6.1-h7f98852_0 \n", " aragorn bioconda/linux-64::aragorn-1.2.41-h031d066_3 \n", - " aria2 conda-forge/linux-64::aria2-1.36.0-h1e4e653_3 \n", - " async-timeout conda-forge/noarch::async-timeout-4.0.3-pyhd8ed1ab_0 \n", - " attrs conda-forge/noarch::attrs-23.2.0-pyh71513ae_0 \n", - " aws-c-auth conda-forge/linux-64::aws-c-auth-0.7.20-h5f1c8d9_0 \n", - " aws-c-cal conda-forge/linux-64::aws-c-cal-0.6.12-h2ba76a8_0 \n", - " aws-c-common conda-forge/linux-64::aws-c-common-0.9.17-h4ab18f5_0 \n", - " aws-c-compression conda-forge/linux-64::aws-c-compression-0.2.18-h36a0aea_4 \n", - " aws-c-event-stream conda-forge/linux-64::aws-c-event-stream-0.4.2-h161de36_10 \n", - " aws-c-http conda-forge/linux-64::aws-c-http-0.8.1-h63f54a0_13 \n", - " aws-c-io conda-forge/linux-64::aws-c-io-0.14.8-h96d4d28_0 \n", - " aws-c-mqtt conda-forge/linux-64::aws-c-mqtt-0.10.4-hcc7299c_2 \n", - " aws-c-s3 conda-forge/linux-64::aws-c-s3-0.5.9-h10bd90f_0 \n", - " aws-c-sdkutils conda-forge/linux-64::aws-c-sdkutils-0.1.16-h36a0aea_0 \n", - " aws-checksums conda-forge/linux-64::aws-checksums-0.1.18-h36a0aea_4 \n", - " aws-crt-cpp conda-forge/linux-64::aws-crt-cpp-0.26.8-h4f3a3cc_11 \n", - " aws-sdk-cpp conda-forge/linux-64::aws-sdk-cpp-1.11.329-h51dfee4_0 \n", - " backports conda-forge/noarch::backports-1.0-pyhd8ed1ab_3 \n", + " aria2 conda-forge/linux-64::aria2-1.37.0-h347180d_1 \n", + " async-timeout conda-forge/noarch::async-timeout-5.0.1-pyhd8ed1ab_0 \n", + " attrs conda-forge/noarch::attrs-24.2.0-pyh71513ae_0 \n", + " aws-c-auth conda-forge/linux-64::aws-c-auth-0.7.22-h96bc93b_2 \n", + " aws-c-cal conda-forge/linux-64::aws-c-cal-0.6.14-h88a6e22_1 \n", + " aws-c-common conda-forge/linux-64::aws-c-common-0.9.19-h4ab18f5_0 \n", + " aws-c-compression conda-forge/linux-64::aws-c-compression-0.2.18-h83b837d_6 \n", + " aws-c-event-stream conda-forge/linux-64::aws-c-event-stream-0.4.2-ha47c788_12 \n", + " aws-c-http conda-forge/linux-64::aws-c-http-0.8.1-h29d6fba_17 \n", + " aws-c-io conda-forge/linux-64::aws-c-io-0.14.8-h21d4f22_5 \n", + " aws-c-mqtt conda-forge/linux-64::aws-c-mqtt-0.10.4-h759edc4_4 \n", + " aws-c-s3 conda-forge/linux-64::aws-c-s3-0.5.9-h594631b_3 \n", + " aws-c-sdkutils conda-forge/linux-64::aws-c-sdkutils-0.1.16-h83b837d_2 \n", + " aws-checksums conda-forge/linux-64::aws-checksums-0.1.18-h83b837d_6 \n", + " aws-crt-cpp conda-forge/linux-64::aws-crt-cpp-0.26.9-he3a8b3b_0 \n", + " aws-sdk-cpp conda-forge/linux-64::aws-sdk-cpp-1.11.329-hba8bd5f_3 \n", + " backports conda-forge/noarch::backports-1.0-pyhd8ed1ab_4 \n", " backports.tempfile conda-forge/noarch::backports.tempfile-1.0-py_0 \n", " backports.weakref conda-forge/noarch::backports.weakref-1.0.post1-pyhd8ed1ab_1003 \n", - " bcbio-gff bioconda/noarch::bcbio-gff-0.7.1-pyh7cba7a3_1 \n", + " bcbio-gff bioconda/noarch::bcbio-gff-0.7.1-pyh7e72e81_2 \n", " biopython conda-forge/linux-64::biopython-1.81-py310h2372a71_1 \n", - " black conda-forge/linux-64::black-24.4.2-py310hff52083_0 \n", - " blast bioconda/linux-64::blast-2.15.0-pl5321h6f7f691_1 \n", - " brotli conda-forge/linux-64::brotli-1.1.0-hd590300_1 \n", - " brotli-bin conda-forge/linux-64::brotli-bin-1.1.0-hd590300_1 \n", - " bx-python bioconda/linux-64::bx-python-0.12.0-py310ha025fb0_0 \n", + " black conda-forge/linux-64::black-24.10.0-py310hff52083_0 \n", + " brotli conda-forge/linux-64::brotli-1.1.0-hb9d3cd8_2 \n", + " brotli-bin conda-forge/linux-64::brotli-bin-1.1.0-hb9d3cd8_2 \n", + " bx-python bioconda/linux-64::bx-python-0.13.0-py310ha025fb0_0 \n", " cached-property conda-forge/noarch::cached-property-1.5.2-hd8ed1ab_1 \n", " cached_property conda-forge/noarch::cached_property-1.5.2-pyha770c72_1 \n", " cairo pkgs/main/linux-64::cairo-1.16.0-hb05425b_5 \n", " capnproto conda-forge/linux-64::capnproto-1.0.2-h2b92303_1 \n", " click conda-forge/noarch::click-8.1.7-unix_pyh707e725_0 \n", " colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0 \n", - " contourpy conda-forge/linux-64::contourpy-1.2.1-py310hd41b1e2_0 \n", - " coverage conda-forge/linux-64::coverage-7.6.0-py310h5b4e0ec_0 \n", - " cuda-cudart conda-forge/linux-64::cuda-cudart-12.5.82-he02047a_0 \n", - " cuda-cudart_linux~ conda-forge/noarch::cuda-cudart_linux-64-12.5.82-h85509e4_0 \n", - " cuda-nvrtc conda-forge/linux-64::cuda-nvrtc-12.5.82-he02047a_0 \n", - " cuda-nvtx conda-forge/linux-64::cuda-nvtx-12.5.82-he02047a_0 \n", - " cuda-version conda-forge/noarch::cuda-version-12.5-hd4f0392_3 \n", + " contourpy conda-forge/linux-64::contourpy-1.3.1-py310h3788b33_0 \n", + " coverage conda-forge/linux-64::coverage-7.6.8-py310h89163eb_0 \n", + " cuda-cudart conda-forge/linux-64::cuda-cudart-12.6.77-h5888daf_0 \n", + " cuda-cudart_linux~ conda-forge/noarch::cuda-cudart_linux-64-12.6.77-h3f2d84a_0 \n", + " cuda-nvrtc conda-forge/linux-64::cuda-nvrtc-12.6.85-hbd13f7d_0 \n", + " cuda-nvtx conda-forge/linux-64::cuda-nvtx-12.6.77-hbd13f7d_0 \n", + " cuda-version conda-forge/noarch::cuda-version-12.6-h7480c83_3 \n", " cudnn conda-forge/linux-64::cudnn-8.9.7.29-h092f7fd_3 \n", - " curl pkgs/main/linux-64::curl-8.7.1-hdbd6064_0 \n", " cycler conda-forge/noarch::cycler-0.12.1-pyhd8ed1ab_0 \n", - " datasets conda-forge/noarch::datasets-2.20.0-pyhd8ed1ab_0 \n", + " datasets conda-forge/noarch::datasets-3.1.0-pyhff2d567_0 \n", " dill conda-forge/noarch::dill-0.3.8-pyhd8ed1ab_0 \n", - " dnaapler bioconda/noarch::dnaapler-0.7.0-pyhdfd78af_0 \n", - " entrez-direct bioconda/linux-64::entrez-direct-22.1-he881be0_0 \n", + " dnaapler bioconda/noarch::dnaapler-1.0.1-pyhdfd78af_0 \n", " exceptiongroup conda-forge/noarch::exceptiongroup-1.2.2-pyhd8ed1ab_0 \n", " fastpath conda-forge/linux-64::fastpath-1.9-py310h2372a71_3 \n", - " filelock conda-forge/noarch::filelock-3.15.4-pyhd8ed1ab_0 \n", + " filelock conda-forge/noarch::filelock-3.16.1-pyhd8ed1ab_0 \n", " foldseek bioconda/linux-64::foldseek-9.427df8a-pl5321hb365157_1 \n", " font-ttf-dejavu-s~ conda-forge/noarch::font-ttf-dejavu-sans-mono-2.37-hab24e00_0 \n", " font-ttf-inconsol~ conda-forge/noarch::font-ttf-inconsolata-3.000-h77eed37_0 \n", " font-ttf-source-c~ conda-forge/noarch::font-ttf-source-code-pro-2.038-h77eed37_0 \n", - " font-ttf-ubuntu conda-forge/noarch::font-ttf-ubuntu-0.83-h77eed37_2 \n", + " font-ttf-ubuntu conda-forge/noarch::font-ttf-ubuntu-0.83-h77eed37_3 \n", " fontconfig conda-forge/linux-64::fontconfig-2.14.2-h14ed4e7_0 \n", " fonts-conda-ecosy~ conda-forge/noarch::fonts-conda-ecosystem-1-0 \n", " fonts-conda-forge conda-forge/noarch::fonts-conda-forge-1-0 \n", - " fonttools conda-forge/linux-64::fonttools-4.53.1-py310h5b4e0ec_0 \n", + " fonttools conda-forge/linux-64::fonttools-4.55.0-py310h89163eb_0 \n", " freetype conda-forge/linux-64::freetype-2.12.1-h267a509_2 \n", - " frozenlist conda-forge/linux-64::frozenlist-1.4.1-py310h2372a71_0 \n", - " fsspec conda-forge/noarch::fsspec-2024.5.0-pyhff2d567_0 \n", - " gawk conda-forge/linux-64::gawk-5.3.0-ha916aea_0 \n", - " gettext conda-forge/linux-64::gettext-0.22.5-h59595ed_2 \n", - " gettext-tools conda-forge/linux-64::gettext-tools-0.22.5-h59595ed_2 \n", - " gflags conda-forge/linux-64::gflags-2.2.2-he1b5a44_1004 \n", + " frozenlist conda-forge/linux-64::frozenlist-1.5.0-py310ha75aee5_0 \n", + " fsspec conda-forge/noarch::fsspec-2024.9.0-pyhff2d567_0 \n", + " gawk conda-forge/linux-64::gawk-5.3.1-hcd3d067_0 \n", + " gettext conda-forge/linux-64::gettext-0.22.5-he02047a_3 \n", + " gettext-tools conda-forge/linux-64::gettext-tools-0.22.5-he02047a_3 \n", + " gflags conda-forge/linux-64::gflags-2.2.2-h5888daf_1005 \n", " giflib conda-forge/linux-64::giflib-5.2.2-hd590300_0 \n", " glib conda-forge/linux-64::glib-2.78.4-hfc55251_0 \n", " glib-tools conda-forge/linux-64::glib-tools-2.78.4-hfc55251_0 \n", " glog conda-forge/linux-64::glog-0.7.1-hbabe93e_0 \n", " gmp conda-forge/linux-64::gmp-6.3.0-hac33072_2 \n", - " gmpy2 conda-forge/linux-64::gmpy2-2.1.5-py310hc7909c9_1 \n", + " gmpy2 conda-forge/linux-64::gmpy2-2.1.5-py310he8512ff_2 \n", " grapheme conda-forge/noarch::grapheme-0.6.0-pyhd8ed1ab_0 \n", " graphite2 pkgs/main/linux-64::graphite2-1.3.14-h295c915_1 \n", " gsl conda-forge/linux-64::gsl-2.7-he838d99_0 \n", " h2 conda-forge/noarch::h2-4.1.0-pyhd8ed1ab_0 \n", - " h5py conda-forge/linux-64::h5py-3.11.0-nompi_py310hf054cd7_102 \n", + " h5py conda-forge/linux-64::h5py-3.12.1-nompi_py310h60e0fe6_102 \n", " harfbuzz pkgs/main/linux-64::harfbuzz-4.3.0-hf52aaf7_2 \n", - " hdf5 conda-forge/linux-64::hdf5-1.14.3-nompi_h4f84152_101 \n", + " hdf5 conda-forge/linux-64::hdf5-1.14.3-nompi_hdf9ad27_105 \n", " hpack conda-forge/noarch::hpack-4.0.0-pyh9f0ad1d_0 \n", - " huggingface_hub conda-forge/noarch::huggingface_hub-0.23.4-pyhd8ed1ab_0 \n", + " huggingface_hub conda-forge/noarch::huggingface_hub-0.26.2-pyh0610db2_0 \n", " hyperframe conda-forge/noarch::hyperframe-6.0.1-pyhd8ed1ab_0 \n", - " infernal bioconda/linux-64::infernal-1.1.5-pl5321h031d066_2 \n", + " infernal bioconda/linux-64::infernal-1.1.5-pl5321h031d066_3 \n", " iniconfig conda-forge/noarch::iniconfig-2.0.0-pyhd8ed1ab_0 \n", " isort conda-forge/noarch::isort-5.13.2-pyhd8ed1ab_0 \n", " jinja2 conda-forge/noarch::jinja2-3.1.4-pyhd8ed1ab_0 \n", " jpeg conda-forge/linux-64::jpeg-9e-h0b41bf4_3 \n", - " kiwisolver conda-forge/linux-64::kiwisolver-1.4.5-py310hd41b1e2_1 \n", + " kiwisolver conda-forge/linux-64::kiwisolver-1.4.7-py310h3788b33_0 \n", " lcms2 conda-forge/linux-64::lcms2-2.15-hfd0df8a_0 \n", " lerc conda-forge/linux-64::lerc-4.0.0-h27087fc_0 \n", " libabseil conda-forge/linux-64::libabseil-20240116.2-cxx17_he02047a_1 \n", " libaec conda-forge/linux-64::libaec-1.1.3-h59595ed_0 \n", - " libarrow conda-forge/linux-64::libarrow-16.1.0-h06228bf_5_cpu \n", - " libarrow-acero conda-forge/linux-64::libarrow-acero-16.1.0-hac33072_5_cpu \n", - " libarrow-dataset conda-forge/linux-64::libarrow-dataset-16.1.0-hac33072_5_cpu \n", - " libarrow-substrait conda-forge/linux-64::libarrow-substrait-16.1.0-h7e0c224_5_cpu \n", - " libasprintf conda-forge/linux-64::libasprintf-0.22.5-h661eb56_2 \n", - " libasprintf-devel conda-forge/linux-64::libasprintf-devel-0.22.5-h661eb56_2 \n", - " libblas conda-forge/linux-64::libblas-3.9.0-22_linux64_openblas \n", - " libbrotlicommon conda-forge/linux-64::libbrotlicommon-1.1.0-hd590300_1 \n", - " libbrotlidec conda-forge/linux-64::libbrotlidec-1.1.0-hd590300_1 \n", - " libbrotlienc conda-forge/linux-64::libbrotlienc-1.1.0-hd590300_1 \n", - " libcblas conda-forge/linux-64::libcblas-3.9.0-22_linux64_openblas \n", + " libarrow conda-forge/linux-64::libarrow-16.1.0-hcb6531f_6_cpu \n", + " libarrow-acero conda-forge/linux-64::libarrow-acero-16.1.0-hac33072_6_cpu \n", + " libarrow-dataset conda-forge/linux-64::libarrow-dataset-16.1.0-hac33072_6_cpu \n", + " libarrow-substrait conda-forge/linux-64::libarrow-substrait-16.1.0-h7e0c224_6_cpu \n", + " libasprintf conda-forge/linux-64::libasprintf-0.22.5-he8f35ee_3 \n", + " libasprintf-devel conda-forge/linux-64::libasprintf-devel-0.22.5-he8f35ee_3 \n", + " libblas conda-forge/linux-64::libblas-3.9.0-25_linux64_openblas \n", + " libbrotlicommon conda-forge/linux-64::libbrotlicommon-1.1.0-hb9d3cd8_2 \n", + " libbrotlidec conda-forge/linux-64::libbrotlidec-1.1.0-hb9d3cd8_2 \n", + " libbrotlienc conda-forge/linux-64::libbrotlienc-1.1.0-hb9d3cd8_2 \n", + " libcblas conda-forge/linux-64::libcblas-3.9.0-25_linux64_openblas \n", " libcrc32c conda-forge/linux-64::libcrc32c-1.1.2-h9c3ff4c_0 \n", - " libcublas conda-forge/linux-64::libcublas-12.5.3.2-he02047a_0 \n", - " libcufft conda-forge/linux-64::libcufft-11.2.3.61-he02047a_0 \n", + " libcublas conda-forge/linux-64::libcublas-12.6.4.1-hbd13f7d_0 \n", + " libcufft conda-forge/linux-64::libcufft-11.3.0.4-hbd13f7d_0 \n", " libcups conda-forge/linux-64::libcups-2.3.3-h36d4200_3 \n", - " libcurand conda-forge/linux-64::libcurand-10.3.6.82-he02047a_0 \n", - " libcusolver conda-forge/linux-64::libcusolver-11.6.3.83-he02047a_0 \n", - " libcusparse conda-forge/linux-64::libcusparse-12.5.1.3-he02047a_0 \n", + " libcurand conda-forge/linux-64::libcurand-10.3.7.77-hbd13f7d_0 \n", + " libcusolver conda-forge/linux-64::libcusolver-11.7.1.2-hbd13f7d_0 \n", + " libcusparse conda-forge/linux-64::libcusparse-12.5.4.2-hbd13f7d_0 \n", " libdeflate conda-forge/linux-64::libdeflate-1.17-h0b41bf4_0 \n", " libevent conda-forge/linux-64::libevent-2.1.12-hf998b51_1 \n", - " libgettextpo conda-forge/linux-64::libgettextpo-0.22.5-h59595ed_2 \n", - " libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.22.5-h59595ed_2 \n", - " libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.1.0-h69a702a_0 \n", - " libgfortran5 conda-forge/linux-64::libgfortran5-14.1.0-hc5f4f2c_0 \n", + " libgcc conda-forge/linux-64::libgcc-14.2.0-h77fa898_1 \n", + " libgettextpo conda-forge/linux-64::libgettextpo-0.22.5-he02047a_3 \n", + " libgettextpo-devel conda-forge/linux-64::libgettextpo-devel-0.22.5-he02047a_3 \n", + " libgfortran conda-forge/linux-64::libgfortran-14.2.0-h69a702a_1 \n", + " libgfortran-ng conda-forge/linux-64::libgfortran-ng-14.2.0-h69a702a_1 \n", + " libgfortran5 conda-forge/linux-64::libgfortran5-14.2.0-hd5240d6_1 \n", " libglib conda-forge/linux-64::libglib-2.78.4-h783c2da_0 \n", " libgoogle-cloud conda-forge/linux-64::libgoogle-cloud-2.24.0-h2736e30_0 \n", " libgoogle-cloud-s~ conda-forge/linux-64::libgoogle-cloud-storage-2.24.0-h3d9a0c8_0 \n", " libgrpc conda-forge/linux-64::libgrpc-1.62.2-h15f2491_0 \n", - " libhwloc conda-forge/linux-64::libhwloc-2.9.1-hd6dc26d_0 \n", + " libhwloc conda-forge/linux-64::libhwloc-2.11.1-default_hecaa2ac_1000 \n", " libiconv conda-forge/linux-64::libiconv-1.17-hd590300_2 \n", " libidn2 conda-forge/linux-64::libidn2-2.3.7-hd590300_0 \n", - " liblapack conda-forge/linux-64::liblapack-3.9.0-22_linux64_openblas \n", - " libmagma conda-forge/linux-64::libmagma-2.7.2-h173bb3b_2 \n", - " libmagma_sparse conda-forge/linux-64::libmagma_sparse-2.7.2-h173bb3b_3 \n", + " liblapack conda-forge/linux-64::liblapack-3.9.0-25_linux64_openblas \n", + " libmagma conda-forge/linux-64::libmagma-2.8.0-h0af6554_0 \n", + " libmagma_sparse conda-forge/linux-64::libmagma_sparse-2.8.0-h0af6554_0 \n", " libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0 \n", - " libnvjitlink conda-forge/linux-64::libnvjitlink-12.5.82-he02047a_0 \n", - " libopenblas conda-forge/linux-64::libopenblas-0.3.27-pthreads_hac2b453_1 \n", - " libparquet conda-forge/linux-64::libparquet-16.1.0-h6a7eafb_5_cpu \n", + " libnvjitlink conda-forge/linux-64::libnvjitlink-12.6.85-hbd13f7d_0 \n", + " libopenblas conda-forge/linux-64::libopenblas-0.3.28-pthreads_h94d23a6_1 \n", + " libparquet conda-forge/linux-64::libparquet-16.1.0-h6a7eafb_6_cpu \n", " libpng conda-forge/linux-64::libpng-1.6.43-h2797004_0 \n", " libprotobuf conda-forge/linux-64::libprotobuf-4.25.3-h08a7969_0 \n", " libre2-11 conda-forge/linux-64::libre2-11-2023.09.01-h5a48ba9_2 \n", - " libsentencepiece conda-forge/linux-64::libsentencepiece-0.2.0-he81a138_2 \n", + " libsentencepiece conda-forge/linux-64::libsentencepiece-0.2.0-hc656cff_4 \n", " libsqlite conda-forge/linux-64::libsqlite-3.46.0-hde9e2c9_0 \n", + " libstdcxx conda-forge/linux-64::libstdcxx-14.2.0-hc0a3c3a_1 \n", " libthrift conda-forge/linux-64::libthrift-0.19.0-hb90f79a_1 \n", " libtiff conda-forge/linux-64::libtiff-4.5.0-h6adf6a1_2 \n", - " libtorch conda-forge/linux-64::libtorch-2.3.1-cuda120_h2b0da52_300 \n", + " libtorch conda-forge/linux-64::libtorch-2.4.0-cuda120_h2b0da52_301 \n", " libunistring conda-forge/linux-64::libunistring-0.9.10-h7f98852_0 \n", " libutf8proc conda-forge/linux-64::libutf8proc-2.8.0-h166bdaf_0 \n", - " libuv conda-forge/linux-64::libuv-1.48.0-hd590300_0 \n", + " libuv conda-forge/linux-64::libuv-1.49.2-hb9d3cd8_0 \n", " libwebp-base conda-forge/linux-64::libwebp-base-1.4.0-hd590300_0 \n", - " libxcb conda-forge/linux-64::libxcb-1.16-hd590300_0 \n", + " libxcb conda-forge/linux-64::libxcb-1.17.0-h8a09558_0 \n", " libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1 \n", " libzlib conda-forge/linux-64::libzlib-1.2.13-h4ab18f5_6 \n", - " llvm-openmp conda-forge/linux-64::llvm-openmp-18.1.7-ha31de31_0 \n", - " loguru conda-forge/linux-64::loguru-0.7.2-py310hff52083_1 \n", - " markupsafe conda-forge/linux-64::markupsafe-2.1.5-py310h2372a71_0 \n", + " llvm-openmp conda-forge/linux-64::llvm-openmp-19.1.4-h024ca30_0 \n", + " loguru conda-forge/linux-64::loguru-0.7.2-py310hff52083_2 \n", + " markupsafe conda-forge/linux-64::markupsafe-3.0.2-py310h89163eb_0 \n", " mash bioconda/linux-64::mash-2.3-hc74b729_7 \n", - " matplotlib-base conda-forge/linux-64::matplotlib-base-3.9.1-py310h0b1de36_0 \n", + " matplotlib-base conda-forge/linux-64::matplotlib-base-3.9.2-py310h68603db_2 \n", " minced bioconda/noarch::minced-0.4.2-hdfd78af_1 \n", " mkl conda-forge/linux-64::mkl-2023.2.0-h84fe81f_50496 \n", " mmseqs2 bioconda/linux-64::mmseqs2-13.45111-pl5321hf1761c0_2 \n", - " mpc conda-forge/linux-64::mpc-1.3.1-hfe3b2da_0 \n", - " mpfr conda-forge/linux-64::mpfr-4.2.1-h9458935_1 \n", + " mpc conda-forge/linux-64::mpc-1.3.1-h24ddda3_1 \n", + " mpfr conda-forge/linux-64::mpfr-4.2.1-h90cbb55_3 \n", " mpmath conda-forge/noarch::mpmath-1.3.0-pyhd8ed1ab_0 \n", - " multidict conda-forge/linux-64::multidict-6.0.5-py310h2372a71_0 \n", - " multiprocess conda-forge/linux-64::multiprocess-0.70.16-py310h2372a71_0 \n", + " multidict conda-forge/linux-64::multidict-6.1.0-py310h89163eb_1 \n", + " multiprocess conda-forge/linux-64::multiprocess-0.70.16-py310ha75aee5_1 \n", " munkres conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0 \n", " mypy_extensions conda-forge/noarch::mypy_extensions-1.0.0-pyha770c72_0 \n", - " ncbi-vdb bioconda/linux-64::ncbi-vdb-3.1.1-h4ac6f70_1 \n", - " nccl conda-forge/linux-64::nccl-2.22.3.1-hbc370b7_0 \n", - " networkx conda-forge/noarch::networkx-3.3-pyhd8ed1ab_1 \n", - " numpy conda-forge/linux-64::numpy-2.0.0-py310h515e003_0 \n", + " nccl conda-forge/linux-64::nccl-2.23.4.1-h2b5d15b_3 \n", + " networkx conda-forge/noarch::networkx-3.4.2-pyh267e887_2 \n", + " numpy conda-forge/linux-64::numpy-2.1.3-py310hd6e36ab_0 \n", " openjdk conda-forge/linux-64::openjdk-11.0.15-hc6918da_0 \n", " openjpeg conda-forge/linux-64::openjpeg-2.5.0-hfec8fc6_2 \n", " orc conda-forge/linux-64::orc-2.0.1-h17fec99_1 \n", - " pandas conda-forge/linux-64::pandas-2.2.2-py310hf9f9076_1 \n", + " pandas conda-forge/linux-64::pandas-2.2.3-py310h5eaa309_1 \n", " pathspec conda-forge/noarch::pathspec-0.12.1-pyhd8ed1ab_0 \n", - " patsy conda-forge/noarch::patsy-0.5.6-pyhd8ed1ab_0 \n", - " pcre conda-forge/linux-64::pcre-8.45-h9c3ff4c_0 \n", + " patsy conda-forge/noarch::patsy-1.0.1-pyhff2d567_0 \n", " perl conda-forge/linux-64::perl-5.32.1-7_hd590300_perl5 \n", - " perl-archive-tar bioconda/noarch::perl-archive-tar-2.40-pl5321hdfd78af_0 \n", - " perl-carp conda-forge/noarch::perl-carp-1.50-pl5321hd8ed1ab_0 \n", - " perl-common-sense conda-forge/noarch::perl-common-sense-3.75-pl5321hd8ed1ab_0 \n", - " perl-compress-raw~ conda-forge/linux-64::perl-compress-raw-bzip2-2.201-pl5321h166bdaf_0 \n", - " perl-compress-raw~ conda-forge/linux-64::perl-compress-raw-zlib-2.202-pl5321h166bdaf_0 \n", - " perl-encode conda-forge/linux-64::perl-encode-3.21-pl5321hd590300_0 \n", - " perl-exporter conda-forge/noarch::perl-exporter-5.74-pl5321hd8ed1ab_0 \n", - " perl-exporter-tiny conda-forge/noarch::perl-exporter-tiny-1.002002-pl5321hd8ed1ab_0 \n", - " perl-extutils-mak~ conda-forge/noarch::perl-extutils-makemaker-7.70-pl5321hd8ed1ab_0 \n", - " perl-io-compress bioconda/linux-64::perl-io-compress-2.201-pl5321hdbdd923_2 \n", - " perl-io-zlib bioconda/noarch::perl-io-zlib-1.14-pl5321hdfd78af_0 \n", - " perl-json bioconda/noarch::perl-json-4.10-pl5321hdfd78af_0 \n", - " perl-json-xs bioconda/linux-64::perl-json-xs-2.34-pl5321h4ac6f70_6 \n", - " perl-list-moreuti~ bioconda/noarch::perl-list-moreutils-0.430-pl5321hdfd78af_0 \n", - " perl-list-moreuti~ bioconda/linux-64::perl-list-moreutils-xs-0.430-pl5321h031d066_2 \n", - " perl-parent conda-forge/noarch::perl-parent-0.241-pl5321hd8ed1ab_0 \n", - " perl-pathtools conda-forge/linux-64::perl-pathtools-3.75-pl5321h166bdaf_0 \n", - " perl-scalar-list-~ conda-forge/linux-64::perl-scalar-list-utils-1.63-pl5321h166bdaf_0 \n", - " perl-storable conda-forge/linux-64::perl-storable-3.15-pl5321h166bdaf_0 \n", - " perl-types-serial~ bioconda/noarch::perl-types-serialiser-1.01-pl5321hdfd78af_0 \n", " phanotate bioconda/linux-64::phanotate-1.5.1-h0dbaff4_1 \n", - " pharokka bioconda/noarch::pharokka-1.7.3-pyhdfd78af_0 \n", + " pharokka bioconda/noarch::pharokka-1.7.4-pyhdfd78af_0 \n", " phold bioconda/noarch::phold-0.2.0-pyhdfd78af_0 \n", - " pillow pkgs/main/linux-64::pillow-10.4.0-py310h5eee18b_0 \n", + " pillow pkgs/main/linux-64::pillow-11.0.0-py310hfdbf927_0 \n", " pixman conda-forge/linux-64::pixman-0.43.2-h59595ed_0 \n", - " psutil conda-forge/linux-64::psutil-6.0.0-py310hc51659f_0 \n", - " pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001 \n", + " propcache conda-forge/linux-64::propcache-0.2.0-py310ha75aee5_2 \n", + " psutil conda-forge/linux-64::psutil-6.1.0-py310ha75aee5_0 \n", + " pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-hb9d3cd8_1002 \n", " pyarrow conda-forge/linux-64::pyarrow-16.1.0-py310hb7f781d_2 \n", " pyarrow-core conda-forge/linux-64::pyarrow-core-16.1.0-py310hcccf80d_2_cpu \n", - " pyarrow-hotfix conda-forge/noarch::pyarrow-hotfix-0.6-pyhd8ed1ab_0 \n", - " pycirclize conda-forge/noarch::pycirclize-1.6.0-pyhd8ed1ab_0 \n", - " pyhmmer bioconda/linux-64::pyhmmer-0.10.14-py310h7c593f9_0 \n", - " pyparsing conda-forge/noarch::pyparsing-3.1.2-pyhd8ed1ab_0 \n", - " pyrodigal bioconda/linux-64::pyrodigal-3.5.0-py310h7c593f9_0 \n", - " pyrodigal-gv bioconda/noarch::pyrodigal-gv-0.3.1-pyh7cba7a3_0 \n", - " pytest conda-forge/noarch::pytest-8.2.2-pyhd8ed1ab_0 \n", - " pytest-cov conda-forge/noarch::pytest-cov-5.0.0-pyhd8ed1ab_0 \n", - " python-dateutil conda-forge/noarch::python-dateutil-2.9.0-pyhd8ed1ab_0 \n", - " python-tzdata conda-forge/noarch::python-tzdata-2024.1-pyhd8ed1ab_0 \n", - " python-xxhash conda-forge/linux-64::python-xxhash-3.4.1-py310h2372a71_0 \n", - " python_abi conda-forge/linux-64::python_abi-3.10-4_cp310 \n", - " pytorch conda-forge/linux-64::pytorch-2.3.1-cuda120_py310h2c91c31_300 \n", + " pycirclize conda-forge/noarch::pycirclize-1.7.1-pyhd8ed1ab_0 \n", + " pyhmmer bioconda/linux-64::pyhmmer-0.10.15-py310h7c593f9_0 \n", + " pyparsing conda-forge/noarch::pyparsing-3.2.0-pyhd8ed1ab_1 \n", + " pyrodigal bioconda/linux-64::pyrodigal-3.6.3-py310h7c593f9_0 \n", + " pyrodigal-gv bioconda/noarch::pyrodigal-gv-0.3.2-pyh7e72e81_0 \n", + " pytest conda-forge/noarch::pytest-8.3.3-pyhd8ed1ab_0 \n", + " pytest-cov conda-forge/noarch::pytest-cov-6.0.0-pyhd8ed1ab_0 \n", + " python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhff2d567_0 \n", + " python-tzdata conda-forge/noarch::python-tzdata-2024.2-pyhd8ed1ab_0 \n", + " python-xxhash conda-forge/linux-64::python-xxhash-3.5.0-py310ha75aee5_1 \n", + " python_abi conda-forge/linux-64::python_abi-3.10-5_cp310 \n", + " pytorch conda-forge/linux-64::pytorch-2.4.0-cuda120_py310h2c91c31_301 \n", " pytz conda-forge/noarch::pytz-2024.1-pyhd8ed1ab_0 \n", - " pyyaml conda-forge/linux-64::pyyaml-6.0.1-py310h2372a71_1 \n", + " pyyaml conda-forge/linux-64::pyyaml-6.0.2-py310ha75aee5_1 \n", " qhull conda-forge/linux-64::qhull-2020.2-h434a139_5 \n", " re2 conda-forge/linux-64::re2-2023.09.01-h7f4b329_2 \n", - " regex conda-forge/linux-64::regex-2024.5.15-py310hc51659f_0 \n", - " ruamel.yaml.clib conda-forge/linux-64::ruamel.yaml.clib-0.2.8-py310h2372a71_0 \n", - " s2n conda-forge/linux-64::s2n-1.4.13-he19d79f_0 \n", - " safetensors conda-forge/linux-64::safetensors-0.4.3-py310hcb5633a_0 \n", - " scipy conda-forge/linux-64::scipy-1.14.0-py310h93e2701_1 \n", + " regex conda-forge/linux-64::regex-2024.11.6-py310ha75aee5_0 \n", + " s2n conda-forge/linux-64::s2n-1.4.15-he19d79f_0 \n", + " safetensors conda-forge/linux-64::safetensors-0.4.5-py310h505e2c1_0 \n", + " scipy conda-forge/linux-64::scipy-1.14.1-py310hfcf56fc_1 \n", " seaborn conda-forge/noarch::seaborn-0.13.2-hd8ed1ab_2 \n", " seaborn-base conda-forge/noarch::seaborn-base-0.13.2-pyhd8ed1ab_2 \n", - " sentencepiece conda-forge/linux-64::sentencepiece-0.2.0-hff52083_2 \n", - " sentencepiece-pyt~ conda-forge/linux-64::sentencepiece-python-0.2.0-py310h91407d4_2 \n", - " sentencepiece-spm conda-forge/linux-64::sentencepiece-spm-0.2.0-he81a138_2 \n", + " sentencepiece conda-forge/linux-64::sentencepiece-0.2.0-hff52083_4 \n", + " sentencepiece-pyt~ conda-forge/linux-64::sentencepiece-python-0.2.0-py310hcf7cfdd_4 \n", + " sentencepiece-spm conda-forge/linux-64::sentencepiece-spm-0.2.0-hc656cff_4 \n", " six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 \n", - " sleef conda-forge/linux-64::sleef-3.6.1-h3400bea_1 \n", + " sleef conda-forge/linux-64::sleef-3.7-h1b44611_2 \n", " snappy conda-forge/linux-64::snappy-1.2.1-ha2e4443_0 \n", - " statsmodels conda-forge/linux-64::statsmodels-0.14.2-py310h261611a_0 \n", - " sympy conda-forge/noarch::sympy-1.13.0-pypyh2585a3b_103 \n", - " tbb conda-forge/linux-64::tbb-2021.9.0-hf52228f_0 \n", + " statsmodels conda-forge/linux-64::statsmodels-0.14.4-py310hf462985_0 \n", + " sympy conda-forge/noarch::sympy-1.13.3-pypyh2585a3b_103 \n", + " tbb conda-forge/linux-64::tbb-2021.13.0-h84d6215_0 \n", " textwrap3 conda-forge/noarch::textwrap3-0.9.2-py_0 \n", - " tokenizers conda-forge/linux-64::tokenizers-0.19.1-py310h320607d_0 \n", + " tokenizers conda-forge/linux-64::tokenizers-0.20.4-py310hb1c6e2c_0 \n", " toml conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0 \n", - " tomli conda-forge/noarch::tomli-2.0.1-pyhd8ed1ab_0 \n", - " transformers conda-forge/noarch::transformers-4.41.2-pyhd8ed1ab_0 \n", - " trnascan-se bioconda/linux-64::trnascan-se-2.0.12-pl5321h031d066_0 \n", + " tomli conda-forge/noarch::tomli-2.1.0-pyhff2d567_0 \n", + " transformers conda-forge/noarch::transformers-4.46.3-pyhd8ed1ab_0 \n", + " trnascan-se bioconda/linux-64::trnascan-se-2.0.12-pl5321h031d066_1 \n", " typing-extensions conda-forge/noarch::typing-extensions-4.12.2-hd8ed1ab_0 \n", " typing_extensions conda-forge/noarch::typing_extensions-4.12.2-pyha770c72_0 \n", - " unicodedata2 conda-forge/linux-64::unicodedata2-15.1.0-py310h2372a71_0 \n", + " unicodedata2 conda-forge/linux-64::unicodedata2-15.1.0-py310ha75aee5_1 \n", " wget conda-forge/linux-64::wget-1.21.4-hda4d442_0 \n", - " xorg-fixesproto conda-forge/linux-64::xorg-fixesproto-5.0-h7f98852_1002 \n", - " xorg-inputproto conda-forge/linux-64::xorg-inputproto-2.3.2-h7f98852_1002 \n", - " xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002 \n", - " xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.9-hb711507_1 \n", - " xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.11-hd590300_0 \n", - " xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0 \n", - " xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h0b41bf4_2 \n", - " xorg-libxfixes conda-forge/linux-64::xorg-libxfixes-5.0.3-h7f98852_1004 \n", - " xorg-libxi conda-forge/linux-64::xorg-libxi-1.7.10-h7f98852_0 \n", - " xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.11-hd590300_0 \n", - " xorg-libxtst conda-forge/linux-64::xorg-libxtst-1.2.3-h7f98852_1002 \n", - " xorg-recordproto conda-forge/linux-64::xorg-recordproto-1.14.2-h7f98852_1002 \n", - " xorg-renderproto conda-forge/linux-64::xorg-renderproto-0.11.1-h7f98852_1002 \n", - " xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h0b41bf4_1003 \n", - " xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007 \n", + " xorg-libx11 conda-forge/linux-64::xorg-libx11-1.8.10-h4f16b4b_0 \n", + " xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.11-hb9d3cd8_1 \n", + " xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.5-hb9d3cd8_0 \n", + " xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.6-hb9d3cd8_0 \n", + " xorg-libxfixes conda-forge/linux-64::xorg-libxfixes-6.0.1-hb9d3cd8_0 \n", + " xorg-libxi conda-forge/linux-64::xorg-libxi-1.8.2-hb9d3cd8_0 \n", + " xorg-libxrender conda-forge/linux-64::xorg-libxrender-0.9.11-hb9d3cd8_1 \n", + " xorg-libxtst conda-forge/linux-64::xorg-libxtst-1.2.5-hb9d3cd8_3 \n", + " xorg-xorgproto conda-forge/linux-64::xorg-xorgproto-2024.1-hb9d3cd8_1 \n", " xxhash conda-forge/linux-64::xxhash-0.8.2-hd590300_0 \n", " yaml conda-forge/linux-64::yaml-0.2.5-h7f98852_2 \n", - " yarl conda-forge/linux-64::yarl-1.9.4-py310h2372a71_0 \n", + " yarl conda-forge/linux-64::yarl-1.18.0-py310ha75aee5_0 \n", "\n", "The following packages will be UPDATED:\n", "\n", + " anaconda-anon-usa~ 0.4.4-py312hfc0e8ea_100 --> 0.5.0-py310hfc0e8ea_100 \n", " boltons pkgs/main/linux-64::boltons-23.0.0-py~ --> conda-forge/noarch::boltons-24.0.0-pyhd8ed1ab_0 \n", - " brotli-python pkgs/main::brotli-python-1.0.9-py312h~ --> conda-forge::brotli-python-1.1.0-py310hc6cd4ac_1 \n", - " c-ares pkgs/main::c-ares-1.19.1-h5eee18b_0 --> conda-forge::c-ares-1.32.2-h4bc722e_0 \n", - " ca-certificates pkgs/main::ca-certificates-2024.3.11-~ --> conda-forge::ca-certificates-2024.7.4-hbcca054_0 \n", - " certifi pkgs/main/linux-64::certifi-2024.6.2-~ --> conda-forge/noarch::certifi-2024.7.4-pyhd8ed1ab_0 \n", - " cryptography pkgs/main::cryptography-42.0.5-py312h~ --> conda-forge::cryptography-42.0.8-py310hb1bd9d3_0 \n", - " frozendict pkgs/main::frozendict-2.4.2-py312h06a~ --> conda-forge::frozendict-2.4.4-py310hc51659f_0 \n", - " libgcc-ng pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-14.1.0-h77fa898_0 \n", - " libgomp pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-14.1.0-h77fa898_0 \n", - " libstdcxx-ng pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-14.1.0-hc0a3c3a_0 \n", + " brotli-python pkgs/main::brotli-python-1.0.9-py312h~ --> conda-forge::brotli-python-1.1.0-py310hf71b8c6_2 \n", + " c-ares pkgs/main::c-ares-1.19.1-h5eee18b_0 --> conda-forge::c-ares-1.34.3-hb9d3cd8_1 \n", + " conda-package-han~ pkgs/main/linux-64::conda-package-han~ --> conda-forge/noarch::conda-package-handling-2.4.0-pyh7900ff3_0 \n", + " conda-package-str~ pkgs/main/linux-64::conda-package-str~ --> conda-forge/noarch::conda-package-streaming-0.11.0-pyhd8ed1ab_0 \n", + " cryptography pkgs/main::cryptography-43.0.0-py312h~ --> conda-forge::cryptography-44.0.0-py310h6c63255_0 \n", + " frozendict pkgs/main::frozendict-2.4.2-py312h06a~ --> conda-forge::frozendict-2.4.6-py310ha75aee5_0 \n", + " idna pkgs/main/linux-64::idna-3.7-py312h06~ --> conda-forge/noarch::idna-3.10-pyhd8ed1ab_0 \n", + " libgcc-ng pkgs/main::libgcc-ng-11.2.0-h1234567_1 --> conda-forge::libgcc-ng-14.2.0-h69a702a_1 \n", + " libgomp pkgs/main::libgomp-11.2.0-h1234567_1 --> conda-forge::libgomp-14.2.0-h77fa898_1 \n", + " libstdcxx-ng pkgs/main::libstdcxx-ng-11.2.0-h12345~ --> conda-forge::libstdcxx-ng-14.2.0-h4852527_1 \n", " libuuid pkgs/main::libuuid-1.41.5-h5eee18b_0 --> conda-forge::libuuid-2.38.1-h0b41bf4_0 \n", - " ncurses pkgs/main::ncurses-6.4-h6a678d5_0 --> conda-forge::ncurses-6.5-h59595ed_0 \n", - " openssl pkgs/main::openssl-3.0.14-h5eee18b_0 --> conda-forge::openssl-3.3.1-h4bc722e_2 \n", - " packaging pkgs/main/linux-64::packaging-23.2-py~ --> conda-forge/noarch::packaging-24.1-pyhd8ed1ab_0 \n", - " platformdirs pkgs/main/linux-64::platformdirs-3.10~ --> conda-forge/noarch::platformdirs-4.2.2-pyhd8ed1ab_0 \n", + " menuinst pkgs/main::menuinst-2.1.2-py312h06a43~ --> conda-forge::menuinst-2.2.0-py310hff52083_0 \n", + " ncurses pkgs/main::ncurses-6.4-h6a678d5_0 --> conda-forge::ncurses-6.5-he02047a_1 \n", + " openssl pkgs/main::openssl-3.0.15-h5eee18b_0 --> conda-forge::openssl-3.4.0-hb9d3cd8_0 \n", + " packaging pkgs/main/linux-64::packaging-24.1-py~ --> conda-forge/noarch::packaging-24.2-pyhff2d567_1 \n", + " pip pkgs/main/linux-64::pip-24.2-py312h06~ --> conda-forge/noarch::pip-24.3.1-pyh8b19718_0 \n", + " platformdirs pkgs/main/linux-64::platformdirs-3.10~ --> conda-forge/noarch::platformdirs-4.3.6-pyhd8ed1ab_0 \n", " pluggy pkgs/main/linux-64::pluggy-1.0.0-py31~ --> conda-forge/noarch::pluggy-1.5.0-pyhd8ed1ab_0 \n", + " pycosat pkgs/main::pycosat-0.6.6-py312h5eee18~ --> conda-forge::pycosat-0.6.6-py310ha75aee5_2 \n", " pysocks pkgs/main/linux-64::pysocks-1.7.1-py3~ --> conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6 \n", - " requests pkgs/main/linux-64::requests-2.32.2-p~ --> conda-forge/noarch::requests-2.32.3-pyhd8ed1ab_0 \n", - " ruamel.yaml pkgs/main::ruamel.yaml-0.17.21-py312h~ --> conda-forge::ruamel.yaml-0.18.6-py310h2372a71_0 \n", - " setuptools pkgs/main/linux-64::setuptools-69.5.1~ --> conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_0 \n", - " urllib3 pkgs/main/linux-64::urllib3-2.2.2-py3~ --> conda-forge/noarch::urllib3-2.2.2-pyhd8ed1ab_1 \n", - " wheel pkgs/main/linux-64::wheel-0.43.0-py31~ --> conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 \n", + " ruamel.yaml pkgs/main::ruamel.yaml-0.18.6-py312h5~ --> conda-forge::ruamel.yaml-0.18.6-py310ha75aee5_1 \n", + " ruamel.yaml.clib pkgs/main::ruamel.yaml.clib-0.2.8-py3~ --> conda-forge::ruamel.yaml.clib-0.2.8-py310ha75aee5_1 \n", + " setuptools pkgs/main/linux-64::setuptools-75.1.0~ --> conda-forge/noarch::setuptools-75.6.0-pyhff2d567_1 \n", + " tqdm pkgs/main/linux-64::tqdm-4.66.5-py312~ --> conda-forge/noarch::tqdm-4.67.1-pyhd8ed1ab_0 \n", + " truststore pkgs/main/linux-64::truststore-0.8.0-~ --> conda-forge/noarch::truststore-0.10.0-pyhd8ed1ab_0 \n", + " wheel pkgs/main/linux-64::wheel-0.44.0-py31~ --> conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_0 \n", " zlib pkgs/main::zlib-1.2.13-h5eee18b_1 --> conda-forge::zlib-1.2.13-h4ab18f5_6 \n", - " zstandard pkgs/main::zstandard-0.22.0-py312h2c3~ --> conda-forge::zstandard-0.23.0-py310h64cae3c_0 \n", - " zstd pkgs/main::zstd-1.5.5-hc292b87_2 --> conda-forge::zstd-1.5.6-ha6fb4c9_0 \n", + " zstandard pkgs/main::zstandard-0.23.0-py312h2c3~ --> conda-forge::zstandard-0.23.0-py310ha39cb0e_1 \n", "\n", "The following packages will be SUPERSEDED by a higher-priority channel:\n", "\n", " _libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge \n", " _openmp_mutex pkgs/main::_openmp_mutex-5.1-1_gnu --> conda-forge::_openmp_mutex-4.5-2_kmp_llvm \n", - " cffi pkgs/main::cffi-1.16.0-py312h5eee18b_1 --> conda-forge::cffi-1.16.0-py310h2fee648_0 \n", - " conda pkgs/main::conda-24.5.0-py312h06a4308~ --> conda-forge::conda-24.5.0-py310hff52083_0 \n", + " certifi pkgs/main/linux-64::certifi-2024.8.30~ --> conda-forge/noarch::certifi-2024.8.30-pyhd8ed1ab_0 \n", + " cffi pkgs/main::cffi-1.17.1-py312h1fdaa30_0 --> conda-forge::cffi-1.17.1-py310h8deb56e_0 \n", + " conda pkgs/main::conda-24.9.2-py312h06a4308~ --> conda-forge::conda-24.9.2-py310hff52083_0 \n", " conda-content-tru~ pkgs/main/linux-64::conda-content-tru~ --> conda-forge/noarch::conda-content-trust-0.2.0-pyhd8ed1ab_0 \n", - " conda-package-han~ pkgs/main/linux-64::conda-package-han~ --> conda-forge/noarch::conda-package-handling-2.3.0-pyh7900ff3_0 \n", - " conda-package-str~ pkgs/main/linux-64::conda-package-str~ --> conda-forge/noarch::conda-package-streaming-0.10.0-pyhd8ed1ab_0 \n", " distro pkgs/main/linux-64::distro-1.9.0-py31~ --> conda-forge/noarch::distro-1.9.0-pyhd8ed1ab_0 \n", - " idna pkgs/main/linux-64::idna-3.7-py312h06~ --> conda-forge/noarch::idna-3.7-pyhd8ed1ab_0 \n", " jsonpatch pkgs/main/linux-64::jsonpatch-1.33-py~ --> conda-forge/noarch::jsonpatch-1.33-pyhd8ed1ab_0 \n", - " menuinst pkgs/main::menuinst-2.1.1-py312h06a43~ --> conda-forge::menuinst-2.1.1-py310hff52083_0 \n", - " pip pkgs/main/linux-64::pip-24.0-py312h06~ --> conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 \n", " pybind11-abi pkgs/main::pybind11-abi-5-hd3eb1b0_0 --> conda-forge::pybind11-abi-4-hd8ed1ab_3 \n", - " pycosat pkgs/main::pycosat-0.6.6-py312h5eee18~ --> conda-forge::pycosat-0.6.6-py310h2372a71_0 \n", - " python pkgs/main::python-3.12.4-h5148396_1 --> conda-forge::python-3.10.14-hd12c33a_0_cpython \n", - " tqdm pkgs/main/linux-64::tqdm-4.66.4-py312~ --> conda-forge/noarch::tqdm-4.66.4-pyhd8ed1ab_0 \n", - " truststore pkgs/main/linux-64::truststore-0.8.0-~ --> conda-forge/noarch::truststore-0.8.0-pyhd8ed1ab_0 \n", + " python pkgs/main::python-3.12.7-h5148396_0 --> conda-forge::python-3.10.14-hd12c33a_0_cpython \n", + " requests pkgs/main/linux-64::requests-2.32.3-p~ --> conda-forge/noarch::requests-2.32.3-pyhd8ed1ab_0 \n", + " urllib3 pkgs/main/linux-64::urllib3-2.2.3-py3~ --> conda-forge/noarch::urllib3-2.2.3-pyhd8ed1ab_0 \n", "\n", "The following packages will be DOWNGRADED:\n", "\n", - " anaconda-anon-usa~ 0.4.4-py312hfc0e8ea_100 --> 0.4.4-py310hfc0e8ea_100 \n", - " libmambapy 1.5.8-py312h2dafd23_2 --> 1.5.8-py310h2dafd23_2 \n", + " libmambapy 1.5.8-py312h2dafd23_3 --> 1.5.8-py310h2dafd23_3 \n", "\n", "\n", "\n", @@ -742,7 +684,7 @@ "set -e\n", "\n", "PYTHON_VERSION=\"3.10\"\n", - "PHAROKKA_VERSION=\"1.7.3\"\n", + "PHAROKKA_VERSION=\"1.7.4\"\n", "PHOLD_VERSION=\"0.2.0\"\n", "\n", "echo \"python version ${PYTHON_VERSION}\"\n", @@ -774,7 +716,7 @@ "base_uri": "https://localhost:8080/" }, "id": "tfltpbZ_QLfZ", - "outputId": "1cf78eef-ccbf-4a36-833f-8c675f9f3bf3" + "outputId": "d5de66ae-7a1b-44f6-bb67-e10beda22c75" }, "outputs": [ { @@ -783,8 +725,8 @@ "text": [ "Downloading pharokka database. This will take a few minutes. Please be patient :)\n", "Downloading phold database. This will take a few minutes. Please be patient :)\n", - "CPU times: user 899 ms, sys: 117 ms, total: 1.02 s\n", - "Wall time: 4min 34s\n" + "CPU times: user 1.22 s, sys: 188 ms, total: 1.41 s\n", + "Wall time: 6min 4s\n" ] }, { @@ -823,7 +765,7 @@ "base_uri": "https://localhost:8080/" }, "id": "Sjdpu6R-Kig9", - "outputId": "573a158f-5578-4d7c-b309-57240101b042" + "outputId": "4a07ee8d-2290-459e-d899-dcd337aeec26" }, "outputs": [ { @@ -836,8 +778,8 @@ "Your output is in output_pharokka.\n", "Zipping the output directory so you can download it all in one go.\n", "Output directory has been zipped to output_pharokka.zip\n", - "CPU times: user 130 ms, sys: 12.7 ms, total: 143 ms\n", - "Wall time: 30 s\n" + "CPU times: user 147 ms, sys: 19.6 ms, total: 167 ms\n", + "Wall time: 32.8 s\n" ] } ], @@ -955,13 +897,13 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 4, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "9QfjP3q-Q04f", - "outputId": "a033f8e9-050d-4630-ab8e-f9ac9fba8000" + "outputId": "91bf9e52-d5dc-4d80-8c61-a5db46b75535" }, "outputs": [ { @@ -973,8 +915,8 @@ "Your output is in output_phold.\n", "Zipping the output directory so you can download it all in one go.\n", "Output directory has been zipped to output_phold.zip\n", - "CPU times: user 348 ms, sys: 46.2 ms, total: 394 ms\n", - "Wall time: 1min 30s\n" + "CPU times: user 451 ms, sys: 61.9 ms, total: 513 ms\n", + "Wall time: 1min 48s\n" ] } ], @@ -1078,105 +1020,182 @@ "base_uri": "https://localhost:8080/" }, "id": "1eUYA415PNRX", - "outputId": "270c6d69-4cd6-4ce8-fc21-1805701a1abb" + "outputId": "80fb0086-058e-42f0-a1c2-9f18cc3823b5" }, - "execution_count": 25, + "execution_count": 5, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "installing phynteny\n", - "Requirement already satisfied: phynteny==0.1.13 in /usr/local/lib/python3.10/site-packages (0.1.13)\n", + "Collecting phynteny==0.1.13\n", + " Downloading phynteny-0.1.13-py3-none-any.whl.metadata (7.9 kB)\n", "Collecting numpy==1.26.4\n", " Downloading numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)\n", - " ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 61.0/61.0 kB 4.2 MB/s eta 0:00:00\n", "Requirement already satisfied: biopython>=1.79 in /usr/local/lib/python3.10/site-packages (from phynteny==0.1.13) (1.81)\n", - 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" Found existing installation: numpy 2.0.0\n", - " Uninstalling numpy-2.0.0:\n", - " Successfully uninstalled numpy-2.0.0\n", - "Successfully installed numpy-1.26.4\n", + " Found existing installation: numpy 2.1.3\n", + " Uninstalling numpy-2.1.3:\n", + " Successfully uninstalled numpy-2.1.3\n", + "Successfully installed absl-py-2.1.0 astunparse-1.6.3 cachetools-5.5.0 flatbuffers-1.12 gast-0.4.0 google-auth-2.36.0 google-auth-oauthlib-0.4.6 google-pasta-0.2.0 grpcio-1.68.0 joblib-1.4.2 keras-2.9.0 keras-preprocessing-1.1.2 libclang-18.1.1 markdown-3.7 numpy-1.26.4 oauthlib-3.2.2 opt-einsum-3.4.0 phynteny-0.1.13 protobuf-3.19.6 pyasn1-0.6.1 pyasn1-modules-0.4.1 requests-oauthlib-2.0.0 rsa-4.9 scikit-learn-1.2.2 tensorboard-2.9.1 tensorboard-data-server-0.6.1 tensorboard-plugin-wit-1.8.1 tensorflow-2.9.1 tensorflow-estimator-2.9.0 tensorflow-io-gcs-filesystem-0.37.1 termcolor-2.5.0 threadpoolctl-3.5.0 werkzeug-3.1.3 wrapt-1.17.0\n", "Downloading phynteny models\n", "Downloading Phynteny models to phynteny_models\n", - "All phynteny models have already been downloaded and checked.\n" - ] - }, - { - "output_type": "stream", - "name": "stderr", - "text": [ - "WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\n" + "Phynteny models are missing.\n", + "Some models are missing.\n", + "Downloading Phynteny Models from https://zenodo.org/record/8198288/files/phynteny_models_v0.1.11.tar.gz.\n", + "path\n", + "https://zenodo.org/record/8198288/files/phynteny_models_v0.1.11.tar.gz\n", + "|████████████████████████████████████████| 381.6M/381.6M [100%] in 7:20.9 (865.49k/s) \n", + "Phynteny Models tarball download OK: 364c1eab8cda872a8757c1187a5c2b53\n", + "Extracting Phynteny Models tarball: file=phynteny_models/phynteny_models_v0.1.11.tar.gz, output=phynteny_models\n", + "Done.\n" ] } ] }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 6, "metadata": { "id": "BlPLP3vlhWYs", "colab": { "base_uri": "https://localhost:8080/" }, - "outputId": "6186a5db-e111-483d-9254-15b210c24096" + "outputId": "e4cc231e-fbc5-4b2d-fb7c-38e102efc849" }, "outputs": [ { @@ -1188,8 +1207,8 @@ "Your output is in output_phynteny.\n", "Zipping the output directory so you can download it all in one go.\n", "Output directory has been zipped to output_phynteny.zip\n", - "CPU times: user 202 ms, sys: 18.8 ms, total: 221 ms\n", - "Wall time: 45.3 s\n" + "CPU times: user 182 ms, sys: 37.7 ms, total: 220 ms\n", + "Wall time: 45.6 s\n" ] } ], @@ -1265,7 +1284,7 @@ "colab": { "provenance": [], "gpuType": "T4", - "authorship_tag": "ABX9TyPhV6L/1JdS3GUiG5UFg6cx", + "authorship_tag": "ABX9TyOn+XbE6ByCGMHehzgMhZLM", "include_colab_link": true }, "kernelspec": {