2025-09-12T05:09:06,137 Created temporary directory: /tmp/pip-build-tracker-w2bg9w1z 2025-09-12T05:09:06,138 Initialized build tracking at /tmp/pip-build-tracker-w2bg9w1z 2025-09-12T05:09:06,138 Created build tracker: /tmp/pip-build-tracker-w2bg9w1z 2025-09-12T05:09:06,139 Entered build tracker: /tmp/pip-build-tracker-w2bg9w1z 2025-09-12T05:09:06,140 Created temporary directory: /tmp/pip-wheel-aufcawnd 2025-09-12T05:09:06,144 Created temporary directory: /tmp/pip-ephem-wheel-cache-nt8ij8sk 2025-09-12T05:09:06,190 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-12T05:09:06,192 2 location(s) to search for versions of gtdbtk: 2025-09-12T05:09:06,192 * https://pypi.org/simple/gtdbtk/ 2025-09-12T05:09:06,192 * https://www.piwheels.org/simple/gtdbtk/ 2025-09-12T05:09:06,193 Fetching project page and analyzing links: https://pypi.org/simple/gtdbtk/ 2025-09-12T05:09:06,194 Getting page https://pypi.org/simple/gtdbtk/ 2025-09-12T05:09:06,196 Found index url 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0.0.4b0 2025-09-12T05:09:06,429 Found link https://files.pythonhosted.org/packages/e7/21/7b30d68267c9ed81610a37c8fdac4b53f7090f9511d963a54754ec49d521/gtdbtk-0.0.4b1.tar.gz (from https://pypi.org/simple/gtdbtk/), version: 0.0.4b1 2025-09-12T05:09:06,429 Found link https://files.pythonhosted.org/packages/d1/f0/970559d46438a2004ccaa4199491188afc1bb13304fb899b26a3530ed841/gtdbtk-0.0.4b2.tar.gz (from https://pypi.org/simple/gtdbtk/), version: 0.0.4b2 2025-09-12T05:09:06,430 Found link https://files.pythonhosted.org/packages/e0/47/a9610df19e2bcf2782fc1ee29e5f85452b20a22d6f80581a23e3c0111c52/gtdbtk-0.0.4b3.tar.gz (from https://pypi.org/simple/gtdbtk/), version: 0.0.4b3 2025-09-12T05:09:06,431 Found link https://files.pythonhosted.org/packages/bf/f1/ebd7ba5d9ac68fc00ec0f7a69b52111d945a70f836dd4ba975600b088a98/gtdbtk-0.0.5.tar.gz (from https://pypi.org/simple/gtdbtk/), version: 0.0.5 2025-09-12T05:09:06,431 Found link 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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 2025-09-12T05:09:06,437 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 2025-09-12T05:09:06,438 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 2025-09-12T05:09:06,438 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 2025-09-12T05:09:06,439 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 2025-09-12T05:09:06,442 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 2025-09-12T05:09:06,443 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) 2025-09-12T05:09:06,443 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 2025-09-12T05:09:06,444 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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2025-09-12T05:09:06,450 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) 2025-09-12T05:09:06,451 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 2025-09-12T05:09:06,451 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) 2025-09-12T05:09:06,452 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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2025-09-12T05:09:06,459 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 2025-09-12T05:09:06,459 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) 2025-09-12T05:09:06,460 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 2025-09-12T05:09:06,460 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/55/a0/82538604d4f39129c5632cf6d8b26a4b2993e9fd4fecc5f8ca6f0a118be0/gtdbtk-2.2.5-py3-none-any.whl (from 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2025-09-12T05:09:06,468 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/7d/49/a5a35b8af03e4e064a4cfa3d1cb6d36b5fdeed84dda368256c3570ff99cf/gtdbtk-2.5.0-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2025-09-12T05:09:06,468 Found link https://files.pythonhosted.org/packages/fb/36/e2400438ac6701fbe3289b285226d04bf3e3882b80ea7383ca548a58da05/gtdbtk-2.5.0.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.5.0 2025-09-12T05:09:06,469 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/16/b2/c3009b7a4002e0f5c5dd4ddcec1b74453cfdba33c11b1e8961db8b61e0e4/gtdbtk-2.5.1-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2025-09-12T05:09:06,469 Found link https://files.pythonhosted.org/packages/3d/d8/f606a77996d44201115b16db4f53b621e7d0bbfff27b9e030172c97c74d5/gtdbtk-2.5.1.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.5.1 2025-09-12T05:09:06,470 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/07/e6/219741ee5df6327ffcfc82e88e7dbb65d4e56cdb143be69bba8b3fe8a355/gtdbtk-2.5.2-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2025-09-12T05:09:06,470 Found link https://files.pythonhosted.org/packages/ca/86/42b6dc1b8025f105a19774e652ff86cb6520b207b9913f5211f8544fdff9/gtdbtk-2.5.2.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.5.2 2025-09-12T05:09:06,471 Fetching project page and analyzing links: https://www.piwheels.org/simple/gtdbtk/ 2025-09-12T05:09:06,472 Getting page https://www.piwheels.org/simple/gtdbtk/ 2025-09-12T05:09:06,473 Found index url https://www.piwheels.org/simple/ 2025-09-12T05:09:06,644 Fetched page https://www.piwheels.org/simple/gtdbtk/ as text/html 2025-09-12T05:09:06,654 Skipping link: No binaries permitted for gtdbtk: 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2025-09-12T05:09:06,673 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.8b1-py3-none-any.whl#sha256=f8404616952a9ef6a46543f35e0263365db7dde0f1010383871c30b5db9fc8db (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,674 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.7-py3-none-any.whl#sha256=ff0ee32028021f53551b42ec4d3ddd9e5f3f046795606fc0612f232672e7bbf4 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,674 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.6-py3-none-any.whl#sha256=ed899d29852d0a5921b1d5319f20e5f5b827f30d0a14fd5afa37e9a4eb02f745 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,675 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.5-py3-none-any.whl#sha256=ae582d50ba58fd74c73ec1a0a37f427d3343e9f20fe45389ee098ed5ef99e3f4 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,675 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.4b3-py3-none-any.whl#sha256=2d5b93346985d7186695de6a4dc010b9abf4e108ec438f449b74705eb7191fc1 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,676 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.4b2-py3-none-any.whl#sha256=177fdc2bb5e28ee60a931441956acff6b853871395a611bc1404c7f78a2a3f85 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,676 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.4b1-py3-none-any.whl#sha256=cffebc36f92b7947522a0e8d0fe11d9a7051a036352eb036ca90db5a14e591e1 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,677 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.4b0-py3-none-any.whl#sha256=1a96ec79753b589c69bb9c881bdedfc0aef683779cb926da47f22e85e77bb203 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,677 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.3-py3-none-any.whl#sha256=6670c151da83c393482600e07c463c74de77ab5776f88a4978d1b7defa71f852 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,678 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.2-py3-none-any.whl#sha256=dac945e10b775b7c8ab5f5b16635bd016d17aacb8a4ad77708ce67dc1b3f3ed6 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,678 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.0.1-py3-none-any.whl#sha256=05d5353a17e20d9bc2a38528bb3b2e2e28d3188d4ebf69192793cd3e0d5199e6 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-12T05:09:06,679 Skipping link: not a file: https://www.piwheels.org/simple/gtdbtk/ 2025-09-12T05:09:06,679 Skipping link: not a file: https://pypi.org/simple/gtdbtk/ 2025-09-12T05:09:06,702 Given no hashes to check 1 links for project 'gtdbtk': discarding no candidates 2025-09-12T05:09:06,704 Collecting gtdbtk==2.5.0 2025-09-12T05:09:06,706 Created temporary directory: /tmp/pip-unpack-88t63vqt 2025-09-12T05:09:06,945 Downloading gtdbtk-2.5.0.tar.gz (1.7 MB) 2025-09-12T05:09:07,549 Added gtdbtk==2.5.0 from https://files.pythonhosted.org/packages/fb/36/e2400438ac6701fbe3289b285226d04bf3e3882b80ea7383ca548a58da05/gtdbtk-2.5.0.tar.gz to build tracker '/tmp/pip-build-tracker-w2bg9w1z' 2025-09-12T05:09:07,551 Running setup.py (path:/tmp/pip-wheel-aufcawnd/gtdbtk_a9e62f48665b447aa9fae5e63a8993b2/setup.py) egg_info for package gtdbtk 2025-09-12T05:09:07,552 Created temporary directory: /tmp/pip-pip-egg-info-e21d2nwi 2025-09-12T05:09:07,552 Preparing metadata (setup.py): started 2025-09-12T05:09:07,554 Running command python setup.py egg_info 2025-09-12T05:09:08,443 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-12T05:09:08,443 !! 2025-09-12T05:09:08,444 ******************************************************************************** 2025-09-12T05:09:08,444 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-12T05:09:08,446 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-09-12T05:09:08,447 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-12T05:09:08,447 ******************************************************************************** 2025-09-12T05:09:08,448 !! 2025-09-12T05:09:08,449 self._finalize_license_expression() 2025-09-12T05:09:08,473 running egg_info 2025-09-12T05:09:08,500 creating /tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info 2025-09-12T05:09:08,501 writing /tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info/PKG-INFO 2025-09-12T05:09:08,504 writing dependency_links to /tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info/dependency_links.txt 2025-09-12T05:09:08,506 writing entry points to /tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info/entry_points.txt 2025-09-12T05:09:08,507 writing requirements to /tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info/requires.txt 2025-09-12T05:09:08,508 writing top-level names to /tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info/top_level.txt 2025-09-12T05:09:08,510 writing manifest file '/tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info/SOURCES.txt' 2025-09-12T05:09:08,641 reading manifest file '/tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info/SOURCES.txt' 2025-09-12T05:09:08,643 adding license file 'LICENSE' 2025-09-12T05:09:08,648 writing manifest file '/tmp/pip-pip-egg-info-e21d2nwi/gtdbtk.egg-info/SOURCES.txt' 2025-09-12T05:09:08,754 Preparing metadata (setup.py): finished with status 'done' 2025-09-12T05:09:08,758 Source in /tmp/pip-wheel-aufcawnd/gtdbtk_a9e62f48665b447aa9fae5e63a8993b2 has version 2.5.0, which satisfies requirement gtdbtk==2.5.0 from https://files.pythonhosted.org/packages/fb/36/e2400438ac6701fbe3289b285226d04bf3e3882b80ea7383ca548a58da05/gtdbtk-2.5.0.tar.gz 2025-09-12T05:09:08,759 Removed gtdbtk==2.5.0 from https://files.pythonhosted.org/packages/fb/36/e2400438ac6701fbe3289b285226d04bf3e3882b80ea7383ca548a58da05/gtdbtk-2.5.0.tar.gz from build tracker '/tmp/pip-build-tracker-w2bg9w1z' 2025-09-12T05:09:08,766 Created temporary directory: /tmp/pip-unpack-bbvup0el 2025-09-12T05:09:08,767 Created temporary directory: /tmp/pip-unpack-fbeni2jv 2025-09-12T05:09:08,768 Building wheels for collected packages: gtdbtk 2025-09-12T05:09:08,771 Created temporary directory: /tmp/pip-wheel-7jfk0oyy 2025-09-12T05:09:08,772 DEPRECATION: Building 'gtdbtk' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'gtdbtk'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-12T05:09:08,773 Building wheel for gtdbtk (setup.py): started 2025-09-12T05:09:08,774 Destination directory: /tmp/pip-wheel-7jfk0oyy 2025-09-12T05:09:08,775 Running command python setup.py bdist_wheel 2025-09-12T05:09:09,589 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-12T05:09:09,589 !! 2025-09-12T05:09:09,590 ******************************************************************************** 2025-09-12T05:09:09,591 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-12T05:09:09,592 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-09-12T05:09:09,593 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-12T05:09:09,593 ******************************************************************************** 2025-09-12T05:09:09,595 !! 2025-09-12T05:09:09,595 self._finalize_license_expression() 2025-09-12T05:09:09,596 running bdist_wheel 2025-09-12T05:09:09,720 running build 2025-09-12T05:09:09,720 running build_py 2025-09-12T05:09:09,749 creating build/lib/tests 2025-09-12T05:09:09,752 copying tests/__init__.py -> build/lib/tests 2025-09-12T05:09:09,753 copying tests/test_cli.py -> build/lib/tests 2025-09-12T05:09:09,756 copying tests/common.py -> build/lib/tests 2025-09-12T05:09:09,758 copying tests/test_classify.py -> build/lib/tests 2025-09-12T05:09:09,761 creating build/lib/gtdbtk 2025-09-12T05:09:09,762 copying gtdbtk/trim_msa.py -> build/lib/gtdbtk 2025-09-12T05:09:09,765 copying gtdbtk/cli.py -> build/lib/gtdbtk 2025-09-12T05:09:09,767 copying gtdbtk/__init__.py -> build/lib/gtdbtk 2025-09-12T05:09:09,769 copying gtdbtk/markers.py -> build/lib/gtdbtk 2025-09-12T05:09:09,773 copying gtdbtk/relative_distance.py -> build/lib/gtdbtk 2025-09-12T05:09:09,775 copying gtdbtk/__main__.py -> build/lib/gtdbtk 2025-09-12T05:09:09,777 copying gtdbtk/decorate.py -> build/lib/gtdbtk 2025-09-12T05:09:09,780 copying gtdbtk/exceptions.py -> build/lib/gtdbtk 2025-09-12T05:09:09,782 copying gtdbtk/misc.py -> build/lib/gtdbtk 2025-09-12T05:09:09,784 copying gtdbtk/infer_ranks.py -> build/lib/gtdbtk 2025-09-12T05:09:09,787 copying gtdbtk/classify.py -> build/lib/gtdbtk 2025-09-12T05:09:09,791 copying gtdbtk/ani_screen.py -> build/lib/gtdbtk 2025-09-12T05:09:09,793 copying gtdbtk/reroot_tree.py -> build/lib/gtdbtk 2025-09-12T05:09:09,796 copying gtdbtk/split.py -> build/lib/gtdbtk 2025-09-12T05:09:09,798 copying gtdbtk/ani_rep.py -> build/lib/gtdbtk 2025-09-12T05:09:09,800 copying gtdbtk/tools.py -> build/lib/gtdbtk 2025-09-12T05:09:09,803 copying gtdbtk/main.py -> build/lib/gtdbtk 2025-09-12T05:09:09,806 creating build/lib/tests/test_gtdbtk 2025-09-12T05:09:09,807 copying tests/test_gtdbtk/__init__.py -> build/lib/tests/test_gtdbtk 2025-09-12T05:09:09,809 copying tests/test_gtdbtk/test__main__.py -> build/lib/tests/test_gtdbtk 2025-09-12T05:09:09,811 copying tests/test_gtdbtk/test_main.py -> build/lib/tests/test_gtdbtk 2025-09-12T05:09:09,814 copying tests/test_gtdbtk/test_markers.py -> build/lib/tests/test_gtdbtk 2025-09-12T05:09:09,815 copying tests/test_gtdbtk/test_trim_msa.py -> build/lib/tests/test_gtdbtk 2025-09-12T05:09:09,817 copying tests/test_gtdbtk/test_tools.py -> build/lib/tests/test_gtdbtk 2025-09-12T05:09:09,820 creating build/lib/tests/test_gtdbtk/test_external 2025-09-12T05:09:09,821 copying tests/test_gtdbtk/test_external/__init__.py -> build/lib/tests/test_gtdbtk/test_external 2025-09-12T05:09:09,822 copying tests/test_gtdbtk/test_external/test_skani.py -> build/lib/tests/test_gtdbtk/test_external 2025-09-12T05:09:09,824 copying tests/test_gtdbtk/test_external/test_fasttree.py -> build/lib/tests/test_gtdbtk/test_external 2025-09-12T05:09:09,826 copying tests/test_gtdbtk/test_external/test_fastani.py -> build/lib/tests/test_gtdbtk/test_external 2025-09-12T05:09:09,829 creating build/lib/tests/test_gtdbtk/test_files 2025-09-12T05:09:09,830 copying tests/test_gtdbtk/test_files/__init__.py -> build/lib/tests/test_gtdbtk/test_files 2025-09-12T05:09:09,832 creating build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:09,833 copying tests/test_gtdbtk/test_biolib_lite/test_newick.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:09,835 copying tests/test_gtdbtk/test_biolib_lite/__init__.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:09,836 copying tests/test_gtdbtk/test_biolib_lite/test_common.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:09,838 copying tests/test_gtdbtk/test_biolib_lite/test_seq_io.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:09,840 copying tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:09,842 creating build/lib/tests/test_gtdbtk/test_files/test_marker 2025-09-12T05:09:09,844 copying tests/test_gtdbtk/test_files/test_marker/__init__.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2025-09-12T05:09:09,845 copying tests/test_gtdbtk/test_files/test_marker/test_tophit.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2025-09-12T05:09:09,847 copying tests/test_gtdbtk/test_files/test_marker/test_copy_number.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2025-09-12T05:09:09,850 creating build/lib/tests/test_gtdbtk/test_files/test_prodigal 2025-09-12T05:09:09,851 copying tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py -> build/lib/tests/test_gtdbtk/test_files/test_prodigal 2025-09-12T05:09:09,853 copying tests/test_gtdbtk/test_files/test_prodigal/__init__.py -> build/lib/tests/test_gtdbtk/test_files/test_prodigal 2025-09-12T05:09:09,855 creating build/lib/gtdbtk/files 2025-09-12T05:09:09,856 copying gtdbtk/files/stage_logger.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,859 copying gtdbtk/files/pplacer_classification.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,861 copying gtdbtk/files/batchfile.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,863 copying gtdbtk/files/marker_info.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,865 copying gtdbtk/files/__init__.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,867 copying gtdbtk/files/red_dict.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,869 copying gtdbtk/files/tree_mapping.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,871 copying gtdbtk/files/missing_genomes.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,873 copying gtdbtk/files/gtdb_radii.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,875 copying gtdbtk/files/classify_summary.py -> build/lib/gtdbtk/files 2025-09-12T05:09:09,878 creating build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,879 copying gtdbtk/biolib_lite/__init__.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,880 copying gtdbtk/biolib_lite/parallel.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,882 copying gtdbtk/biolib_lite/prodigal_biolib.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,885 copying gtdbtk/biolib_lite/taxonomy.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,888 copying gtdbtk/biolib_lite/execute.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,890 copying gtdbtk/biolib_lite/common.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,892 copying gtdbtk/biolib_lite/exceptions.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,894 copying gtdbtk/biolib_lite/custom_help_formatter.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,897 copying gtdbtk/biolib_lite/logger.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,899 copying gtdbtk/biolib_lite/newick.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,901 copying gtdbtk/biolib_lite/seq_io.py -> build/lib/gtdbtk/biolib_lite 2025-09-12T05:09:09,904 creating build/lib/gtdbtk/model 2025-09-12T05:09:09,906 copying gtdbtk/model/__init__.py -> build/lib/gtdbtk/model 2025-09-12T05:09:09,907 copying gtdbtk/model/enum.py -> build/lib/gtdbtk/model 2025-09-12T05:09:09,910 creating build/lib/gtdbtk/pipeline 2025-09-12T05:09:09,911 copying gtdbtk/pipeline/__init__.py -> build/lib/gtdbtk/pipeline 2025-09-12T05:09:09,913 copying gtdbtk/pipeline/export_msa.py -> build/lib/gtdbtk/pipeline 2025-09-12T05:09:09,915 copying gtdbtk/pipeline/align.py -> build/lib/gtdbtk/pipeline 2025-09-12T05:09:09,918 creating build/lib/gtdbtk/external 2025-09-12T05:09:09,919 copying gtdbtk/external/__init__.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,921 copying gtdbtk/external/hmm_aligner.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,924 copying gtdbtk/external/skani.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,927 copying gtdbtk/external/prodigal.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,929 copying gtdbtk/external/pfam_search.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,932 copying gtdbtk/external/fasttree.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,934 copying gtdbtk/external/pplacer.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,937 copying gtdbtk/external/fastani.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,940 copying gtdbtk/external/tigrfam_search.py -> build/lib/gtdbtk/external 2025-09-12T05:09:09,943 creating build/lib/gtdbtk/config 2025-09-12T05:09:09,944 copying gtdbtk/config/output.py -> build/lib/gtdbtk/config 2025-09-12T05:09:09,946 copying gtdbtk/config/__init__.py -> build/lib/gtdbtk/config 2025-09-12T05:09:09,948 copying gtdbtk/config/common.py -> build/lib/gtdbtk/config 2025-09-12T05:09:09,951 creating build/lib/gtdbtk/files/prodigal 2025-09-12T05:09:09,953 copying gtdbtk/files/prodigal/__init__.py -> build/lib/gtdbtk/files/prodigal 2025-09-12T05:09:09,955 copying gtdbtk/files/prodigal/tln_table.py -> build/lib/gtdbtk/files/prodigal 2025-09-12T05:09:09,957 copying gtdbtk/files/prodigal/tln_table_summary.py -> build/lib/gtdbtk/files/prodigal 2025-09-12T05:09:09,960 creating build/lib/gtdbtk/files/marker 2025-09-12T05:09:09,961 copying gtdbtk/files/marker/__init__.py -> build/lib/gtdbtk/files/marker 2025-09-12T05:09:09,963 copying gtdbtk/files/marker/copy_number.py -> build/lib/gtdbtk/files/marker 2025-09-12T05:09:09,966 copying gtdbtk/files/marker/tophit.py -> build/lib/gtdbtk/files/marker 2025-09-12T05:09:09,969 creating build/lib/gtdbtk/external/pypfam 2025-09-12T05:09:09,970 copying gtdbtk/external/pypfam/__init__.py -> build/lib/gtdbtk/external/pypfam 2025-09-12T05:09:09,972 creating build/lib/gtdbtk/external/pypfam/Scan 2025-09-12T05:09:09,974 copying gtdbtk/external/pypfam/Scan/__init__.py -> build/lib/gtdbtk/external/pypfam/Scan 2025-09-12T05:09:09,976 copying gtdbtk/external/pypfam/Scan/PfamScan.py -> build/lib/gtdbtk/external/pypfam/Scan 2025-09-12T05:09:09,979 creating build/lib/gtdbtk/external/pypfam/HMM 2025-09-12T05:09:09,980 copying gtdbtk/external/pypfam/HMM/__init__.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-12T05:09:09,982 copying gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-12T05:09:09,984 copying gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-12T05:09:09,986 copying gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-12T05:09:09,989 copying gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-12T05:09:09,991 copying gtdbtk/external/pypfam/HMM/HMMResults.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-12T05:09:10,002 creating build/lib/gtdbtk/tests/data/genomes 2025-09-12T05:09:10,005 copying gtdbtk/tests/data/genomes/genome_1.fna -> build/lib/gtdbtk/tests/data/genomes 2025-09-12T05:09:10,054 copying gtdbtk/tests/data/genomes/genome_3.fna -> build/lib/gtdbtk/tests/data/genomes 2025-09-12T05:09:10,074 copying gtdbtk/tests/data/genomes/genome_2.fna -> build/lib/gtdbtk/tests/data/genomes 2025-09-12T05:09:10,104 running build_scripts 2025-09-12T05:09:10,105 creating build/scripts-3.11 2025-09-12T05:09:10,107 copying and adjusting scripts/gtdb_to_ncbi_majority_vote.py -> build/scripts-3.11 2025-09-12T05:09:10,110 changing mode of build/scripts-3.11/gtdb_to_ncbi_majority_vote.py from 644 to 755 2025-09-12T05:09:10,136 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-12T05:09:10,137 !! 2025-09-12T05:09:10,138 ******************************************************************************** 2025-09-12T05:09:10,138 Please avoid running ``setup.py`` directly. 2025-09-12T05:09:10,139 Instead, use pypa/build, pypa/installer or other 2025-09-12T05:09:10,139 standards-based tools. 2025-09-12T05:09:10,140 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-12T05:09:10,141 or your builds will no longer be supported. 2025-09-12T05:09:10,142 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-12T05:09:10,142 ******************************************************************************** 2025-09-12T05:09:10,144 !! 2025-09-12T05:09:10,144 self.initialize_options() 2025-09-12T05:09:10,167 installing to build/bdist.linux-armv7l/wheel 2025-09-12T05:09:10,167 running install 2025-09-12T05:09:10,191 running install_lib 2025-09-12T05:09:10,218 creating build/bdist.linux-armv7l/wheel 2025-09-12T05:09:10,220 creating build/bdist.linux-armv7l/wheel/tests 2025-09-12T05:09:10,221 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-09-12T05:09:10,223 copying build/lib/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/./tests 2025-09-12T05:09:10,226 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2025-09-12T05:09:10,228 copying build/lib/tests/test_classify.py -> build/bdist.linux-armv7l/wheel/./tests 2025-09-12T05:09:10,230 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2025-09-12T05:09:10,232 copying build/lib/tests/test_gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-12T05:09:10,234 copying build/lib/tests/test_gtdbtk/test__main__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-12T05:09:10,237 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2025-09-12T05:09:10,238 copying build/lib/tests/test_gtdbtk/test_external/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_external 2025-09-12T05:09:10,241 copying build/lib/tests/test_gtdbtk/test_external/test_skani.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_external 2025-09-12T05:09:10,243 copying build/lib/tests/test_gtdbtk/test_external/test_fasttree.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_external 2025-09-12T05:09:10,246 copying build/lib/tests/test_gtdbtk/test_external/test_fastani.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_external 2025-09-12T05:09:10,249 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files 2025-09-12T05:09:10,250 copying build/lib/tests/test_gtdbtk/test_files/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_files 2025-09-12T05:09:10,252 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_marker 2025-09-12T05:09:10,253 copying build/lib/tests/test_gtdbtk/test_files/test_marker/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_files/test_marker 2025-09-12T05:09:10,255 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 2025-09-12T05:09:10,258 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 2025-09-12T05:09:10,260 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_prodigal 2025-09-12T05:09:10,262 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 2025-09-12T05:09:10,264 copying build/lib/tests/test_gtdbtk/test_files/test_prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_files/test_prodigal 2025-09-12T05:09:10,266 copying build/lib/tests/test_gtdbtk/test_main.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-12T05:09:10,269 copying build/lib/tests/test_gtdbtk/test_markers.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-12T05:09:10,271 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:10,273 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_newick.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:10,275 copying build/lib/tests/test_gtdbtk/test_biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:10,277 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_common.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:10,279 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_seq_io.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:10,282 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-12T05:09:10,284 copying build/lib/tests/test_gtdbtk/test_trim_msa.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-12T05:09:10,287 copying build/lib/tests/test_gtdbtk/test_tools.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-12T05:09:10,290 creating build/bdist.linux-armv7l/wheel/gtdbtk 2025-09-12T05:09:10,291 copying build/lib/gtdbtk/trim_msa.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,295 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests 2025-09-12T05:09:10,296 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data 2025-09-12T05:09:10,298 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2025-09-12T05:09:10,300 copying build/lib/gtdbtk/tests/data/genomes/genome_1.fna -> build/bdist.linux-armv7l/wheel/./gtdbtk/tests/data/genomes 2025-09-12T05:09:10,346 copying build/lib/gtdbtk/tests/data/genomes/genome_3.fna -> build/bdist.linux-armv7l/wheel/./gtdbtk/tests/data/genomes 2025-09-12T05:09:10,365 copying build/lib/gtdbtk/tests/data/genomes/genome_2.fna -> build/bdist.linux-armv7l/wheel/./gtdbtk/tests/data/genomes 2025-09-12T05:09:10,386 copying build/lib/gtdbtk/cli.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,389 copying build/lib/gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,391 creating build/bdist.linux-armv7l/wheel/gtdbtk/files 2025-09-12T05:09:10,392 copying build/lib/gtdbtk/files/stage_logger.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,394 copying build/lib/gtdbtk/files/pplacer_classification.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,396 copying build/lib/gtdbtk/files/batchfile.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,398 copying build/lib/gtdbtk/files/marker_info.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,400 copying build/lib/gtdbtk/files/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,401 copying build/lib/gtdbtk/files/red_dict.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,404 creating build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2025-09-12T05:09:10,405 copying build/lib/gtdbtk/files/prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/prodigal 2025-09-12T05:09:10,406 copying build/lib/gtdbtk/files/prodigal/tln_table.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/prodigal 2025-09-12T05:09:10,408 copying build/lib/gtdbtk/files/prodigal/tln_table_summary.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/prodigal 2025-09-12T05:09:10,410 copying build/lib/gtdbtk/files/tree_mapping.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,412 copying build/lib/gtdbtk/files/missing_genomes.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,414 copying build/lib/gtdbtk/files/gtdb_radii.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,416 creating build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2025-09-12T05:09:10,417 copying build/lib/gtdbtk/files/marker/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/marker 2025-09-12T05:09:10,419 copying build/lib/gtdbtk/files/marker/copy_number.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/marker 2025-09-12T05:09:10,421 copying build/lib/gtdbtk/files/marker/tophit.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/marker 2025-09-12T05:09:10,423 copying build/lib/gtdbtk/files/classify_summary.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-12T05:09:10,425 copying build/lib/gtdbtk/markers.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,428 copying build/lib/gtdbtk/relative_distance.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,430 copying build/lib/gtdbtk/__main__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,433 creating build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2025-09-12T05:09:10,434 copying build/lib/gtdbtk/biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,436 copying build/lib/gtdbtk/biolib_lite/parallel.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,438 copying build/lib/gtdbtk/biolib_lite/prodigal_biolib.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,440 copying build/lib/gtdbtk/biolib_lite/taxonomy.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,443 copying build/lib/gtdbtk/biolib_lite/execute.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,445 copying build/lib/gtdbtk/biolib_lite/common.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,447 copying build/lib/gtdbtk/biolib_lite/exceptions.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,449 copying build/lib/gtdbtk/biolib_lite/custom_help_formatter.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,451 copying build/lib/gtdbtk/biolib_lite/logger.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,453 copying build/lib/gtdbtk/biolib_lite/newick.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,455 copying build/lib/gtdbtk/biolib_lite/seq_io.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-12T05:09:10,457 copying build/lib/gtdbtk/decorate.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,460 creating build/bdist.linux-armv7l/wheel/gtdbtk/model 2025-09-12T05:09:10,460 copying build/lib/gtdbtk/model/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/model 2025-09-12T05:09:10,462 copying build/lib/gtdbtk/model/enum.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/model 2025-09-12T05:09:10,464 copying build/lib/gtdbtk/exceptions.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,466 copying build/lib/gtdbtk/misc.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,468 copying build/lib/gtdbtk/infer_ranks.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,470 copying build/lib/gtdbtk/classify.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,474 copying build/lib/gtdbtk/ani_screen.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,476 copying build/lib/gtdbtk/reroot_tree.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,478 creating build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2025-09-12T05:09:10,480 copying build/lib/gtdbtk/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/pipeline 2025-09-12T05:09:10,481 copying build/lib/gtdbtk/pipeline/export_msa.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/pipeline 2025-09-12T05:09:10,483 copying build/lib/gtdbtk/pipeline/align.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/pipeline 2025-09-12T05:09:10,485 copying build/lib/gtdbtk/split.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,488 copying build/lib/gtdbtk/ani_rep.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,490 creating build/bdist.linux-armv7l/wheel/gtdbtk/external 2025-09-12T05:09:10,491 copying build/lib/gtdbtk/external/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,493 copying build/lib/gtdbtk/external/hmm_aligner.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,495 copying build/lib/gtdbtk/external/skani.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,497 copying build/lib/gtdbtk/external/prodigal.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,500 copying build/lib/gtdbtk/external/pfam_search.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,502 copying build/lib/gtdbtk/external/fasttree.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,505 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam 2025-09-12T05:09:10,506 copying build/lib/gtdbtk/external/pypfam/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam 2025-09-12T05:09:10,508 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan 2025-09-12T05:09:10,509 copying build/lib/gtdbtk/external/pypfam/Scan/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/Scan 2025-09-12T05:09:10,510 copying build/lib/gtdbtk/external/pypfam/Scan/PfamScan.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/Scan 2025-09-12T05:09:10,513 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2025-09-12T05:09:10,514 copying build/lib/gtdbtk/external/pypfam/HMM/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-12T05:09:10,516 copying build/lib/gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-12T05:09:10,518 copying build/lib/gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-12T05:09:10,520 copying build/lib/gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-12T05:09:10,521 copying build/lib/gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-12T05:09:10,524 copying build/lib/gtdbtk/external/pypfam/HMM/HMMResults.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-12T05:09:10,526 copying build/lib/gtdbtk/external/pplacer.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,528 copying build/lib/gtdbtk/external/fastani.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,531 copying build/lib/gtdbtk/external/tigrfam_search.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-12T05:09:10,533 copying build/lib/gtdbtk/tools.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,536 creating build/bdist.linux-armv7l/wheel/gtdbtk/config 2025-09-12T05:09:10,537 copying build/lib/gtdbtk/config/output.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/config 2025-09-12T05:09:10,539 copying build/lib/gtdbtk/config/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/config 2025-09-12T05:09:10,540 copying build/lib/gtdbtk/config/common.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/config 2025-09-12T05:09:10,543 copying build/lib/gtdbtk/main.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-12T05:09:10,545 running install_data 2025-09-12T05:09:10,573 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.5.0.data/data 2025-09-12T05:09:10,575 copying LICENSE -> build/bdist.linux-armv7l/wheel/gtdbtk-2.5.0.data/data/. 2025-09-12T05:09:10,577 running install_egg_info 2025-09-12T05:09:10,611 running egg_info 2025-09-12T05:09:10,639 writing gtdbtk.egg-info/PKG-INFO 2025-09-12T05:09:10,642 writing dependency_links to gtdbtk.egg-info/dependency_links.txt 2025-09-12T05:09:10,644 writing entry points to gtdbtk.egg-info/entry_points.txt 2025-09-12T05:09:10,645 writing requirements to gtdbtk.egg-info/requires.txt 2025-09-12T05:09:10,646 writing top-level names to gtdbtk.egg-info/top_level.txt 2025-09-12T05:09:10,701 reading manifest file 'gtdbtk.egg-info/SOURCES.txt' 2025-09-12T05:09:10,711 adding license file 'LICENSE' 2025-09-12T05:09:10,720 writing manifest file 'gtdbtk.egg-info/SOURCES.txt' 2025-09-12T05:09:10,722 Copying gtdbtk.egg-info to build/bdist.linux-armv7l/wheel/./gtdbtk-2.5.0-py3.11.egg-info 2025-09-12T05:09:10,736 running install_scripts 2025-09-12T05:09:10,737 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.5.0.data/scripts 2025-09-12T05:09:10,738 copying build/scripts-3.11/gtdb_to_ncbi_majority_vote.py -> build/bdist.linux-armv7l/wheel/gtdbtk-2.5.0.data/scripts 2025-09-12T05:09:10,741 changing mode of build/bdist.linux-armv7l/wheel/gtdbtk-2.5.0.data/scripts/gtdb_to_ncbi_majority_vote.py to 755 2025-09-12T05:09:10,757 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.5.0.dist-info/WHEEL 2025-09-12T05:09:10,760 creating '/tmp/pip-wheel-7jfk0oyy/gtdbtk-2.5.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-12T05:09:10,764 adding 'gtdbtk/__init__.py' 2025-09-12T05:09:10,766 adding 'gtdbtk/__main__.py' 2025-09-12T05:09:10,769 adding 'gtdbtk/ani_rep.py' 2025-09-12T05:09:10,770 adding 'gtdbtk/ani_screen.py' 2025-09-12T05:09:10,781 adding 'gtdbtk/classify.py' 2025-09-12T05:09:10,785 adding 'gtdbtk/cli.py' 2025-09-12T05:09:10,787 adding 'gtdbtk/decorate.py' 2025-09-12T05:09:10,789 adding 'gtdbtk/exceptions.py' 2025-09-12T05:09:10,791 adding 'gtdbtk/infer_ranks.py' 2025-09-12T05:09:10,795 adding 'gtdbtk/main.py' 2025-09-12T05:09:10,800 adding 'gtdbtk/markers.py' 2025-09-12T05:09:10,802 adding 'gtdbtk/misc.py' 2025-09-12T05:09:10,804 adding 'gtdbtk/relative_distance.py' 2025-09-12T05:09:10,806 adding 'gtdbtk/reroot_tree.py' 2025-09-12T05:09:10,809 adding 'gtdbtk/split.py' 2025-09-12T05:09:10,811 adding 'gtdbtk/tools.py' 2025-09-12T05:09:10,813 adding 'gtdbtk/trim_msa.py' 2025-09-12T05:09:10,815 adding 'gtdbtk/biolib_lite/__init__.py' 2025-09-12T05:09:10,816 adding 'gtdbtk/biolib_lite/common.py' 2025-09-12T05:09:10,818 adding 'gtdbtk/biolib_lite/custom_help_formatter.py' 2025-09-12T05:09:10,819 adding 'gtdbtk/biolib_lite/exceptions.py' 2025-09-12T05:09:10,821 adding 'gtdbtk/biolib_lite/execute.py' 2025-09-12T05:09:10,822 adding 'gtdbtk/biolib_lite/logger.py' 2025-09-12T05:09:10,824 adding 'gtdbtk/biolib_lite/newick.py' 2025-09-12T05:09:10,825 adding 'gtdbtk/biolib_lite/parallel.py' 2025-09-12T05:09:10,828 adding 'gtdbtk/biolib_lite/prodigal_biolib.py' 2025-09-12T05:09:10,829 adding 'gtdbtk/biolib_lite/seq_io.py' 2025-09-12T05:09:10,833 adding 'gtdbtk/biolib_lite/taxonomy.py' 2025-09-12T05:09:10,834 adding 'gtdbtk/config/__init__.py' 2025-09-12T05:09:10,836 adding 'gtdbtk/config/common.py' 2025-09-12T05:09:10,838 adding 'gtdbtk/config/output.py' 2025-09-12T05:09:10,840 adding 'gtdbtk/external/__init__.py' 2025-09-12T05:09:10,842 adding 'gtdbtk/external/fastani.py' 2025-09-12T05:09:10,843 adding 'gtdbtk/external/fasttree.py' 2025-09-12T05:09:10,845 adding 'gtdbtk/external/hmm_aligner.py' 2025-09-12T05:09:10,847 adding 'gtdbtk/external/pfam_search.py' 2025-09-12T05:09:10,849 adding 'gtdbtk/external/pplacer.py' 2025-09-12T05:09:10,851 adding 'gtdbtk/external/prodigal.py' 2025-09-12T05:09:10,853 adding 'gtdbtk/external/skani.py' 2025-09-12T05:09:10,855 adding 'gtdbtk/external/tigrfam_search.py' 2025-09-12T05:09:10,857 adding 'gtdbtk/external/pypfam/__init__.py' 2025-09-12T05:09:10,858 adding 'gtdbtk/external/pypfam/HMM/HMMMatch.py' 2025-09-12T05:09:10,860 adding 'gtdbtk/external/pypfam/HMM/HMMResults.py' 2025-09-12T05:09:10,862 adding 'gtdbtk/external/pypfam/HMM/HMMResultsIO.py' 2025-09-12T05:09:10,864 adding 'gtdbtk/external/pypfam/HMM/HMMSequence.py' 2025-09-12T05:09:10,865 adding 'gtdbtk/external/pypfam/HMM/HMMUnit.py' 2025-09-12T05:09:10,866 adding 'gtdbtk/external/pypfam/HMM/__init__.py' 2025-09-12T05:09:10,869 adding 'gtdbtk/external/pypfam/Scan/PfamScan.py' 2025-09-12T05:09:10,870 adding 'gtdbtk/external/pypfam/Scan/__init__.py' 2025-09-12T05:09:10,871 adding 'gtdbtk/files/__init__.py' 2025-09-12T05:09:10,873 adding 'gtdbtk/files/batchfile.py' 2025-09-12T05:09:10,874 adding 'gtdbtk/files/classify_summary.py' 2025-09-12T05:09:10,876 adding 'gtdbtk/files/gtdb_radii.py' 2025-09-12T05:09:10,877 adding 'gtdbtk/files/marker_info.py' 2025-09-12T05:09:10,879 adding 'gtdbtk/files/missing_genomes.py' 2025-09-12T05:09:10,880 adding 'gtdbtk/files/pplacer_classification.py' 2025-09-12T05:09:10,881 adding 'gtdbtk/files/red_dict.py' 2025-09-12T05:09:10,883 adding 'gtdbtk/files/stage_logger.py' 2025-09-12T05:09:10,884 adding 'gtdbtk/files/tree_mapping.py' 2025-09-12T05:09:10,886 adding 'gtdbtk/files/marker/__init__.py' 2025-09-12T05:09:10,887 adding 'gtdbtk/files/marker/copy_number.py' 2025-09-12T05:09:10,889 adding 'gtdbtk/files/marker/tophit.py' 2025-09-12T05:09:10,891 adding 'gtdbtk/files/prodigal/__init__.py' 2025-09-12T05:09:10,892 adding 'gtdbtk/files/prodigal/tln_table.py' 2025-09-12T05:09:10,894 adding 'gtdbtk/files/prodigal/tln_table_summary.py' 2025-09-12T05:09:10,895 adding 'gtdbtk/model/__init__.py' 2025-09-12T05:09:10,896 adding 'gtdbtk/model/enum.py' 2025-09-12T05:09:10,898 adding 'gtdbtk/pipeline/__init__.py' 2025-09-12T05:09:10,900 adding 'gtdbtk/pipeline/align.py' 2025-09-12T05:09:10,901 adding 'gtdbtk/pipeline/export_msa.py' 2025-09-12T05:09:12,488 adding 'gtdbtk/tests/data/genomes/genome_1.fna' 2025-09-12T05:09:13,215 adding 'gtdbtk/tests/data/genomes/genome_2.fna' 2025-09-12T05:09:13,878 adding 'gtdbtk/tests/data/genomes/genome_3.fna' 2025-09-12T05:09:13,893 adding 'gtdbtk-2.5.0.data/data/LICENSE' 2025-09-12T05:09:13,897 adding 'gtdbtk-2.5.0.data/scripts/gtdb_to_ncbi_majority_vote.py' 2025-09-12T05:09:13,905 adding 'gtdbtk-2.5.0.dist-info/licenses/LICENSE' 2025-09-12T05:09:13,907 adding 'tests/__init__.py' 2025-09-12T05:09:13,908 adding 'tests/common.py' 2025-09-12T05:09:13,910 adding 'tests/test_classify.py' 2025-09-12T05:09:13,912 adding 'tests/test_cli.py' 2025-09-12T05:09:13,913 adding 'tests/test_gtdbtk/__init__.py' 2025-09-12T05:09:13,915 adding 'tests/test_gtdbtk/test__main__.py' 2025-09-12T05:09:13,917 adding 'tests/test_gtdbtk/test_main.py' 2025-09-12T05:09:13,919 adding 'tests/test_gtdbtk/test_markers.py' 2025-09-12T05:09:13,920 adding 'tests/test_gtdbtk/test_tools.py' 2025-09-12T05:09:13,921 adding 'tests/test_gtdbtk/test_trim_msa.py' 2025-09-12T05:09:13,923 adding 'tests/test_gtdbtk/test_biolib_lite/__init__.py' 2025-09-12T05:09:13,925 adding 'tests/test_gtdbtk/test_biolib_lite/test_common.py' 2025-09-12T05:09:13,926 adding 'tests/test_gtdbtk/test_biolib_lite/test_newick.py' 2025-09-12T05:09:13,927 adding 'tests/test_gtdbtk/test_biolib_lite/test_seq_io.py' 2025-09-12T05:09:13,929 adding 'tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py' 2025-09-12T05:09:13,931 adding 'tests/test_gtdbtk/test_external/__init__.py' 2025-09-12T05:09:13,933 adding 'tests/test_gtdbtk/test_external/test_fastani.py' 2025-09-12T05:09:13,934 adding 'tests/test_gtdbtk/test_external/test_fasttree.py' 2025-09-12T05:09:13,936 adding 'tests/test_gtdbtk/test_external/test_skani.py' 2025-09-12T05:09:13,937 adding 'tests/test_gtdbtk/test_files/__init__.py' 2025-09-12T05:09:13,939 adding 'tests/test_gtdbtk/test_files/test_marker/__init__.py' 2025-09-12T05:09:13,940 adding 'tests/test_gtdbtk/test_files/test_marker/test_copy_number.py' 2025-09-12T05:09:13,942 adding 'tests/test_gtdbtk/test_files/test_marker/test_tophit.py' 2025-09-12T05:09:13,944 adding 'tests/test_gtdbtk/test_files/test_prodigal/__init__.py' 2025-09-12T05:09:13,945 adding 'tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py' 2025-09-12T05:09:13,947 adding 'gtdbtk-2.5.0.dist-info/METADATA' 2025-09-12T05:09:13,948 adding 'gtdbtk-2.5.0.dist-info/WHEEL' 2025-09-12T05:09:13,949 adding 'gtdbtk-2.5.0.dist-info/entry_points.txt' 2025-09-12T05:09:13,950 adding 'gtdbtk-2.5.0.dist-info/top_level.txt' 2025-09-12T05:09:13,952 adding 'gtdbtk-2.5.0.dist-info/RECORD' 2025-09-12T05:09:13,975 removing build/bdist.linux-armv7l/wheel 2025-09-12T05:09:14,114 Building wheel for gtdbtk (setup.py): finished with status 'done' 2025-09-12T05:09:14,135 Created wheel for gtdbtk: filename=gtdbtk-2.5.0-py3-none-any.whl size=1840276 sha256=18300c5358f39da88a24647ba331bedf4c66d2072d282e5b32cd923cf2aaf629 2025-09-12T05:09:14,136 Stored in directory: /tmp/pip-ephem-wheel-cache-nt8ij8sk/wheels/23/37/e0/f2da27c6aa46e9f705645773405f437cf609a78b6f3e2219b1 2025-09-12T05:09:14,152 Successfully built gtdbtk 2025-09-12T05:09:14,209 Removed build tracker: '/tmp/pip-build-tracker-w2bg9w1z'