2023-03-16T04:27:39,662 Created temporary directory: /tmp/pip-ephem-wheel-cache-11oak7ot 2023-03-16T04:27:39,667 Created temporary directory: /tmp/pip-build-tracker-424uunun 2023-03-16T04:27:39,668 Initialized build tracking at /tmp/pip-build-tracker-424uunun 2023-03-16T04:27:39,668 Created build tracker: /tmp/pip-build-tracker-424uunun 2023-03-16T04:27:39,669 Entered build tracker: /tmp/pip-build-tracker-424uunun 2023-03-16T04:27:39,670 Created temporary directory: /tmp/pip-wheel-cttts9xt 2023-03-16T04:27:39,680 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2023-03-16T04:27:39,686 Created temporary directory: /tmp/pip-ephem-wheel-cache-_dm5rcyn 2023-03-16T04:27:39,747 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-03-16T04:27:39,753 2 location(s) to search for versions of gtdbtk: 2023-03-16T04:27:39,753 * https://pypi.org/simple/gtdbtk/ 2023-03-16T04:27:39,753 * https://www.piwheels.org/simple/gtdbtk/ 2023-03-16T04:27:39,754 Fetching project page and analyzing links: https://pypi.org/simple/gtdbtk/ 2023-03-16T04:27:39,756 Getting page https://pypi.org/simple/gtdbtk/ 2023-03-16T04:27:39,759 Found index url https://pypi.org/simple 2023-03-16T04:27:39,956 Fetched page https://pypi.org/simple/gtdbtk/ as application/vnd.pypi.simple.v1+json 2023-03-16T04:27:39,990 Found link https://files.pythonhosted.org/packages/77/1d/a47e727062761ea6108b1be340d24c711131df11415d82cdb30bcb51738b/gtdbtk-0.0.1.tar.gz (from https://pypi.org/simple/gtdbtk/), 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2023-03-16T04:27:40,039 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/48/bc/6f4c477f7fe9d4d67abd5a2843c88533570cd482a63e35c1f2589393126f/gtdbtk-2.2.2-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-03-16T04:27:40,040 Found link https://files.pythonhosted.org/packages/ee/bb/539be0884928b9906f9a4ffb0118e4501f6f203afda9fe1a5c40b231d150/gtdbtk-2.2.2.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.2.2 2023-03-16T04:27:40,040 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/02/43/0ba90c5591bea3ec5f2340724f0b5a12da4fe2cebe5a79022be66b406917/gtdbtk-2.2.3-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-03-16T04:27:40,042 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 2023-03-16T04:27:40,042 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) 2023-03-16T04:27:40,044 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 2023-03-16T04:27:40,044 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) 2023-03-16T04:27:40,046 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 2023-03-16T04:27:40,047 Fetching project page and analyzing links: https://www.piwheels.org/simple/gtdbtk/ 2023-03-16T04:27:40,047 Getting page https://www.piwheels.org/simple/gtdbtk/ 2023-03-16T04:27:40,050 Found index url https://www.piwheels.org/simple 2023-03-16T04:27:40,262 Fetched page https://www.piwheels.org/simple/gtdbtk/ as text/html 2023-03-16T04:27:40,295 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-2.2.4-py3-none-any.whl#sha256=f20682a7cd468122eebde8ada2d62256fda4c792fb24359eb3cec4802065cfb3 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-03-16T04:27:40,295 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) 2023-03-16T04:27:40,296 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) 2023-03-16T04:27:40,296 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) 2023-03-16T04:27:40,297 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-2.1.1-py3-none-any.whl#sha256=9ab09353c8901bf41d042f5dd678b8e4a0b44bd88b9edf99c113095e719fa689 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-03-16T04:27:40,297 Skipping link: No binaries permitted for gtdbtk: 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(from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-03-16T04:27:40,299 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) 2023-03-16T04:27:40,300 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) 2023-03-16T04:27:40,300 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-1.4.1-py3-none-any.whl#sha256=5bf60e34c9532ee96689ca34330f5f4ad6d344bac28ebdd1925ee4d0326e4345 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-03-16T04:27:40,301 Skipping link: No binaries permitted for gtdbtk: 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(from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-03-16T04:27:40,303 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) 2023-03-16T04:27:40,304 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) 2023-03-16T04:27:40,304 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-1.0.1-py3-none-any.whl#sha256=4f17b5e884096c03286b38720b63f262572ca3f8c6fcce36fb3a543aa1c45840 (from https://www.piwheels.org/simple/gtdbtk/) (requires-python:>=3.6) 2023-03-16T04:27:40,305 Skipping link: No binaries permitted for gtdbtk: 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2023-03-16T04:27:40,307 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.3.0-py3-none-any.whl#sha256=967042d7d0fb425c296cb4370268936f5efab1086c93bba32aa75b05eb61d5eb (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,307 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.2.2-py3-none-any.whl#sha256=0f2f51b4c73c58071c0e693201460c6b3d67d4a956368ed7b2df1555a9a2d5e3 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,308 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.2.1-py3-none-any.whl#sha256=c3dda689b923a8788e648223335928c657b054fecd8eeb78e5e48e7be5cd3df4 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,308 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.1.6-py3-none-any.whl#sha256=dd5a03ce2b22ffe66b776fb405e95f4f7a70fed4ba1a7087db1de973f4e22fef (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,309 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.1.3-py3-none-any.whl#sha256=02c694c6199f0c5db1056131515f4272e703ea6beceffb16678ad3eb24358d8d (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,309 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.1.2-py3-none-any.whl#sha256=4b75117a7c332187dfb858bffe54fbadf2a9f39960fcc21d2bce0db59b6e114d (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,310 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.1.1-py3-none-any.whl#sha256=c971843754fb3c11f48ead52c04bc7bd86ddeab289fd362e9e24a9c0fd1f2879 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,310 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-0.0.5-py3-none-any.whl#sha256=ae582d50ba58fd74c73ec1a0a37f427d3343e9f20fe45389ee098ed5ef99e3f4 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,313 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.0.4b3-py3-none-any.whl#sha256=2d5b93346985d7186695de6a4dc010b9abf4e108ec438f449b74705eb7191fc1 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,313 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.0.4b2-py3-none-any.whl#sha256=177fdc2bb5e28ee60a931441956acff6b853871395a611bc1404c7f78a2a3f85 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,314 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.0.4b1-py3-none-any.whl#sha256=cffebc36f92b7947522a0e8d0fe11d9a7051a036352eb036ca90db5a14e591e1 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,314 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.0.4b0-py3-none-any.whl#sha256=1a96ec79753b589c69bb9c881bdedfc0aef683779cb926da47f22e85e77bb203 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,315 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-0.0.3-py3-none-any.whl#sha256=6670c151da83c393482600e07c463c74de77ab5776f88a4978d1b7defa71f852 (from https://www.piwheels.org/simple/gtdbtk/) 2023-03-16T04:27:40,315 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/) 2023-03-16T04:27:40,316 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/) 2023-03-16T04:27:40,316 Skipping link: not a file: https://www.piwheels.org/simple/gtdbtk/ 2023-03-16T04:27:40,317 Skipping link: not a file: https://pypi.org/simple/gtdbtk/ 2023-03-16T04:27:40,364 Given no hashes to check 1 links for project 'gtdbtk': discarding no candidates 2023-03-16T04:27:40,395 Collecting gtdbtk==2.2.5 2023-03-16T04:27:40,399 Created temporary directory: /tmp/pip-unpack-xtw2x39t 2023-03-16T04:27:40,680 Downloading gtdbtk-2.2.5.tar.gz (1.7 MB) 2023-03-16T04:27:42,271 Added gtdbtk==2.2.5 from https://files.pythonhosted.org/packages/29/7b/3aed07a21e615b1b3f0a2fbcf8c7032ffe50d45fd4ffba50f59a12aab20f/gtdbtk-2.2.5.tar.gz to build tracker '/tmp/pip-build-tracker-424uunun' 2023-03-16T04:27:42,275 Running setup.py (path:/tmp/pip-wheel-cttts9xt/gtdbtk_a295eb167e744d3fb1bd95e00c689b09/setup.py) egg_info for package gtdbtk 2023-03-16T04:27:42,276 Created temporary directory: /tmp/pip-pip-egg-info-3c84a64t 2023-03-16T04:27:42,277 Preparing metadata (setup.py): started 2023-03-16T04:27:42,279 Running command python setup.py egg_info 2023-03-16T04:27:43,787 running egg_info 2023-03-16T04:27:43,789 creating /tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info 2023-03-16T04:27:43,846 writing /tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info/PKG-INFO 2023-03-16T04:27:43,851 writing dependency_links to /tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info/dependency_links.txt 2023-03-16T04:27:43,855 writing entry points to /tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info/entry_points.txt 2023-03-16T04:27:43,858 writing requirements to /tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info/requires.txt 2023-03-16T04:27:43,860 writing top-level names to /tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info/top_level.txt 2023-03-16T04:27:43,862 writing manifest file '/tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info/SOURCES.txt' 2023-03-16T04:27:44,077 reading manifest file '/tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info/SOURCES.txt' 2023-03-16T04:27:44,081 adding license file 'LICENSE' 2023-03-16T04:27:44,094 writing manifest file '/tmp/pip-pip-egg-info-3c84a64t/gtdbtk.egg-info/SOURCES.txt' 2023-03-16T04:27:44,211 Preparing metadata (setup.py): finished with status 'done' 2023-03-16T04:27:44,225 Source in /tmp/pip-wheel-cttts9xt/gtdbtk_a295eb167e744d3fb1bd95e00c689b09 has version 2.2.5, which satisfies requirement gtdbtk==2.2.5 from https://files.pythonhosted.org/packages/29/7b/3aed07a21e615b1b3f0a2fbcf8c7032ffe50d45fd4ffba50f59a12aab20f/gtdbtk-2.2.5.tar.gz 2023-03-16T04:27:44,227 Removed gtdbtk==2.2.5 from https://files.pythonhosted.org/packages/29/7b/3aed07a21e615b1b3f0a2fbcf8c7032ffe50d45fd4ffba50f59a12aab20f/gtdbtk-2.2.5.tar.gz from build tracker '/tmp/pip-build-tracker-424uunun' 2023-03-16T04:27:44,243 Created temporary directory: /tmp/pip-unpack-1y29m4rd 2023-03-16T04:27:44,245 Building wheels for collected packages: gtdbtk 2023-03-16T04:27:44,254 Created temporary directory: /tmp/pip-wheel-vqaen2j6 2023-03-16T04:27:44,255 Building wheel for gtdbtk (setup.py): started 2023-03-16T04:27:44,257 Destination directory: /tmp/pip-wheel-vqaen2j6 2023-03-16T04:27:44,257 Running command python setup.py bdist_wheel 2023-03-16T04:27:46,310 running bdist_wheel 2023-03-16T04:27:46,494 running build 2023-03-16T04:27:46,494 running build_py 2023-03-16T04:27:46,563 creating build 2023-03-16T04:27:46,563 creating build/lib 2023-03-16T04:27:46,566 creating build/lib/gtdbtk 2023-03-16T04:27:46,568 copying gtdbtk/infer_ranks.py -> build/lib/gtdbtk 2023-03-16T04:27:46,573 copying gtdbtk/reroot_tree.py -> build/lib/gtdbtk 2023-03-16T04:27:46,577 copying gtdbtk/main.py -> build/lib/gtdbtk 2023-03-16T04:27:46,585 copying gtdbtk/__init__.py -> build/lib/gtdbtk 2023-03-16T04:27:46,592 copying gtdbtk/tools.py -> build/lib/gtdbtk 2023-03-16T04:27:46,603 copying gtdbtk/misc.py -> build/lib/gtdbtk 2023-03-16T04:27:46,607 copying gtdbtk/ani_screen.py -> build/lib/gtdbtk 2023-03-16T04:27:46,612 copying gtdbtk/decorate.py -> build/lib/gtdbtk 2023-03-16T04:27:46,619 copying gtdbtk/cli.py -> build/lib/gtdbtk 2023-03-16T04:27:46,626 copying gtdbtk/split.py -> build/lib/gtdbtk 2023-03-16T04:27:46,631 copying gtdbtk/relative_distance.py -> build/lib/gtdbtk 2023-03-16T04:27:46,638 copying gtdbtk/__main__.py -> build/lib/gtdbtk 2023-03-16T04:27:46,645 copying gtdbtk/classify.py -> build/lib/gtdbtk 2023-03-16T04:27:46,663 copying gtdbtk/exceptions.py -> build/lib/gtdbtk 2023-03-16T04:27:46,675 copying gtdbtk/ani_rep.py -> build/lib/gtdbtk 2023-03-16T04:27:46,684 copying gtdbtk/trim_msa.py -> build/lib/gtdbtk 2023-03-16T04:27:46,692 copying gtdbtk/markers.py -> build/lib/gtdbtk 2023-03-16T04:27:46,703 creating build/lib/tests 2023-03-16T04:27:46,707 copying tests/test_classify.py -> build/lib/tests 2023-03-16T04:27:46,714 copying tests/__init__.py -> build/lib/tests 2023-03-16T04:27:46,718 copying tests/test_cli.py -> build/lib/tests 2023-03-16T04:27:46,723 copying tests/common.py -> build/lib/tests 2023-03-16T04:27:46,730 creating build/lib/gtdbtk/model 2023-03-16T04:27:46,732 copying gtdbtk/model/__init__.py -> build/lib/gtdbtk/model 2023-03-16T04:27:46,736 copying gtdbtk/model/enum.py -> build/lib/gtdbtk/model 2023-03-16T04:27:46,743 creating build/lib/gtdbtk/files 2023-03-16T04:27:46,745 copying gtdbtk/files/tree_mapping.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,750 copying gtdbtk/files/__init__.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,754 copying gtdbtk/files/stage_logger.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,759 copying gtdbtk/files/pplacer_classification.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,764 copying gtdbtk/files/gtdb_radii.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,768 copying gtdbtk/files/classify_summary.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,773 copying gtdbtk/files/red_dict.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,778 copying gtdbtk/files/marker_info.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,781 copying gtdbtk/files/batchfile.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,785 copying gtdbtk/files/missing_genomes.py -> build/lib/gtdbtk/files 2023-03-16T04:27:46,790 creating build/lib/gtdbtk/pipeline 2023-03-16T04:27:46,791 copying gtdbtk/pipeline/__init__.py -> build/lib/gtdbtk/pipeline 2023-03-16T04:27:46,795 copying gtdbtk/pipeline/export_msa.py -> build/lib/gtdbtk/pipeline 2023-03-16T04:27:46,805 copying gtdbtk/pipeline/align.py -> build/lib/gtdbtk/pipeline 2023-03-16T04:27:46,812 creating build/lib/gtdbtk/external 2023-03-16T04:27:46,814 copying gtdbtk/external/fasttree.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,818 copying gtdbtk/external/__init__.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,821 copying gtdbtk/external/fastani.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,826 copying gtdbtk/external/pfam_search.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,830 copying gtdbtk/external/mash.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,835 copying gtdbtk/external/prodigal.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,839 copying gtdbtk/external/hmm_aligner.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,844 copying gtdbtk/external/pplacer.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,849 copying gtdbtk/external/tigrfam_search.py -> build/lib/gtdbtk/external 2023-03-16T04:27:46,856 creating build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,858 copying gtdbtk/biolib_lite/seq_io.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,862 copying gtdbtk/biolib_lite/__init__.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,865 copying gtdbtk/biolib_lite/taxonomy.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,871 copying gtdbtk/biolib_lite/prodigal_biolib.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,877 copying gtdbtk/biolib_lite/common.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,881 copying gtdbtk/biolib_lite/parallel.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,886 copying gtdbtk/biolib_lite/execute.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,890 copying gtdbtk/biolib_lite/newick.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,894 copying gtdbtk/biolib_lite/exceptions.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,897 copying gtdbtk/biolib_lite/custom_help_formatter.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,901 copying gtdbtk/biolib_lite/logger.py -> build/lib/gtdbtk/biolib_lite 2023-03-16T04:27:46,907 creating build/lib/gtdbtk/config 2023-03-16T04:27:46,908 copying gtdbtk/config/output.py -> build/lib/gtdbtk/config 2023-03-16T04:27:46,913 copying gtdbtk/config/__init__.py -> build/lib/gtdbtk/config 2023-03-16T04:27:46,916 copying gtdbtk/config/config.py -> build/lib/gtdbtk/config 2023-03-16T04:27:46,922 creating build/lib/gtdbtk/files/marker 2023-03-16T04:27:46,924 copying gtdbtk/files/marker/copy_number.py -> build/lib/gtdbtk/files/marker 2023-03-16T04:27:46,929 copying gtdbtk/files/marker/__init__.py -> build/lib/gtdbtk/files/marker 2023-03-16T04:27:46,932 copying gtdbtk/files/marker/tophit.py -> build/lib/gtdbtk/files/marker 2023-03-16T04:27:46,937 creating build/lib/gtdbtk/files/prodigal 2023-03-16T04:27:46,939 copying gtdbtk/files/prodigal/__init__.py -> build/lib/gtdbtk/files/prodigal 2023-03-16T04:27:46,942 copying gtdbtk/files/prodigal/tln_table.py -> build/lib/gtdbtk/files/prodigal 2023-03-16T04:27:46,946 copying gtdbtk/files/prodigal/tln_table_summary.py -> build/lib/gtdbtk/files/prodigal 2023-03-16T04:27:46,951 creating build/lib/gtdbtk/external/pypfam 2023-03-16T04:27:46,953 copying gtdbtk/external/pypfam/__init__.py -> build/lib/gtdbtk/external/pypfam 2023-03-16T04:27:46,957 creating build/lib/gtdbtk/external/pypfam/Scan 2023-03-16T04:27:46,959 copying gtdbtk/external/pypfam/Scan/__init__.py -> build/lib/gtdbtk/external/pypfam/Scan 2023-03-16T04:27:46,962 copying gtdbtk/external/pypfam/Scan/PfamScan.py -> build/lib/gtdbtk/external/pypfam/Scan 2023-03-16T04:27:46,969 creating build/lib/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:46,971 copying gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:46,977 copying gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:46,980 copying gtdbtk/external/pypfam/HMM/__init__.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:46,983 copying gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:46,987 copying gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:46,991 copying gtdbtk/external/pypfam/HMM/HMMResults.py -> build/lib/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:46,997 creating build/lib/tests/test_gtdbtk 2023-03-16T04:27:46,998 copying tests/test_gtdbtk/__init__.py -> build/lib/tests/test_gtdbtk 2023-03-16T04:27:47,002 copying tests/test_gtdbtk/test_trim_msa.py -> build/lib/tests/test_gtdbtk 2023-03-16T04:27:47,006 copying tests/test_gtdbtk/test_tools.py -> build/lib/tests/test_gtdbtk 2023-03-16T04:27:47,010 copying tests/test_gtdbtk/test__main__.py -> build/lib/tests/test_gtdbtk 2023-03-16T04:27:47,015 copying tests/test_gtdbtk/test_main.py -> build/lib/tests/test_gtdbtk 2023-03-16T04:27:47,019 copying tests/test_gtdbtk/test_markers.py -> build/lib/tests/test_gtdbtk 2023-03-16T04:27:47,024 creating build/lib/tests/test_gtdbtk/test_external 2023-03-16T04:27:47,026 copying tests/test_gtdbtk/test_external/__init__.py -> build/lib/tests/test_gtdbtk/test_external 2023-03-16T04:27:47,029 copying tests/test_gtdbtk/test_external/test_fastani.py -> build/lib/tests/test_gtdbtk/test_external 2023-03-16T04:27:47,033 copying tests/test_gtdbtk/test_external/test_fasttree.py -> build/lib/tests/test_gtdbtk/test_external 2023-03-16T04:27:47,038 creating build/lib/tests/test_gtdbtk/test_files 2023-03-16T04:27:47,040 copying tests/test_gtdbtk/test_files/__init__.py -> build/lib/tests/test_gtdbtk/test_files 2023-03-16T04:27:47,045 creating build/lib/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:47,047 copying tests/test_gtdbtk/test_biolib_lite/test_seq_io.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:47,053 copying tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:47,057 copying tests/test_gtdbtk/test_biolib_lite/__init__.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:47,060 copying tests/test_gtdbtk/test_biolib_lite/test_newick.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:47,064 copying tests/test_gtdbtk/test_biolib_lite/test_common.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:47,069 creating build/lib/tests/test_gtdbtk/test_files/test_prodigal 2023-03-16T04:27:47,070 copying tests/test_gtdbtk/test_files/test_prodigal/__init__.py -> build/lib/tests/test_gtdbtk/test_files/test_prodigal 2023-03-16T04:27:47,074 copying tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py -> build/lib/tests/test_gtdbtk/test_files/test_prodigal 2023-03-16T04:27:47,079 creating build/lib/tests/test_gtdbtk/test_files/test_marker 2023-03-16T04:27:47,080 copying tests/test_gtdbtk/test_files/test_marker/__init__.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2023-03-16T04:27:47,084 copying tests/test_gtdbtk/test_files/test_marker/test_copy_number.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2023-03-16T04:27:47,089 copying tests/test_gtdbtk/test_files/test_marker/test_tophit.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2023-03-16T04:27:47,101 creating build/lib/gtdbtk/tests 2023-03-16T04:27:47,102 creating build/lib/gtdbtk/tests/data 2023-03-16T04:27:47,103 creating build/lib/gtdbtk/tests/data/genomes 2023-03-16T04:27:47,105 copying gtdbtk/tests/data/genomes/genome_1.fna -> build/lib/gtdbtk/tests/data/genomes 2023-03-16T04:27:47,264 copying gtdbtk/tests/data/genomes/genome_2.fna -> build/lib/gtdbtk/tests/data/genomes 2023-03-16T04:27:47,332 copying gtdbtk/tests/data/genomes/genome_3.fna -> build/lib/gtdbtk/tests/data/genomes 2023-03-16T04:27:47,493 /usr/local/lib/python3.7/dist-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 2023-03-16T04:27:47,494 setuptools.SetuptoolsDeprecationWarning, 2023-03-16T04:27:47,556 installing to build/bdist.linux-armv7l/wheel 2023-03-16T04:27:47,557 running install 2023-03-16T04:27:47,616 running install_lib 2023-03-16T04:27:47,680 creating build/bdist.linux-armv7l 2023-03-16T04:27:47,681 creating build/bdist.linux-armv7l/wheel 2023-03-16T04:27:47,686 creating build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,689 creating build/bdist.linux-armv7l/wheel/gtdbtk/model 2023-03-16T04:27:47,691 copying build/lib/gtdbtk/model/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/model 2023-03-16T04:27:47,695 copying build/lib/gtdbtk/model/enum.py -> build/bdist.linux-armv7l/wheel/gtdbtk/model 2023-03-16T04:27:47,699 copying build/lib/gtdbtk/infer_ranks.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,704 copying build/lib/gtdbtk/reroot_tree.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,708 copying build/lib/gtdbtk/main.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,715 copying build/lib/gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,718 copying build/lib/gtdbtk/tools.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,725 creating build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,726 copying build/lib/gtdbtk/files/tree_mapping.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,731 copying build/lib/gtdbtk/files/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,733 copying build/lib/gtdbtk/files/stage_logger.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,738 copying build/lib/gtdbtk/files/pplacer_classification.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,742 creating build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2023-03-16T04:27:47,744 copying build/lib/gtdbtk/files/marker/copy_number.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2023-03-16T04:27:47,749 copying build/lib/gtdbtk/files/marker/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2023-03-16T04:27:47,752 copying build/lib/gtdbtk/files/marker/tophit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2023-03-16T04:27:47,756 copying build/lib/gtdbtk/files/gtdb_radii.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,760 copying build/lib/gtdbtk/files/classify_summary.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,765 creating build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2023-03-16T04:27:47,767 copying build/lib/gtdbtk/files/prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2023-03-16T04:27:47,770 copying build/lib/gtdbtk/files/prodigal/tln_table.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2023-03-16T04:27:47,773 copying build/lib/gtdbtk/files/prodigal/tln_table_summary.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2023-03-16T04:27:47,777 copying build/lib/gtdbtk/files/red_dict.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,781 copying build/lib/gtdbtk/files/marker_info.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,784 copying build/lib/gtdbtk/files/batchfile.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,788 copying build/lib/gtdbtk/files/missing_genomes.py -> build/bdist.linux-armv7l/wheel/gtdbtk/files 2023-03-16T04:27:47,791 copying build/lib/gtdbtk/misc.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,796 copying build/lib/gtdbtk/ani_screen.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,799 copying build/lib/gtdbtk/decorate.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:47,805 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests 2023-03-16T04:27:47,808 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data 2023-03-16T04:27:47,811 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2023-03-16T04:27:47,812 copying build/lib/gtdbtk/tests/data/genomes/genome_1.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2023-03-16T04:27:47,955 copying build/lib/gtdbtk/tests/data/genomes/genome_2.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2023-03-16T04:27:48,019 copying build/lib/gtdbtk/tests/data/genomes/genome_3.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2023-03-16T04:27:48,081 copying build/lib/gtdbtk/cli.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,087 copying build/lib/gtdbtk/split.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,093 creating build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2023-03-16T04:27:48,095 copying build/lib/gtdbtk/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2023-03-16T04:27:48,099 copying build/lib/gtdbtk/pipeline/export_msa.py -> build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2023-03-16T04:27:48,103 copying build/lib/gtdbtk/pipeline/align.py -> build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2023-03-16T04:27:48,108 copying build/lib/gtdbtk/relative_distance.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,115 creating build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,117 copying build/lib/gtdbtk/external/fasttree.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,123 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam 2023-03-16T04:27:48,126 copying build/lib/gtdbtk/external/pypfam/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam 2023-03-16T04:27:48,131 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan 2023-03-16T04:27:48,133 copying build/lib/gtdbtk/external/pypfam/Scan/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan 2023-03-16T04:27:48,137 copying build/lib/gtdbtk/external/pypfam/Scan/PfamScan.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan 2023-03-16T04:27:48,143 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:48,146 copying build/lib/gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:48,152 copying build/lib/gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:48,157 copying build/lib/gtdbtk/external/pypfam/HMM/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:48,160 copying build/lib/gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:48,164 copying build/lib/gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:48,169 copying build/lib/gtdbtk/external/pypfam/HMM/HMMResults.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2023-03-16T04:27:48,173 copying build/lib/gtdbtk/external/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,177 copying build/lib/gtdbtk/external/fastani.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,182 copying build/lib/gtdbtk/external/pfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,187 copying build/lib/gtdbtk/external/mash.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,192 copying build/lib/gtdbtk/external/prodigal.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,197 copying build/lib/gtdbtk/external/hmm_aligner.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,203 copying build/lib/gtdbtk/external/pplacer.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,208 copying build/lib/gtdbtk/external/tigrfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external 2023-03-16T04:27:48,213 copying build/lib/gtdbtk/__main__.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,218 copying build/lib/gtdbtk/classify.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,229 copying build/lib/gtdbtk/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,233 copying build/lib/gtdbtk/ani_rep.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,239 copying build/lib/gtdbtk/trim_msa.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,245 creating build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,248 copying build/lib/gtdbtk/biolib_lite/seq_io.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,253 copying build/lib/gtdbtk/biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,257 copying build/lib/gtdbtk/biolib_lite/taxonomy.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,263 copying build/lib/gtdbtk/biolib_lite/prodigal_biolib.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,268 copying build/lib/gtdbtk/biolib_lite/common.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,273 copying build/lib/gtdbtk/biolib_lite/parallel.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,279 copying build/lib/gtdbtk/biolib_lite/execute.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,283 copying build/lib/gtdbtk/biolib_lite/newick.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,287 copying build/lib/gtdbtk/biolib_lite/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,290 copying build/lib/gtdbtk/biolib_lite/custom_help_formatter.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,295 copying build/lib/gtdbtk/biolib_lite/logger.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2023-03-16T04:27:48,300 copying build/lib/gtdbtk/markers.py -> build/bdist.linux-armv7l/wheel/gtdbtk 2023-03-16T04:27:48,307 creating build/bdist.linux-armv7l/wheel/gtdbtk/config 2023-03-16T04:27:48,309 copying build/lib/gtdbtk/config/output.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config 2023-03-16T04:27:48,314 copying build/lib/gtdbtk/config/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config 2023-03-16T04:27:48,317 copying build/lib/gtdbtk/config/config.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config 2023-03-16T04:27:48,323 creating build/bdist.linux-armv7l/wheel/tests 2023-03-16T04:27:48,325 copying build/lib/tests/test_classify.py -> build/bdist.linux-armv7l/wheel/tests 2023-03-16T04:27:48,330 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests 2023-03-16T04:27:48,333 copying build/lib/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/tests 2023-03-16T04:27:48,338 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/tests 2023-03-16T04:27:48,343 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-03-16T04:27:48,345 copying build/lib/tests/test_gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-03-16T04:27:48,348 copying build/lib/tests/test_gtdbtk/test_trim_msa.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-03-16T04:27:48,352 copying build/lib/tests/test_gtdbtk/test_tools.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-03-16T04:27:48,358 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2023-03-16T04:27:48,359 copying build/lib/tests/test_gtdbtk/test_external/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2023-03-16T04:27:48,363 copying build/lib/tests/test_gtdbtk/test_external/test_fastani.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2023-03-16T04:27:48,367 copying build/lib/tests/test_gtdbtk/test_external/test_fasttree.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2023-03-16T04:27:48,372 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files 2023-03-16T04:27:48,373 copying build/lib/tests/test_gtdbtk/test_files/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files 2023-03-16T04:27:48,378 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_prodigal 2023-03-16T04:27:48,380 copying build/lib/tests/test_gtdbtk/test_files/test_prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_prodigal 2023-03-16T04:27:48,383 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 2023-03-16T04:27:48,388 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_marker 2023-03-16T04:27:48,390 copying build/lib/tests/test_gtdbtk/test_files/test_marker/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_marker 2023-03-16T04:27:48,393 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 2023-03-16T04:27:48,398 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 2023-03-16T04:27:48,402 copying build/lib/tests/test_gtdbtk/test__main__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-03-16T04:27:48,407 copying build/lib/tests/test_gtdbtk/test_main.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-03-16T04:27:48,426 copying build/lib/tests/test_gtdbtk/test_markers.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2023-03-16T04:27:48,431 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:48,433 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_seq_io.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:48,437 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:48,440 copying build/lib/tests/test_gtdbtk/test_biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:48,443 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_newick.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:48,447 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_common.py -> build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2023-03-16T04:27:48,450 running install_data 2023-03-16T04:27:48,513 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.2.5.data 2023-03-16T04:27:48,514 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.2.5.data/data 2023-03-16T04:27:48,517 copying LICENSE -> build/bdist.linux-armv7l/wheel/gtdbtk-2.2.5.data/data/ 2023-03-16T04:27:48,523 running install_egg_info 2023-03-16T04:27:48,674 running egg_info 2023-03-16T04:27:48,735 writing gtdbtk.egg-info/PKG-INFO 2023-03-16T04:27:48,740 writing dependency_links to gtdbtk.egg-info/dependency_links.txt 2023-03-16T04:27:48,745 writing entry points to gtdbtk.egg-info/entry_points.txt 2023-03-16T04:27:48,748 writing requirements to gtdbtk.egg-info/requires.txt 2023-03-16T04:27:48,751 writing top-level names to gtdbtk.egg-info/top_level.txt 2023-03-16T04:27:48,847 reading manifest file 'gtdbtk.egg-info/SOURCES.txt' 2023-03-16T04:27:48,857 adding license file 'LICENSE' 2023-03-16T04:27:48,874 writing manifest file 'gtdbtk.egg-info/SOURCES.txt' 2023-03-16T04:27:48,878 Copying gtdbtk.egg-info to build/bdist.linux-armv7l/wheel/gtdbtk-2.2.5-py3.7.egg-info 2023-03-16T04:27:48,903 running install_scripts 2023-03-16T04:27:48,943 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2023-03-16T04:27:48,955 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.2.5.dist-info/WHEEL 2023-03-16T04:27:48,961 creating '/tmp/pip-wheel-vqaen2j6/gtdbtk-2.2.5-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-03-16T04:27:48,968 adding 'gtdbtk/__init__.py' 2023-03-16T04:27:48,972 adding 'gtdbtk/__main__.py' 2023-03-16T04:27:48,977 adding 'gtdbtk/ani_rep.py' 2023-03-16T04:27:48,981 adding 'gtdbtk/ani_screen.py' 2023-03-16T04:27:49,009 adding 'gtdbtk/classify.py' 2023-03-16T04:27:49,018 adding 'gtdbtk/cli.py' 2023-03-16T04:27:49,025 adding 'gtdbtk/decorate.py' 2023-03-16T04:27:49,029 adding 'gtdbtk/exceptions.py' 2023-03-16T04:27:49,034 adding 'gtdbtk/infer_ranks.py' 2023-03-16T04:27:49,046 adding 'gtdbtk/main.py' 2023-03-16T04:27:49,058 adding 'gtdbtk/markers.py' 2023-03-16T04:27:49,063 adding 'gtdbtk/misc.py' 2023-03-16T04:27:49,069 adding 'gtdbtk/relative_distance.py' 2023-03-16T04:27:49,073 adding 'gtdbtk/reroot_tree.py' 2023-03-16T04:27:49,079 adding 'gtdbtk/split.py' 2023-03-16T04:27:49,084 adding 'gtdbtk/tools.py' 2023-03-16T04:27:49,089 adding 'gtdbtk/trim_msa.py' 2023-03-16T04:27:49,093 adding 'gtdbtk/biolib_lite/__init__.py' 2023-03-16T04:27:49,096 adding 'gtdbtk/biolib_lite/common.py' 2023-03-16T04:27:49,099 adding 'gtdbtk/biolib_lite/custom_help_formatter.py' 2023-03-16T04:27:49,102 adding 'gtdbtk/biolib_lite/exceptions.py' 2023-03-16T04:27:49,105 adding 'gtdbtk/biolib_lite/execute.py' 2023-03-16T04:27:49,109 adding 'gtdbtk/biolib_lite/logger.py' 2023-03-16T04:27:49,112 adding 'gtdbtk/biolib_lite/newick.py' 2023-03-16T04:27:49,116 adding 'gtdbtk/biolib_lite/parallel.py' 2023-03-16T04:27:49,121 adding 'gtdbtk/biolib_lite/prodigal_biolib.py' 2023-03-16T04:27:49,125 adding 'gtdbtk/biolib_lite/seq_io.py' 2023-03-16T04:27:49,133 adding 'gtdbtk/biolib_lite/taxonomy.py' 2023-03-16T04:27:49,137 adding 'gtdbtk/config/__init__.py' 2023-03-16T04:27:49,141 adding 'gtdbtk/config/config.py' 2023-03-16T04:27:49,145 adding 'gtdbtk/config/output.py' 2023-03-16T04:27:49,148 adding 'gtdbtk/external/__init__.py' 2023-03-16T04:27:49,153 adding 'gtdbtk/external/fastani.py' 2023-03-16T04:27:49,157 adding 'gtdbtk/external/fasttree.py' 2023-03-16T04:27:49,162 adding 'gtdbtk/external/hmm_aligner.py' 2023-03-16T04:27:49,167 adding 'gtdbtk/external/mash.py' 2023-03-16T04:27:49,171 adding 'gtdbtk/external/pfam_search.py' 2023-03-16T04:27:49,175 adding 'gtdbtk/external/pplacer.py' 2023-03-16T04:27:49,179 adding 'gtdbtk/external/prodigal.py' 2023-03-16T04:27:49,183 adding 'gtdbtk/external/tigrfam_search.py' 2023-03-16T04:27:49,186 adding 'gtdbtk/external/pypfam/__init__.py' 2023-03-16T04:27:49,190 adding 'gtdbtk/external/pypfam/HMM/HMMMatch.py' 2023-03-16T04:27:49,193 adding 'gtdbtk/external/pypfam/HMM/HMMResults.py' 2023-03-16T04:27:49,199 adding 'gtdbtk/external/pypfam/HMM/HMMResultsIO.py' 2023-03-16T04:27:49,202 adding 'gtdbtk/external/pypfam/HMM/HMMSequence.py' 2023-03-16T04:27:49,205 adding 'gtdbtk/external/pypfam/HMM/HMMUnit.py' 2023-03-16T04:27:49,207 adding 'gtdbtk/external/pypfam/HMM/__init__.py' 2023-03-16T04:27:49,214 adding 'gtdbtk/external/pypfam/Scan/PfamScan.py' 2023-03-16T04:27:49,217 adding 'gtdbtk/external/pypfam/Scan/__init__.py' 2023-03-16T04:27:49,220 adding 'gtdbtk/files/__init__.py' 2023-03-16T04:27:49,223 adding 'gtdbtk/files/batchfile.py' 2023-03-16T04:27:49,227 adding 'gtdbtk/files/classify_summary.py' 2023-03-16T04:27:49,230 adding 'gtdbtk/files/gtdb_radii.py' 2023-03-16T04:27:49,233 adding 'gtdbtk/files/marker_info.py' 2023-03-16T04:27:49,235 adding 'gtdbtk/files/missing_genomes.py' 2023-03-16T04:27:49,239 adding 'gtdbtk/files/pplacer_classification.py' 2023-03-16T04:27:49,241 adding 'gtdbtk/files/red_dict.py' 2023-03-16T04:27:49,245 adding 'gtdbtk/files/stage_logger.py' 2023-03-16T04:27:49,248 adding 'gtdbtk/files/tree_mapping.py' 2023-03-16T04:27:49,252 adding 'gtdbtk/files/marker/__init__.py' 2023-03-16T04:27:49,255 adding 'gtdbtk/files/marker/copy_number.py' 2023-03-16T04:27:49,259 adding 'gtdbtk/files/marker/tophit.py' 2023-03-16T04:27:49,262 adding 'gtdbtk/files/prodigal/__init__.py' 2023-03-16T04:27:49,265 adding 'gtdbtk/files/prodigal/tln_table.py' 2023-03-16T04:27:49,268 adding 'gtdbtk/files/prodigal/tln_table_summary.py' 2023-03-16T04:27:49,271 adding 'gtdbtk/model/__init__.py' 2023-03-16T04:27:49,274 adding 'gtdbtk/model/enum.py' 2023-03-16T04:27:49,277 adding 'gtdbtk/pipeline/__init__.py' 2023-03-16T04:27:49,281 adding 'gtdbtk/pipeline/align.py' 2023-03-16T04:27:49,283 adding 'gtdbtk/pipeline/export_msa.py' 2023-03-16T04:27:53,245 adding 'gtdbtk/tests/data/genomes/genome_1.fna' 2023-03-16T04:27:55,055 adding 'gtdbtk/tests/data/genomes/genome_2.fna' 2023-03-16T04:27:56,701 adding 'gtdbtk/tests/data/genomes/genome_3.fna' 2023-03-16T04:27:56,742 adding 'gtdbtk-2.2.5.data/data/LICENSE' 2023-03-16T04:27:56,749 adding 'tests/__init__.py' 2023-03-16T04:27:56,752 adding 'tests/common.py' 2023-03-16T04:27:56,755 adding 'tests/test_classify.py' 2023-03-16T04:27:56,759 adding 'tests/test_cli.py' 2023-03-16T04:27:56,763 adding 'tests/test_gtdbtk/__init__.py' 2023-03-16T04:27:56,767 adding 'tests/test_gtdbtk/test__main__.py' 2023-03-16T04:27:56,771 adding 'tests/test_gtdbtk/test_main.py' 2023-03-16T04:27:56,774 adding 'tests/test_gtdbtk/test_markers.py' 2023-03-16T04:27:56,777 adding 'tests/test_gtdbtk/test_tools.py' 2023-03-16T04:27:56,780 adding 'tests/test_gtdbtk/test_trim_msa.py' 2023-03-16T04:27:56,784 adding 'tests/test_gtdbtk/test_biolib_lite/__init__.py' 2023-03-16T04:27:56,787 adding 'tests/test_gtdbtk/test_biolib_lite/test_common.py' 2023-03-16T04:27:56,790 adding 'tests/test_gtdbtk/test_biolib_lite/test_newick.py' 2023-03-16T04:27:56,793 adding 'tests/test_gtdbtk/test_biolib_lite/test_seq_io.py' 2023-03-16T04:27:56,796 adding 'tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py' 2023-03-16T04:27:56,800 adding 'tests/test_gtdbtk/test_external/__init__.py' 2023-03-16T04:27:56,803 adding 'tests/test_gtdbtk/test_external/test_fastani.py' 2023-03-16T04:27:56,806 adding 'tests/test_gtdbtk/test_external/test_fasttree.py' 2023-03-16T04:27:56,809 adding 'tests/test_gtdbtk/test_files/__init__.py' 2023-03-16T04:27:56,813 adding 'tests/test_gtdbtk/test_files/test_marker/__init__.py' 2023-03-16T04:27:56,817 adding 'tests/test_gtdbtk/test_files/test_marker/test_copy_number.py' 2023-03-16T04:27:56,820 adding 'tests/test_gtdbtk/test_files/test_marker/test_tophit.py' 2023-03-16T04:27:56,824 adding 'tests/test_gtdbtk/test_files/test_prodigal/__init__.py' 2023-03-16T04:27:56,827 adding 'tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py' 2023-03-16T04:27:56,841 adding 'gtdbtk-2.2.5.dist-info/LICENSE' 2023-03-16T04:27:56,846 adding 'gtdbtk-2.2.5.dist-info/METADATA' 2023-03-16T04:27:56,848 adding 'gtdbtk-2.2.5.dist-info/WHEEL' 2023-03-16T04:27:56,849 adding 'gtdbtk-2.2.5.dist-info/entry_points.txt' 2023-03-16T04:27:56,851 adding 'gtdbtk-2.2.5.dist-info/top_level.txt' 2023-03-16T04:27:56,855 adding 'gtdbtk-2.2.5.dist-info/RECORD' 2023-03-16T04:27:56,928 removing build/bdist.linux-armv7l/wheel 2023-03-16T04:27:57,151 Building wheel for gtdbtk (setup.py): finished with status 'done' 2023-03-16T04:27:57,212 Created wheel for gtdbtk: filename=gtdbtk-2.2.5-py3-none-any.whl size=1828677 sha256=373f24c03ca4a533fc30378cc753ef810c9943df2fe1f361d39b11133869f81e 2023-03-16T04:27:57,214 Stored in directory: /tmp/pip-ephem-wheel-cache-_dm5rcyn/wheels/90/24/9b/6d29b5f6d0b34312b02255c09a9db195e77b59a124f0ab9756 2023-03-16T04:27:57,254 Successfully built gtdbtk 2023-03-16T04:27:57,414 Removed build tracker: '/tmp/pip-build-tracker-424uunun'