2023-05-14T06:32:27,182 Created temporary directory: /tmp/pip-build-tracker-5ggcvboj 2023-05-14T06:32:27,185 Initialized build tracking at /tmp/pip-build-tracker-5ggcvboj 2023-05-14T06:32:27,185 Created build tracker: /tmp/pip-build-tracker-5ggcvboj 2023-05-14T06:32:27,185 Entered build tracker: /tmp/pip-build-tracker-5ggcvboj 2023-05-14T06:32:27,187 Created temporary directory: /tmp/pip-wheel-7umqmwf5 2023-05-14T06:32:27,195 Created temporary directory: /tmp/pip-ephem-wheel-cache-67fq5ora 2023-05-14T06:32:27,252 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-05-14T06:32:27,260 2 location(s) to search for versions of gtdbtk: 2023-05-14T06:32:27,260 * https://pypi.org/simple/gtdbtk/ 2023-05-14T06:32:27,260 * https://www.piwheels.org/simple/gtdbtk/ 2023-05-14T06:32:27,261 Fetching project page and analyzing links: https://pypi.org/simple/gtdbtk/ 2023-05-14T06:32:27,262 Getting page https://pypi.org/simple/gtdbtk/ 2023-05-14T06:32:27,266 Found index url 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https://files.pythonhosted.org/packages/0a/74/8cbe8afea3aa0f7d6b948210b8937f3edcf541b3212cae2ce6aa560276a9/gtdbtk-0.2.2.tar.gz (from https://pypi.org/simple/gtdbtk/), version: 0.2.2 2023-05-14T06:32:27,500 Found link https://files.pythonhosted.org/packages/45/de/019db6634299b4086a49646891c9e99347e2908713baa14641e15687e4af/gtdbtk-0.3.0.tar.gz (from https://pypi.org/simple/gtdbtk/), version: 0.3.0 2023-05-14T06:32:27,501 Found link https://files.pythonhosted.org/packages/6e/46/14181ed7f443fd8f70353250d09c94d2a2d867e68cc687167a8546ef4926/gtdbtk-0.3.1.tar.gz (from https://pypi.org/simple/gtdbtk/), version: 0.3.1 2023-05-14T06:32:27,501 Found link https://files.pythonhosted.org/packages/91/64/06be7ada30b1895a1205feac310a92929a5e135b5821036632aa36d1354c/gtdbtk-0.3.2.tar.gz (from https://pypi.org/simple/gtdbtk/), version: 0.3.2 2023-05-14T06:32:27,502 Found link https://files.pythonhosted.org/packages/7d/90/a62620e2c5c5799d0271f097a83c356dd7d458bf85651da24a353e93d669/gtdbtk-0.3.3.tar.gz (from 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version: 1.1.0 2023-05-14T06:32:27,509 Found link https://files.pythonhosted.org/packages/68/d0/bcdb38880ed7e0d0ae563c62b1f192b1d77a35a0d00b193f9e5a01817454/gtdbtk-1.1.1.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.1.1 2023-05-14T06:32:27,510 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/f3/56/60ff2a296580b4e5741592ad17ca874ba024f7f5c9c225d7cadfb9cfd54f/gtdbtk-1.2.0-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,511 Found link https://files.pythonhosted.org/packages/fd/9d/2060d8cdefde94050a969360e8b1343d6c441b35f57ca3000ec2b8c0c950/gtdbtk-1.2.0.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.2.0 2023-05-14T06:32:27,512 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/ef/47/293fd1fa9548d876d0da7f2a99a3784614850d84f9667dc08c1d28a50737/gtdbtk-1.3.0-py3-none-any.whl (from 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2023-05-14T06:32:27,524 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/4a/cc/631e798a8f921fc6c504591472e34a04c2868f7ce7fdfc1b3c1cb5a81c05/gtdbtk-1.7.0-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,525 Found link https://files.pythonhosted.org/packages/a0/eb/859b20c3adeb96ca72f242bc31cd30319c2bd6e4d130c13aba0b76d2fe34/gtdbtk-1.7.0.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.7.0 2023-05-14T06:32:27,526 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/c5/ac/fd59f08a268eab7c094ee1e9b14004c591c3477b11628c9e08aaad2bbaa6/gtdbtk-2.0.0-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,527 Found link https://files.pythonhosted.org/packages/7e/43/9b3c861f07fa420e9595fdf5f2261c0d1519a01f9e994b6445fb2e263d98/gtdbtk-2.0.0.tar.gz (from https://pypi.org/simple/gtdbtk/) 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2023-05-14T06:32:27,539 Found link https://files.pythonhosted.org/packages/51/6d/8a161d447e0d3db86dffe2c684272be3969254b056ef819a270a10e5bdbd/gtdbtk-2.2.3.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.2.3 2023-05-14T06:32:27,540 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/a5/32/24f75f992865e4e5c761bb04a48ebc510dd91b9f04d5f1424eb5e4161ac4/gtdbtk-2.2.4-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,541 Found link https://files.pythonhosted.org/packages/70/ee/8ae2325f1f084a901575e9dffe8c8e7dae4bb89df809858983281177c0d1/gtdbtk-2.2.4.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.2.4 2023-05-14T06:32:27,541 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/55/a0/82538604d4f39129c5632cf6d8b26a4b2993e9fd4fecc5f8ca6f0a118be0/gtdbtk-2.2.5-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,543 Found link https://files.pythonhosted.org/packages/29/7b/3aed07a21e615b1b3f0a2fbcf8c7032ffe50d45fd4ffba50f59a12aab20f/gtdbtk-2.2.5.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.2.5 2023-05-14T06:32:27,543 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/f6/a2/877a99121b5cc2071ef2cff154c037418df0dce5d4512ed5eebcac3adff1/gtdbtk-2.2.6-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,545 Found link https://files.pythonhosted.org/packages/43/1d/f650449e249a128023732c98dc8f570d4033d52b81d64e442c0ea49175cc/gtdbtk-2.2.6.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.2.6 2023-05-14T06:32:27,545 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/4e/be/72ff9d9e718e08898e8f9817ae91d06c8364b288d3c082026ddab01ba4e0/gtdbtk-2.3.0-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,547 Found link https://files.pythonhosted.org/packages/17/7f/8e724eb5b29d4a3d73d4530e8c9f18296a1f69fde82d634772ed6f0a267a/gtdbtk-2.3.0.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.3.0 2023-05-14T06:32:27,548 Fetching project page and analyzing links: https://www.piwheels.org/simple/gtdbtk/ 2023-05-14T06:32:27,548 Getting page https://www.piwheels.org/simple/gtdbtk/ 2023-05-14T06:32:27,551 Found index url https://www.piwheels.org/simple/ 2023-05-14T06:32:27,834 Fetched page https://www.piwheels.org/simple/gtdbtk/ as text/html 2023-05-14T06:32:27,867 Skipping link: No binaries permitted for gtdbtk: 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(from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,873 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-2.2.3-py3-none-any.whl#sha256=06f93a7c81ad0d432168b3c6813c6b41c6c62c8c772d3f5a3f7a07026002e417 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,874 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-2.2.2-py3-none-any.whl#sha256=b2a2470befeb113d05b7e439d383b55fa4a7bf604d4de4b947eceb0cdd11feb9 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,874 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-2.2.1-py3-none-any.whl#sha256=2cf336d7981cf9e722bb1ab210ad70a0fdc421364d66f121ba0ed2764f49d831 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,875 Skipping link: No binaries permitted for gtdbtk: 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(from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,877 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-1.6.0-py3-none-any.whl#sha256=b5a207597ad94381e816d097e1e1925df4e5570643272ed7b76db5dd3001ebde (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,878 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-1.5.1-py3-none-any.whl#sha256=ed5d3a99e31ba670781bfdc0b376d6269e1d683d7385d3508bdfd574f1a16b5c (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,878 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-1.5.0-py3-none-any.whl#sha256=4d5f2ecca5c2f1e7b279ff1bba63edd378e64f1195c8da6f8d2fe1c37bb1a02e (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,879 Skipping link: No binaries permitted for gtdbtk: 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(from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,881 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-1.1.1-py3-none-any.whl#sha256=6015c83a790205e33f5f1a6b18e6dc3f59ed21785e21e2335e333d2a0c2b6149 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,881 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-1.1.0-py3-none-any.whl#sha256=74644ddd23fa626c60834924b75ff2461cfe146825dfe8cb56ba7aa87f80065c (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,882 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-1.0.2-py3-none-any.whl#sha256=bcb2aff77a5de8e7ee657b155c07cef65e54ed4c69e75f792746eeb1a116d7d8 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-05-14T06:32:27,882 Skipping link: No binaries permitted for gtdbtk: 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Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.0.2-py3-none-any.whl#sha256=dac945e10b775b7c8ab5f5b16635bd016d17aacb8a4ad77708ce67dc1b3f3ed6 (from https://www.piwheels.org/simple/gtdbtk/) 2023-05-14T06:32:27,894 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.0.1-py3-none-any.whl#sha256=05d5353a17e20d9bc2a38528bb3b2e2e28d3188d4ebf69192793cd3e0d5199e6 (from https://www.piwheels.org/simple/gtdbtk/) 2023-05-14T06:32:27,895 Skipping link: not a file: https://www.piwheels.org/simple/gtdbtk/ 2023-05-14T06:32:27,895 Skipping link: not a file: https://pypi.org/simple/gtdbtk/ 2023-05-14T06:32:27,941 Given no hashes to check 1 links for project 'gtdbtk': discarding no candidates 2023-05-14T06:32:27,969 Collecting gtdbtk==2.3.0 2023-05-14T06:32:27,974 Created temporary directory: /tmp/pip-unpack-i6ijrt91 2023-05-14T06:32:28,173 Downloading gtdbtk-2.3.0.tar.gz (1.7 MB) 2023-05-14T06:32:29,909 Added gtdbtk==2.3.0 from https://files.pythonhosted.org/packages/17/7f/8e724eb5b29d4a3d73d4530e8c9f18296a1f69fde82d634772ed6f0a267a/gtdbtk-2.3.0.tar.gz to build tracker '/tmp/pip-build-tracker-5ggcvboj' 2023-05-14T06:32:29,914 Running setup.py (path:/tmp/pip-wheel-7umqmwf5/gtdbtk_07f9614f07284186b702a5e2e0e485b3/setup.py) egg_info for package gtdbtk 2023-05-14T06:32:29,915 Created temporary directory: /tmp/pip-pip-egg-info-m_xxl8hn 2023-05-14T06:32:29,916 Preparing metadata (setup.py): started 2023-05-14T06:32:29,918 Running command python setup.py egg_info 2023-05-14T06:32:31,647 running egg_info 2023-05-14T06:32:31,649 creating /tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info 2023-05-14T06:32:31,707 writing /tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info/PKG-INFO 2023-05-14T06:32:31,711 writing dependency_links to /tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info/dependency_links.txt 2023-05-14T06:32:31,715 writing entry points to /tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info/entry_points.txt 2023-05-14T06:32:31,718 writing requirements to /tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info/requires.txt 2023-05-14T06:32:31,720 writing top-level names to /tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info/top_level.txt 2023-05-14T06:32:31,723 writing manifest file '/tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info/SOURCES.txt' 2023-05-14T06:32:31,947 reading manifest file '/tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info/SOURCES.txt' 2023-05-14T06:32:31,957 adding license file 'LICENSE' 2023-05-14T06:32:31,970 writing manifest file '/tmp/pip-pip-egg-info-m_xxl8hn/gtdbtk.egg-info/SOURCES.txt' 2023-05-14T06:32:32,095 Preparing metadata (setup.py): finished with status 'done' 2023-05-14T06:32:32,109 Source in /tmp/pip-wheel-7umqmwf5/gtdbtk_07f9614f07284186b702a5e2e0e485b3 has version 2.3.0, which satisfies requirement gtdbtk==2.3.0 from https://files.pythonhosted.org/packages/17/7f/8e724eb5b29d4a3d73d4530e8c9f18296a1f69fde82d634772ed6f0a267a/gtdbtk-2.3.0.tar.gz 2023-05-14T06:32:32,111 Removed gtdbtk==2.3.0 from https://files.pythonhosted.org/packages/17/7f/8e724eb5b29d4a3d73d4530e8c9f18296a1f69fde82d634772ed6f0a267a/gtdbtk-2.3.0.tar.gz from build tracker '/tmp/pip-build-tracker-5ggcvboj' 2023-05-14T06:32:32,127 Created temporary directory: /tmp/pip-unpack-qhbjy552 2023-05-14T06:32:32,128 Building wheels for collected packages: gtdbtk 2023-05-14T06:32:32,137 Created temporary directory: /tmp/pip-wheel-9hrm8n0l 2023-05-14T06:32:32,138 Building wheel for gtdbtk (setup.py): started 2023-05-14T06:32:32,140 Destination directory: /tmp/pip-wheel-9hrm8n0l 2023-05-14T06:32:32,140 Running command python setup.py bdist_wheel 2023-05-14T06:32:34,081 running bdist_wheel 2023-05-14T06:32:34,257 running build 2023-05-14T06:32:34,257 running build_py 2023-05-14T06:32:34,322 creating build 2023-05-14T06:32:34,323 creating build/lib 2023-05-14T06:32:34,324 creating build/lib/gtdbtk 2023-05-14T06:32:34,327 copying gtdbtk/ani_rep.py -> build/lib/gtdbtk 2023-05-14T06:32:34,332 copying gtdbtk/tools.py -> build/lib/gtdbtk 2023-05-14T06:32:34,336 copying gtdbtk/misc.py -> build/lib/gtdbtk 2023-05-14T06:32:34,341 copying gtdbtk/infer_ranks.py -> build/lib/gtdbtk 2023-05-14T06:32:34,346 copying gtdbtk/ani_screen.py -> build/lib/gtdbtk 2023-05-14T06:32:34,350 copying gtdbtk/relative_distance.py -> build/lib/gtdbtk 2023-05-14T06:32:34,355 copying gtdbtk/classify.py -> build/lib/gtdbtk 2023-05-14T06:32:34,366 copying gtdbtk/trim_msa.py -> build/lib/gtdbtk 2023-05-14T06:32:34,370 copying gtdbtk/markers.py -> build/lib/gtdbtk 2023-05-14T06:32:34,376 copying gtdbtk/main.py -> build/lib/gtdbtk 2023-05-14T06:32:34,383 copying gtdbtk/__init__.py -> build/lib/gtdbtk 2023-05-14T06:32:34,386 copying gtdbtk/decorate.py -> build/lib/gtdbtk 2023-05-14T06:32:34,391 copying gtdbtk/exceptions.py -> build/lib/gtdbtk 2023-05-14T06:32:34,395 copying gtdbtk/split.py -> build/lib/gtdbtk 2023-05-14T06:32:34,400 copying gtdbtk/__main__.py -> build/lib/gtdbtk 2023-05-14T06:32:34,404 copying gtdbtk/cli.py -> build/lib/gtdbtk 2023-05-14T06:32:34,409 copying gtdbtk/reroot_tree.py -> build/lib/gtdbtk 2023-05-14T06:32:34,415 creating build/lib/tests 2023-05-14T06:32:34,417 copying tests/test_classify.py -> build/lib/tests 2023-05-14T06:32:34,421 copying tests/__init__.py -> build/lib/tests 2023-05-14T06:32:34,424 copying tests/test_cli.py -> build/lib/tests 2023-05-14T06:32:34,429 copying tests/common.py -> build/lib/tests 2023-05-14T06:32:34,435 creating build/lib/gtdbtk/files 2023-05-14T06:32:34,436 copying gtdbtk/files/classify_summary.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,441 copying gtdbtk/files/batchfile.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,445 copying gtdbtk/files/pplacer_classification.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,449 copying gtdbtk/files/tree_mapping.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,453 copying gtdbtk/files/__init__.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,456 copying gtdbtk/files/gtdb_radii.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,460 copying gtdbtk/files/stage_logger.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,464 copying gtdbtk/files/red_dict.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,467 copying gtdbtk/files/missing_genomes.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,471 copying gtdbtk/files/marker_info.py -> build/lib/gtdbtk/files 2023-05-14T06:32:34,477 creating build/lib/gtdbtk/external 2023-05-14T06:32:34,479 copying gtdbtk/external/prodigal.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,484 copying gtdbtk/external/pplacer.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,488 copying gtdbtk/external/hmm_aligner.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,493 copying gtdbtk/external/fasttree.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,497 copying gtdbtk/external/__init__.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,500 copying gtdbtk/external/fastani.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,504 copying gtdbtk/external/mash.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,509 copying gtdbtk/external/tigrfam_search.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,514 copying gtdbtk/external/pfam_search.py -> build/lib/gtdbtk/external 2023-05-14T06:32:34,519 creating build/lib/gtdbtk/model 2023-05-14T06:32:34,521 copying gtdbtk/model/enum.py -> build/lib/gtdbtk/model 2023-05-14T06:32:34,525 copying gtdbtk/model/__init__.py -> build/lib/gtdbtk/model 2023-05-14T06:32:34,529 creating build/lib/gtdbtk/config 2023-05-14T06:32:34,531 copying gtdbtk/config/output.py -> build/lib/gtdbtk/config 2023-05-14T06:32:34,535 copying gtdbtk/config/__init__.py -> build/lib/gtdbtk/config 2023-05-14T06:32:34,538 copying gtdbtk/config/common.py -> build/lib/gtdbtk/config 2023-05-14T06:32:34,544 creating build/lib/gtdbtk/pipeline 2023-05-14T06:32:34,546 copying gtdbtk/pipeline/align.py -> build/lib/gtdbtk/pipeline 2023-05-14T06:32:34,550 copying gtdbtk/pipeline/__init__.py -> build/lib/gtdbtk/pipeline 2023-05-14T06:32:34,553 copying gtdbtk/pipeline/export_msa.py -> build/lib/gtdbtk/pipeline 2023-05-14T06:32:34,560 creating build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,562 copying gtdbtk/biolib_lite/logger.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,566 copying gtdbtk/biolib_lite/prodigal_biolib.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,571 copying gtdbtk/biolib_lite/taxonomy.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,577 copying gtdbtk/biolib_lite/__init__.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,580 copying gtdbtk/biolib_lite/newick.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,583 copying gtdbtk/biolib_lite/custom_help_formatter.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,588 copying gtdbtk/biolib_lite/exceptions.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,591 copying gtdbtk/biolib_lite/seq_io.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,596 copying gtdbtk/biolib_lite/parallel.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,600 copying gtdbtk/biolib_lite/execute.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,604 copying gtdbtk/biolib_lite/common.py -> build/lib/gtdbtk/biolib_lite 2023-05-14T06:32:34,610 creating build/lib/gtdbtk/files/marker 2023-05-14T06:32:34,612 copying gtdbtk/files/marker/tophit.py -> build/lib/gtdbtk/files/marker 2023-05-14T06:32:34,617 copying gtdbtk/files/marker/copy_number.py -> build/lib/gtdbtk/files/marker 2023-05-14T06:32:34,621 copying gtdbtk/files/marker/__init__.py -> build/lib/gtdbtk/files/marker 2023-05-14T06:32:34,626 creating build/lib/gtdbtk/files/prodigal 2023-05-14T06:32:34,628 copying gtdbtk/files/prodigal/tln_table_summary.py -> build/lib/gtdbtk/files/prodigal 2023-05-14T06:32:34,632 copying gtdbtk/files/prodigal/__init__.py -> build/lib/gtdbtk/files/prodigal 2023-05-14T06:32:34,635 copying gtdbtk/files/prodigal/tln_table.py -> build/lib/gtdbtk/files/prodigal 2023-05-14T06:32:34,641 creating build/lib/gtdbtk/external/pypfam 2023-05-14T06:32:34,643 copying gtdbtk/external/pypfam/__init__.py -> build/lib/gtdbtk/external/pypfam 2023-05-14T06:32:34,648 creating build/lib/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:34,651 copying gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:34,656 copying gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:34,661 copying gtdbtk/external/pypfam/HMM/HMMResults.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:34,666 copying gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:34,670 copying gtdbtk/external/pypfam/HMM/__init__.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:34,674 copying gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:34,680 creating build/lib/gtdbtk/external/pypfam/Scan 2023-05-14T06:32:34,683 copying gtdbtk/external/pypfam/Scan/PfamScan.py -> build/lib/gtdbtk/external/pypfam/Scan 2023-05-14T06:32:34,688 copying gtdbtk/external/pypfam/Scan/__init__.py -> build/lib/gtdbtk/external/pypfam/Scan 2023-05-14T06:32:34,694 creating build/lib/tests/test_gtdbtk 2023-05-14T06:32:34,696 copying tests/test_gtdbtk/test_trim_msa.py -> build/lib/tests/test_gtdbtk 2023-05-14T06:32:34,701 copying tests/test_gtdbtk/test_tools.py -> build/lib/tests/test_gtdbtk 2023-05-14T06:32:34,707 copying tests/test_gtdbtk/test_markers.py -> build/lib/tests/test_gtdbtk 2023-05-14T06:32:34,711 copying tests/test_gtdbtk/test__main__.py -> build/lib/tests/test_gtdbtk 2023-05-14T06:32:34,716 copying tests/test_gtdbtk/__init__.py -> build/lib/tests/test_gtdbtk 2023-05-14T06:32:34,720 copying tests/test_gtdbtk/test_main.py -> build/lib/tests/test_gtdbtk 2023-05-14T06:32:34,727 creating build/lib/tests/test_gtdbtk/test_external 2023-05-14T06:32:34,730 copying tests/test_gtdbtk/test_external/test_fasttree.py -> build/lib/tests/test_gtdbtk/test_external 2023-05-14T06:32:34,734 copying tests/test_gtdbtk/test_external/__init__.py -> build/lib/tests/test_gtdbtk/test_external 2023-05-14T06:32:34,738 copying tests/test_gtdbtk/test_external/test_fastani.py -> build/lib/tests/test_gtdbtk/test_external 2023-05-14T06:32:34,744 creating build/lib/tests/test_gtdbtk/test_files 2023-05-14T06:32:34,746 copying tests/test_gtdbtk/test_files/__init__.py -> build/lib/tests/test_gtdbtk/test_files 2023-05-14T06:32:34,752 creating build/lib/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:34,754 copying tests/test_gtdbtk/test_biolib_lite/test_seq_io.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:34,759 copying tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:34,763 copying tests/test_gtdbtk/test_biolib_lite/test_newick.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:34,767 copying tests/test_gtdbtk/test_biolib_lite/__init__.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:34,771 copying tests/test_gtdbtk/test_biolib_lite/test_common.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:34,777 creating build/lib/tests/test_gtdbtk/test_files/test_marker 2023-05-14T06:32:34,780 copying tests/test_gtdbtk/test_files/test_marker/test_tophit.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2023-05-14T06:32:34,786 copying tests/test_gtdbtk/test_files/test_marker/test_copy_number.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2023-05-14T06:32:34,791 copying tests/test_gtdbtk/test_files/test_marker/__init__.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2023-05-14T06:32:34,796 creating build/lib/tests/test_gtdbtk/test_files/test_prodigal 2023-05-14T06:32:34,798 copying tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py -> build/lib/tests/test_gtdbtk/test_files/test_prodigal 2023-05-14T06:32:34,802 copying tests/test_gtdbtk/test_files/test_prodigal/__init__.py -> build/lib/tests/test_gtdbtk/test_files/test_prodigal 2023-05-14T06:32:34,810 creating build/lib/gtdbtk/tests 2023-05-14T06:32:34,812 creating build/lib/gtdbtk/tests/data 2023-05-14T06:32:34,814 creating build/lib/gtdbtk/tests/data/genomes 2023-05-14T06:32:34,817 copying gtdbtk/tests/data/genomes/genome_3.fna -> build/lib/gtdbtk/tests/data/genomes 2023-05-14T06:32:34,877 copying gtdbtk/tests/data/genomes/genome_1.fna -> build/lib/gtdbtk/tests/data/genomes 2023-05-14T06:32:35,019 copying gtdbtk/tests/data/genomes/genome_2.fna -> build/lib/gtdbtk/tests/data/genomes 2023-05-14T06:32:35,174 /usr/local/lib/python3.7/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-05-14T06:32:35,175 !! 2023-05-14T06:32:35,175 ******************************************************************************** 2023-05-14T06:32:35,176 Please avoid running ``setup.py`` directly. 2023-05-14T06:32:35,176 Instead, use pypa/build, pypa/installer, pypa/build or 2023-05-14T06:32:35,177 other standards-based tools. 2023-05-14T06:32:35,177 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-05-14T06:32:35,178 ******************************************************************************** 2023-05-14T06:32:35,178 !! 2023-05-14T06:32:35,179 self.initialize_options() 2023-05-14T06:32:35,235 installing to build/bdist.linux-armv7l/wheel 2023-05-14T06:32:35,235 running install 2023-05-14T06:32:35,295 running install_lib 2023-05-14T06:32:35,357 creating build/bdist.linux-armv7l 2023-05-14T06:32:35,358 creating build/bdist.linux-armv7l/wheel 2023-05-14T06:32:35,362 creating build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,364 copying build/lib/gtdbtk/ani_rep.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,371 creating build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,372 copying build/lib/gtdbtk/files/classify_summary.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,378 copying build/lib/gtdbtk/files/batchfile.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,382 copying build/lib/gtdbtk/files/pplacer_classification.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,387 creating build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2023-05-14T06:32:35,389 copying build/lib/gtdbtk/files/marker/tophit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2023-05-14T06:32:35,394 copying build/lib/gtdbtk/files/marker/copy_number.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2023-05-14T06:32:35,398 copying build/lib/gtdbtk/files/marker/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2023-05-14T06:32:35,401 copying build/lib/gtdbtk/files/tree_mapping.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,406 copying build/lib/gtdbtk/files/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,408 copying build/lib/gtdbtk/files/gtdb_radii.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,413 creating build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2023-05-14T06:32:35,415 copying build/lib/gtdbtk/files/prodigal/tln_table_summary.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2023-05-14T06:32:35,419 copying build/lib/gtdbtk/files/prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2023-05-14T06:32:35,422 copying build/lib/gtdbtk/files/prodigal/tln_table.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2023-05-14T06:32:35,426 copying build/lib/gtdbtk/files/stage_logger.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,430 copying build/lib/gtdbtk/files/red_dict.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,434 copying build/lib/gtdbtk/files/missing_genomes.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,437 copying build/lib/gtdbtk/files/marker_info.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-05-14T06:32:35,441 copying build/lib/gtdbtk/tools.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,446 copying build/lib/gtdbtk/misc.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,451 creating build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,453 copying build/lib/gtdbtk/external/prodigal.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,458 copying build/lib/gtdbtk/external/pplacer.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,464 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam 2023-05-14T06:32:35,465 copying build/lib/gtdbtk/external/pypfam/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam 2023-05-14T06:32:35,470 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:35,471 copying build/lib/gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:35,476 copying build/lib/gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:35,481 copying build/lib/gtdbtk/external/pypfam/HMM/HMMResults.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:35,485 copying build/lib/gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:35,488 copying build/lib/gtdbtk/external/pypfam/HMM/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:35,491 copying build/lib/gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-05-14T06:32:35,495 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan 2023-05-14T06:32:35,497 copying build/lib/gtdbtk/external/pypfam/Scan/PfamScan.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan 2023-05-14T06:32:35,502 copying build/lib/gtdbtk/external/pypfam/Scan/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan 2023-05-14T06:32:35,505 copying build/lib/gtdbtk/external/hmm_aligner.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,509 copying build/lib/gtdbtk/external/fasttree.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,514 copying build/lib/gtdbtk/external/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,516 copying build/lib/gtdbtk/external/fastani.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,521 copying build/lib/gtdbtk/external/mash.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,525 copying build/lib/gtdbtk/external/tigrfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,529 copying build/lib/gtdbtk/external/pfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-05-14T06:32:35,533 copying build/lib/gtdbtk/infer_ranks.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,537 copying build/lib/gtdbtk/ani_screen.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,542 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests 2023-05-14T06:32:35,545 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data 2023-05-14T06:32:35,548 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2023-05-14T06:32:35,549 copying build/lib/gtdbtk/tests/data/genomes/genome_3.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2023-05-14T06:32:35,617 copying build/lib/gtdbtk/tests/data/genomes/genome_1.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2023-05-14T06:32:35,772 copying build/lib/gtdbtk/tests/data/genomes/genome_2.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2023-05-14T06:32:35,844 copying build/lib/gtdbtk/relative_distance.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,850 creating build/bdist.linux-armv7l/wheel/gtdbtk/model 2023-05-14T06:32:35,851 copying build/lib/gtdbtk/model/enum.py -> build/bdist.linux-armv7l/wheel/gtdbtk/model 2023-05-14T06:32:35,855 copying build/lib/gtdbtk/model/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/model 2023-05-14T06:32:35,858 copying build/lib/gtdbtk/classify.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,868 copying build/lib/gtdbtk/trim_msa.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,873 copying build/lib/gtdbtk/markers.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,879 copying build/lib/gtdbtk/main.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,885 copying build/lib/gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,890 creating build/bdist.linux-armv7l/wheel/gtdbtk/config 2023-05-14T06:32:35,891 copying build/lib/gtdbtk/config/output.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config 2023-05-14T06:32:35,896 copying build/lib/gtdbtk/config/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config 2023-05-14T06:32:35,899 copying build/lib/gtdbtk/config/common.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config 2023-05-14T06:32:35,903 copying build/lib/gtdbtk/decorate.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,908 copying build/lib/gtdbtk/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,912 copying build/lib/gtdbtk/split.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,917 copying build/lib/gtdbtk/__main__.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,921 copying build/lib/gtdbtk/cli.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,927 creating build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2023-05-14T06:32:35,929 copying build/lib/gtdbtk/pipeline/align.py -> build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2023-05-14T06:32:35,933 copying build/lib/gtdbtk/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2023-05-14T06:32:35,936 copying build/lib/gtdbtk/pipeline/export_msa.py -> build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2023-05-14T06:32:35,941 creating build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,942 copying build/lib/gtdbtk/biolib_lite/logger.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,947 copying build/lib/gtdbtk/biolib_lite/prodigal_biolib.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,952 copying build/lib/gtdbtk/biolib_lite/taxonomy.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,957 copying build/lib/gtdbtk/biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,960 copying build/lib/gtdbtk/biolib_lite/newick.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,963 copying build/lib/gtdbtk/biolib_lite/custom_help_formatter.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,967 copying build/lib/gtdbtk/biolib_lite/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,971 copying build/lib/gtdbtk/biolib_lite/seq_io.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,975 copying build/lib/gtdbtk/biolib_lite/parallel.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,980 copying build/lib/gtdbtk/biolib_lite/execute.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,985 copying build/lib/gtdbtk/biolib_lite/common.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-05-14T06:32:35,990 copying build/lib/gtdbtk/reroot_tree.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-05-14T06:32:35,995 creating build/bdist.linux-armv7l/wheel/tests 2023-05-14T06:32:35,998 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-05-14T06:32:36,000 copying build/lib/tests/test_gtdbtk/test_trim_msa.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-05-14T06:32:36,005 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2023-05-14T06:32:36,007 copying build/lib/tests/test_gtdbtk/test_external/test_fasttree.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2023-05-14T06:32:36,010 copying build/lib/tests/test_gtdbtk/test_external/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2023-05-14T06:32:36,013 copying build/lib/tests/test_gtdbtk/test_external/test_fastani.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2023-05-14T06:32:36,017 copying build/lib/tests/test_gtdbtk/test_tools.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-05-14T06:32:36,021 copying build/lib/tests/test_gtdbtk/test_markers.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-05-14T06:32:36,026 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files 2023-05-14T06:32:36,027 copying build/lib/tests/test_gtdbtk/test_files/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files 2023-05-14T06:32:36,032 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_marker 2023-05-14T06:32:36,033 copying build/lib/tests/test_gtdbtk/test_files/test_marker/test_tophit.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_marker 2023-05-14T06:32:36,038 copying build/lib/tests/test_gtdbtk/test_files/test_marker/test_copy_number.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_marker 2023-05-14T06:32:36,043 copying build/lib/tests/test_gtdbtk/test_files/test_marker/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_marker 2023-05-14T06:32:36,046 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_prodigal 2023-05-14T06:32:36,048 copying build/lib/tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_prodigal 2023-05-14T06:32:36,052 copying build/lib/tests/test_gtdbtk/test_files/test_prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_prodigal 2023-05-14T06:32:36,055 copying build/lib/tests/test_gtdbtk/test__main__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-05-14T06:32:36,059 copying build/lib/tests/test_gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-05-14T06:32:36,062 copying build/lib/tests/test_gtdbtk/test_main.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-05-14T06:32:36,067 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:36,069 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_seq_io.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:36,073 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:36,077 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_newick.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:36,080 copying build/lib/tests/test_gtdbtk/test_biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:36,083 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_common.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-05-14T06:32:36,087 copying build/lib/tests/test_classify.py -> build/bdist.linux-armv7l/wheel/tests 2023-05-14T06:32:36,091 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests 2023-05-14T06:32:36,093 copying build/lib/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/tests 2023-05-14T06:32:36,098 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/tests 2023-05-14T06:32:36,101 running install_data 2023-05-14T06:32:36,158 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.3.0.data 2023-05-14T06:32:36,159 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.3.0.data/data 2023-05-14T06:32:36,161 copying LICENSE -> build/bdist.linux-armv7l/wheel/gtdbtk-2.3.0.data/data/ 2023-05-14T06:32:36,167 running install_egg_info 2023-05-14T06:32:36,313 running egg_info 2023-05-14T06:32:36,370 writing gtdbtk.egg-info/PKG-INFO 2023-05-14T06:32:36,375 writing dependency_links to gtdbtk.egg-info/dependency_links.txt 2023-05-14T06:32:36,378 writing entry points to gtdbtk.egg-info/entry_points.txt 2023-05-14T06:32:36,381 writing requirements to gtdbtk.egg-info/requires.txt 2023-05-14T06:32:36,383 writing top-level names to gtdbtk.egg-info/top_level.txt 2023-05-14T06:32:36,475 reading manifest file 'gtdbtk.egg-info/SOURCES.txt' 2023-05-14T06:32:36,484 adding license file 'LICENSE' 2023-05-14T06:32:36,501 writing manifest file 'gtdbtk.egg-info/SOURCES.txt' 2023-05-14T06:32:36,504 Copying gtdbtk.egg-info to build/bdist.linux-armv7l/wheel/gtdbtk-2.3.0-py3.7.egg-info 2023-05-14T06:32:36,528 running install_scripts 2023-05-14T06:32:36,572 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2023-05-14T06:32:36,584 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.3.0.dist-info/WHEEL 2023-05-14T06:32:36,589 creating '/tmp/pip-wheel-9hrm8n0l/gtdbtk-2.3.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-05-14T06:32:36,595 adding 'gtdbtk/__init__.py' 2023-05-14T06:32:36,599 adding 'gtdbtk/__main__.py' 2023-05-14T06:32:36,603 adding 'gtdbtk/ani_rep.py' 2023-05-14T06:32:36,606 adding 'gtdbtk/ani_screen.py' 2023-05-14T06:32:36,633 adding 'gtdbtk/classify.py' 2023-05-14T06:32:36,641 adding 'gtdbtk/cli.py' 2023-05-14T06:32:36,647 adding 'gtdbtk/decorate.py' 2023-05-14T06:32:36,651 adding 'gtdbtk/exceptions.py' 2023-05-14T06:32:36,655 adding 'gtdbtk/infer_ranks.py' 2023-05-14T06:32:36,667 adding 'gtdbtk/main.py' 2023-05-14T06:32:36,677 adding 'gtdbtk/markers.py' 2023-05-14T06:32:36,683 adding 'gtdbtk/misc.py' 2023-05-14T06:32:36,688 adding 'gtdbtk/relative_distance.py' 2023-05-14T06:32:36,692 adding 'gtdbtk/reroot_tree.py' 2023-05-14T06:32:36,697 adding 'gtdbtk/split.py' 2023-05-14T06:32:36,703 adding 'gtdbtk/tools.py' 2023-05-14T06:32:36,708 adding 'gtdbtk/trim_msa.py' 2023-05-14T06:32:36,711 adding 'gtdbtk/biolib_lite/__init__.py' 2023-05-14T06:32:36,714 adding 'gtdbtk/biolib_lite/common.py' 2023-05-14T06:32:36,718 adding 'gtdbtk/biolib_lite/custom_help_formatter.py' 2023-05-14T06:32:36,720 adding 'gtdbtk/biolib_lite/exceptions.py' 2023-05-14T06:32:36,723 adding 'gtdbtk/biolib_lite/execute.py' 2023-05-14T06:32:36,727 adding 'gtdbtk/biolib_lite/logger.py' 2023-05-14T06:32:36,730 adding 'gtdbtk/biolib_lite/newick.py' 2023-05-14T06:32:36,734 adding 'gtdbtk/biolib_lite/parallel.py' 2023-05-14T06:32:36,739 adding 'gtdbtk/biolib_lite/prodigal_biolib.py' 2023-05-14T06:32:36,743 adding 'gtdbtk/biolib_lite/seq_io.py' 2023-05-14T06:32:36,751 adding 'gtdbtk/biolib_lite/taxonomy.py' 2023-05-14T06:32:36,755 adding 'gtdbtk/config/__init__.py' 2023-05-14T06:32:36,759 adding 'gtdbtk/config/common.py' 2023-05-14T06:32:36,762 adding 'gtdbtk/config/output.py' 2023-05-14T06:32:36,766 adding 'gtdbtk/external/__init__.py' 2023-05-14T06:32:36,771 adding 'gtdbtk/external/fastani.py' 2023-05-14T06:32:36,774 adding 'gtdbtk/external/fasttree.py' 2023-05-14T06:32:36,779 adding 'gtdbtk/external/hmm_aligner.py' 2023-05-14T06:32:36,783 adding 'gtdbtk/external/mash.py' 2023-05-14T06:32:36,787 adding 'gtdbtk/external/pfam_search.py' 2023-05-14T06:32:36,791 adding 'gtdbtk/external/pplacer.py' 2023-05-14T06:32:36,795 adding 'gtdbtk/external/prodigal.py' 2023-05-14T06:32:36,799 adding 'gtdbtk/external/tigrfam_search.py' 2023-05-14T06:32:36,802 adding 'gtdbtk/external/pypfam/__init__.py' 2023-05-14T06:32:36,806 adding 'gtdbtk/external/pypfam/HMM/HMMMatch.py' 2023-05-14T06:32:36,809 adding 'gtdbtk/external/pypfam/HMM/HMMResults.py' 2023-05-14T06:32:36,815 adding 'gtdbtk/external/pypfam/HMM/HMMResultsIO.py' 2023-05-14T06:32:36,818 adding 'gtdbtk/external/pypfam/HMM/HMMSequence.py' 2023-05-14T06:32:36,821 adding 'gtdbtk/external/pypfam/HMM/HMMUnit.py' 2023-05-14T06:32:36,823 adding 'gtdbtk/external/pypfam/HMM/__init__.py' 2023-05-14T06:32:36,830 adding 'gtdbtk/external/pypfam/Scan/PfamScan.py' 2023-05-14T06:32:36,833 adding 'gtdbtk/external/pypfam/Scan/__init__.py' 2023-05-14T06:32:36,837 adding 'gtdbtk/files/__init__.py' 2023-05-14T06:32:36,839 adding 'gtdbtk/files/batchfile.py' 2023-05-14T06:32:36,843 adding 'gtdbtk/files/classify_summary.py' 2023-05-14T06:32:36,846 adding 'gtdbtk/files/gtdb_radii.py' 2023-05-14T06:32:36,848 adding 'gtdbtk/files/marker_info.py' 2023-05-14T06:32:36,851 adding 'gtdbtk/files/missing_genomes.py' 2023-05-14T06:32:36,854 adding 'gtdbtk/files/pplacer_classification.py' 2023-05-14T06:32:36,857 adding 'gtdbtk/files/red_dict.py' 2023-05-14T06:32:36,860 adding 'gtdbtk/files/stage_logger.py' 2023-05-14T06:32:36,864 adding 'gtdbtk/files/tree_mapping.py' 2023-05-14T06:32:36,867 adding 'gtdbtk/files/marker/__init__.py' 2023-05-14T06:32:36,870 adding 'gtdbtk/files/marker/copy_number.py' 2023-05-14T06:32:36,874 adding 'gtdbtk/files/marker/tophit.py' 2023-05-14T06:32:36,878 adding 'gtdbtk/files/prodigal/__init__.py' 2023-05-14T06:32:36,880 adding 'gtdbtk/files/prodigal/tln_table.py' 2023-05-14T06:32:36,883 adding 'gtdbtk/files/prodigal/tln_table_summary.py' 2023-05-14T06:32:36,887 adding 'gtdbtk/model/__init__.py' 2023-05-14T06:32:36,889 adding 'gtdbtk/model/enum.py' 2023-05-14T06:32:36,892 adding 'gtdbtk/pipeline/__init__.py' 2023-05-14T06:32:36,896 adding 'gtdbtk/pipeline/align.py' 2023-05-14T06:32:36,899 adding 'gtdbtk/pipeline/export_msa.py' 2023-05-14T06:32:40,893 adding 'gtdbtk/tests/data/genomes/genome_1.fna' 2023-05-14T06:32:42,728 adding 'gtdbtk/tests/data/genomes/genome_2.fna' 2023-05-14T06:32:44,400 adding 'gtdbtk/tests/data/genomes/genome_3.fna' 2023-05-14T06:32:44,441 adding 'gtdbtk-2.3.0.data/data/LICENSE' 2023-05-14T06:32:44,448 adding 'tests/__init__.py' 2023-05-14T06:32:44,450 adding 'tests/common.py' 2023-05-14T06:32:44,453 adding 'tests/test_classify.py' 2023-05-14T06:32:44,458 adding 'tests/test_cli.py' 2023-05-14T06:32:44,461 adding 'tests/test_gtdbtk/__init__.py' 2023-05-14T06:32:44,465 adding 'tests/test_gtdbtk/test__main__.py' 2023-05-14T06:32:44,469 adding 'tests/test_gtdbtk/test_main.py' 2023-05-14T06:32:44,472 adding 'tests/test_gtdbtk/test_markers.py' 2023-05-14T06:32:44,476 adding 'tests/test_gtdbtk/test_tools.py' 2023-05-14T06:32:44,478 adding 'tests/test_gtdbtk/test_trim_msa.py' 2023-05-14T06:32:44,482 adding 'tests/test_gtdbtk/test_biolib_lite/__init__.py' 2023-05-14T06:32:44,485 adding 'tests/test_gtdbtk/test_biolib_lite/test_common.py' 2023-05-14T06:32:44,487 adding 'tests/test_gtdbtk/test_biolib_lite/test_newick.py' 2023-05-14T06:32:44,490 adding 'tests/test_gtdbtk/test_biolib_lite/test_seq_io.py' 2023-05-14T06:32:44,493 adding 'tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py' 2023-05-14T06:32:44,496 adding 'tests/test_gtdbtk/test_external/__init__.py' 2023-05-14T06:32:44,499 adding 'tests/test_gtdbtk/test_external/test_fastani.py' 2023-05-14T06:32:44,502 adding 'tests/test_gtdbtk/test_external/test_fasttree.py' 2023-05-14T06:32:44,506 adding 'tests/test_gtdbtk/test_files/__init__.py' 2023-05-14T06:32:44,509 adding 'tests/test_gtdbtk/test_files/test_marker/__init__.py' 2023-05-14T06:32:44,512 adding 'tests/test_gtdbtk/test_files/test_marker/test_copy_number.py' 2023-05-14T06:32:44,516 adding 'tests/test_gtdbtk/test_files/test_marker/test_tophit.py' 2023-05-14T06:32:44,519 adding 'tests/test_gtdbtk/test_files/test_prodigal/__init__.py' 2023-05-14T06:32:44,522 adding 'tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py' 2023-05-14T06:32:44,536 adding 'gtdbtk-2.3.0.dist-info/LICENSE' 2023-05-14T06:32:44,540 adding 'gtdbtk-2.3.0.dist-info/METADATA' 2023-05-14T06:32:44,543 adding 'gtdbtk-2.3.0.dist-info/WHEEL' 2023-05-14T06:32:44,545 adding 'gtdbtk-2.3.0.dist-info/entry_points.txt' 2023-05-14T06:32:44,546 adding 'gtdbtk-2.3.0.dist-info/top_level.txt' 2023-05-14T06:32:44,550 adding 'gtdbtk-2.3.0.dist-info/RECORD' 2023-05-14T06:32:44,629 removing build/bdist.linux-armv7l/wheel 2023-05-14T06:32:44,847 Building wheel for gtdbtk (setup.py): finished with status 'done' 2023-05-14T06:32:44,907 Created wheel for gtdbtk: filename=gtdbtk-2.3.0-py3-none-any.whl size=1829444 sha256=c67a62ad20275141b009be21cc871ec657a8ad737c61d0e6866b1b0b25778f2f 2023-05-14T06:32:44,909 Stored in directory: /tmp/pip-ephem-wheel-cache-67fq5ora/wheels/8d/29/48/6aa38b5653a8190718c44d59c5db1e45ea682b41b1581d5604 2023-05-14T06:32:44,951 Successfully built gtdbtk 2023-05-14T06:32:45,077 Removed build tracker: '/tmp/pip-build-tracker-5ggcvboj'