2025-09-17T00:39:05,933 Created temporary directory: /tmp/pip-ephem-wheel-cache-h4cg7cgx 2025-09-17T00:39:05,935 Created temporary directory: /tmp/pip-build-tracker-oxogx523 2025-09-17T00:39:05,935 Initialized build tracking at /tmp/pip-build-tracker-oxogx523 2025-09-17T00:39:05,936 Created build tracker: /tmp/pip-build-tracker-oxogx523 2025-09-17T00:39:05,936 Entered build tracker: /tmp/pip-build-tracker-oxogx523 2025-09-17T00:39:05,937 Created temporary directory: /tmp/pip-wheel-ht87k0f7 2025-09-17T00:39:05,940 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 2025-09-17T00:39:05,942 Created temporary directory: /tmp/pip-ephem-wheel-cache-tg9g5jog 2025-09-17T00:39:05,964 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-17T00:39:05,967 2 location(s) to search for versions of gtdbtk: 2025-09-17T00:39:05,967 * https://pypi.org/simple/gtdbtk/ 2025-09-17T00:39:05,967 * https://www.piwheels.org/simple/gtdbtk/ 2025-09-17T00:39:05,968 Fetching project page and analyzing links: https://pypi.org/simple/gtdbtk/ 2025-09-17T00:39:05,969 Getting page https://pypi.org/simple/gtdbtk/ 2025-09-17T00:39:05,970 Found index url https://pypi.org/simple 2025-09-17T00:39:06,191 Fetched page https://pypi.org/simple/gtdbtk/ as application/vnd.pypi.simple.v1+json 2025-09-17T00:39:06,205 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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2025-09-17T00:39:06,233 Found link https://files.pythonhosted.org/packages/46/7d/42643d2bed1eb3406a32c8cedd4be15aa03a47a29d09c2be1498b0602428/gtdbtk-1.5.1.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.5.1 2025-09-17T00:39:06,234 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/34/43/30519d579e26c5b2bf8370bcdc49e4b7805bf0445b766f54459e2fa1560c/gtdbtk-1.6.0-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2025-09-17T00:39:06,234 Found link https://files.pythonhosted.org/packages/e5/0b/c809fdd5da93a76edcb388c8ce5bf0f9836df548fb5e73c1bd4a90de0c3c/gtdbtk-1.6.0.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.6.0 2025-09-17T00:39:06,235 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/4a/cc/631e798a8f921fc6c504591472e34a04c2868f7ce7fdfc1b3c1cb5a81c05/gtdbtk-1.7.0-py3-none-any.whl (from 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2025-09-17T00:39:06,255 Found link https://files.pythonhosted.org/packages/c6/bd/b66510b12e1b143fcd6fd45a78a8c50cf8750e95d98ebcb5b496421ab279/gtdbtk-2.4.0.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.4.0 2025-09-17T00:39:06,256 Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/da/51/c225874c4531225f5031b6d583852164334046ba28a62e9a015f4ab75038/gtdbtk-2.4.1-py3-none-any.whl (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6) 2025-09-17T00:39:06,257 Found link https://files.pythonhosted.org/packages/cc/06/89b8f6b9d637f29c6d9e45d837dda960c096b02a130cba4b61ef7629730a/gtdbtk-2.4.1.tar.gz (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 2.4.1 2025-09-17T00:39:06,257 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) 2025-09-17T00:39:06,258 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 2025-09-17T00:39:06,259 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) 2025-09-17T00:39:06,259 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 2025-09-17T00:39:06,260 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) 2025-09-17T00:39:06,261 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 2025-09-17T00:39:06,262 Fetching project page and analyzing links: https://www.piwheels.org/simple/gtdbtk/ 2025-09-17T00:39:06,262 Getting page https://www.piwheels.org/simple/gtdbtk/ 2025-09-17T00:39:06,263 Found index url https://www.piwheels.org/simple 2025-09-17T00:39:06,436 Fetched page https://www.piwheels.org/simple/gtdbtk/ as text/html 2025-09-17T00:39:06,450 Skipping link: No binaries permitted for gtdbtk: https://www.piwheels.org/simple/gtdbtk/gtdbtk-2.5.1-py3-none-any.whl#sha256=6263cad08107a6fabc14415718d9c856bb493de32495d6dd93b1cc8d7818202b 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2025-09-17T00:39:06,471 Skipping link: No binaries permitted for gtdbtk: https://archive1.piwheels.org/simple/gtdbtk/gtdbtk-0.1.0-py3-none-any.whl#sha256=3133231730578803c78146b89d575c44b9ac4419b598cbb7a3178c13e5175428 (from https://www.piwheels.org/simple/gtdbtk/) 2025-09-17T00:39:06,472 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/) 2025-09-17T00:39:06,472 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/) 2025-09-17T00:39:06,473 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/) 2025-09-17T00:39:06,474 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/) 2025-09-17T00:39:06,474 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/) 2025-09-17T00:39:06,474 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/) 2025-09-17T00:39:06,475 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/) 2025-09-17T00:39:06,475 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/) 2025-09-17T00:39:06,476 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/) 2025-09-17T00:39:06,476 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/) 2025-09-17T00:39:06,477 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/) 2025-09-17T00:39:06,477 Skipping link: not a file: https://www.piwheels.org/simple/gtdbtk/ 2025-09-17T00:39:06,478 Skipping link: not a file: https://pypi.org/simple/gtdbtk/ 2025-09-17T00:39:06,502 Given no hashes to check 1 links for project 'gtdbtk': discarding no candidates 2025-09-17T00:39:06,520 Collecting gtdbtk==2.5.2 2025-09-17T00:39:06,523 Created temporary directory: /tmp/pip-unpack-y78jo3bx 2025-09-17T00:39:07,011 Downloading gtdbtk-2.5.2.tar.gz (1.7 MB) 2025-09-17T00:39:07,713 Added gtdbtk==2.5.2 from https://files.pythonhosted.org/packages/ca/86/42b6dc1b8025f105a19774e652ff86cb6520b207b9913f5211f8544fdff9/gtdbtk-2.5.2.tar.gz to build tracker '/tmp/pip-build-tracker-oxogx523' 2025-09-17T00:39:07,715 Running setup.py (path:/tmp/pip-wheel-ht87k0f7/gtdbtk_44071b4c009d4423ad5cb7f62e16ab81/setup.py) egg_info for package gtdbtk 2025-09-17T00:39:07,716 Created temporary directory: /tmp/pip-pip-egg-info-fhxz2nwx 2025-09-17T00:39:07,717 Preparing metadata (setup.py): started 2025-09-17T00:39:07,718 Running command python setup.py egg_info 2025-09-17T00:39:08,587 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-17T00:39:08,587 !! 2025-09-17T00:39:08,589 ******************************************************************************** 2025-09-17T00:39:08,590 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-17T00:39:08,592 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-09-17T00:39:08,593 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-17T00:39:08,594 ******************************************************************************** 2025-09-17T00:39:08,596 !! 2025-09-17T00:39:08,597 self._finalize_license_expression() 2025-09-17T00:39:08,629 running egg_info 2025-09-17T00:39:08,671 creating /tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info 2025-09-17T00:39:08,672 writing /tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info/PKG-INFO 2025-09-17T00:39:08,676 writing dependency_links to /tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info/dependency_links.txt 2025-09-17T00:39:08,678 writing entry points to /tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info/entry_points.txt 2025-09-17T00:39:08,680 writing requirements to /tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info/requires.txt 2025-09-17T00:39:08,681 writing top-level names to /tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info/top_level.txt 2025-09-17T00:39:08,683 writing manifest file '/tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info/SOURCES.txt' 2025-09-17T00:39:08,875 reading manifest file '/tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info/SOURCES.txt' 2025-09-17T00:39:08,877 adding license file 'LICENSE' 2025-09-17T00:39:08,882 writing manifest file '/tmp/pip-pip-egg-info-fhxz2nwx/gtdbtk.egg-info/SOURCES.txt' 2025-09-17T00:39:08,989 Preparing metadata (setup.py): finished with status 'done' 2025-09-17T00:39:08,995 Source in /tmp/pip-wheel-ht87k0f7/gtdbtk_44071b4c009d4423ad5cb7f62e16ab81 has version 2.5.2, which satisfies requirement gtdbtk==2.5.2 from https://files.pythonhosted.org/packages/ca/86/42b6dc1b8025f105a19774e652ff86cb6520b207b9913f5211f8544fdff9/gtdbtk-2.5.2.tar.gz 2025-09-17T00:39:08,996 Removed gtdbtk==2.5.2 from https://files.pythonhosted.org/packages/ca/86/42b6dc1b8025f105a19774e652ff86cb6520b207b9913f5211f8544fdff9/gtdbtk-2.5.2.tar.gz from build tracker '/tmp/pip-build-tracker-oxogx523' 2025-09-17T00:39:09,002 Created temporary directory: /tmp/pip-unpack-5ostebbj 2025-09-17T00:39:09,003 Building wheels for collected packages: gtdbtk 2025-09-17T00:39:09,007 Created temporary directory: /tmp/pip-wheel-x869ic2y 2025-09-17T00:39:09,008 Building wheel for gtdbtk (setup.py): started 2025-09-17T00:39:09,009 Destination directory: /tmp/pip-wheel-x869ic2y 2025-09-17T00:39:09,010 Running command python setup.py bdist_wheel 2025-09-17T00:39:09,840 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-17T00:39:09,840 !! 2025-09-17T00:39:09,841 ******************************************************************************** 2025-09-17T00:39:09,841 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-17T00:39:09,843 License :: OSI Approved :: GNU General Public License v3 (GPLv3) 2025-09-17T00:39:09,844 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-17T00:39:09,844 ******************************************************************************** 2025-09-17T00:39:09,845 !! 2025-09-17T00:39:09,846 self._finalize_license_expression() 2025-09-17T00:39:09,846 running bdist_wheel 2025-09-17T00:39:09,976 running build 2025-09-17T00:39:09,976 running build_py 2025-09-17T00:39:10,007 creating build/lib/tests 2025-09-17T00:39:10,010 copying tests/common.py -> build/lib/tests 2025-09-17T00:39:10,012 copying tests/test_classify.py -> build/lib/tests 2025-09-17T00:39:10,014 copying tests/test_cli.py -> build/lib/tests 2025-09-17T00:39:10,017 copying tests/__init__.py -> build/lib/tests 2025-09-17T00:39:10,019 creating build/lib/gtdbtk 2025-09-17T00:39:10,020 copying gtdbtk/classify.py -> build/lib/gtdbtk 2025-09-17T00:39:10,025 copying gtdbtk/exceptions.py -> build/lib/gtdbtk 2025-09-17T00:39:10,027 copying gtdbtk/relative_distance.py -> build/lib/gtdbtk 2025-09-17T00:39:10,029 copying gtdbtk/__main__.py -> build/lib/gtdbtk 2025-09-17T00:39:10,032 copying gtdbtk/trim_msa.py -> build/lib/gtdbtk 2025-09-17T00:39:10,034 copying gtdbtk/markers.py -> build/lib/gtdbtk 2025-09-17T00:39:10,037 copying gtdbtk/tools.py -> build/lib/gtdbtk 2025-09-17T00:39:10,039 copying gtdbtk/cli.py -> build/lib/gtdbtk 2025-09-17T00:39:10,042 copying gtdbtk/ani_rep.py -> build/lib/gtdbtk 2025-09-17T00:39:10,045 copying gtdbtk/split.py -> build/lib/gtdbtk 2025-09-17T00:39:10,048 copying gtdbtk/main.py -> build/lib/gtdbtk 2025-09-17T00:39:10,051 copying gtdbtk/__init__.py -> build/lib/gtdbtk 2025-09-17T00:39:10,054 copying gtdbtk/infer_ranks.py -> build/lib/gtdbtk 2025-09-17T00:39:10,056 copying gtdbtk/ani_screen.py -> build/lib/gtdbtk 2025-09-17T00:39:10,059 copying gtdbtk/reroot_tree.py -> build/lib/gtdbtk 2025-09-17T00:39:10,061 copying gtdbtk/misc.py -> build/lib/gtdbtk 2025-09-17T00:39:10,064 copying gtdbtk/decorate.py -> build/lib/gtdbtk 2025-09-17T00:39:10,068 creating build/lib/tests/test_gtdbtk 2025-09-17T00:39:10,069 copying tests/test_gtdbtk/test_main.py -> build/lib/tests/test_gtdbtk 2025-09-17T00:39:10,072 copying tests/test_gtdbtk/test_trim_msa.py -> build/lib/tests/test_gtdbtk 2025-09-17T00:39:10,075 copying tests/test_gtdbtk/test_tools.py -> build/lib/tests/test_gtdbtk 2025-09-17T00:39:10,077 copying tests/test_gtdbtk/__init__.py -> build/lib/tests/test_gtdbtk 2025-09-17T00:39:10,079 copying tests/test_gtdbtk/test_markers.py -> build/lib/tests/test_gtdbtk 2025-09-17T00:39:10,081 copying tests/test_gtdbtk/test__main__.py -> build/lib/tests/test_gtdbtk 2025-09-17T00:39:10,084 creating build/lib/tests/test_gtdbtk/test_files 2025-09-17T00:39:10,085 copying tests/test_gtdbtk/test_files/__init__.py -> build/lib/tests/test_gtdbtk/test_files 2025-09-17T00:39:10,088 creating build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,089 copying tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,091 copying tests/test_gtdbtk/test_biolib_lite/test_seq_io.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,094 copying tests/test_gtdbtk/test_biolib_lite/test_newick.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,096 copying tests/test_gtdbtk/test_biolib_lite/__init__.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,098 copying tests/test_gtdbtk/test_biolib_lite/test_common.py -> build/lib/tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,101 creating build/lib/tests/test_gtdbtk/test_external 2025-09-17T00:39:10,102 copying tests/test_gtdbtk/test_external/test_fasttree.py -> build/lib/tests/test_gtdbtk/test_external 2025-09-17T00:39:10,104 copying tests/test_gtdbtk/test_external/test_skani.py -> build/lib/tests/test_gtdbtk/test_external 2025-09-17T00:39:10,107 copying tests/test_gtdbtk/test_external/test_fastani.py -> build/lib/tests/test_gtdbtk/test_external 2025-09-17T00:39:10,109 copying tests/test_gtdbtk/test_external/__init__.py -> build/lib/tests/test_gtdbtk/test_external 2025-09-17T00:39:10,111 creating build/lib/tests/test_gtdbtk/test_files/test_marker 2025-09-17T00:39:10,113 copying tests/test_gtdbtk/test_files/test_marker/test_copy_number.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2025-09-17T00:39:10,116 copying tests/test_gtdbtk/test_files/test_marker/test_tophit.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2025-09-17T00:39:10,119 copying tests/test_gtdbtk/test_files/test_marker/__init__.py -> build/lib/tests/test_gtdbtk/test_files/test_marker 2025-09-17T00:39:10,121 creating build/lib/tests/test_gtdbtk/test_files/test_prodigal 2025-09-17T00:39:10,123 copying tests/test_gtdbtk/test_files/test_prodigal/__init__.py -> build/lib/tests/test_gtdbtk/test_files/test_prodigal 2025-09-17T00:39:10,125 copying tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py -> build/lib/tests/test_gtdbtk/test_files/test_prodigal 2025-09-17T00:39:10,127 creating build/lib/gtdbtk/config 2025-09-17T00:39:10,129 copying gtdbtk/config/common.py -> build/lib/gtdbtk/config 2025-09-17T00:39:10,132 copying gtdbtk/config/__init__.py -> build/lib/gtdbtk/config 2025-09-17T00:39:10,133 copying gtdbtk/config/output.py -> build/lib/gtdbtk/config 2025-09-17T00:39:10,136 creating build/lib/gtdbtk/files 2025-09-17T00:39:10,138 copying gtdbtk/files/tree_mapping.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,140 copying gtdbtk/files/missing_genomes.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,142 copying gtdbtk/files/classify_summary.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,145 copying gtdbtk/files/red_dict.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,147 copying gtdbtk/files/pplacer_classification.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,149 copying gtdbtk/files/stage_logger.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,152 copying gtdbtk/files/gtdb_radii.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,154 copying gtdbtk/files/batchfile.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,157 copying gtdbtk/files/__init__.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,159 copying gtdbtk/files/marker_info.py -> build/lib/gtdbtk/files 2025-09-17T00:39:10,162 creating build/lib/gtdbtk/pipeline 2025-09-17T00:39:10,163 copying gtdbtk/pipeline/__init__.py -> build/lib/gtdbtk/pipeline 2025-09-17T00:39:10,165 copying gtdbtk/pipeline/align.py -> build/lib/gtdbtk/pipeline 2025-09-17T00:39:10,168 copying gtdbtk/pipeline/export_msa.py -> build/lib/gtdbtk/pipeline 2025-09-17T00:39:10,170 creating build/lib/gtdbtk/external 2025-09-17T00:39:10,172 copying gtdbtk/external/hmm_aligner.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,175 copying gtdbtk/external/pfam_search.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,178 copying gtdbtk/external/pplacer.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,181 copying gtdbtk/external/tigrfam_search.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,184 copying gtdbtk/external/prodigal.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,188 copying gtdbtk/external/fastani.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,191 copying gtdbtk/external/__init__.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,193 copying gtdbtk/external/fasttree.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,196 copying gtdbtk/external/skani.py -> build/lib/gtdbtk/external 2025-09-17T00:39:10,199 creating build/lib/gtdbtk/model 2025-09-17T00:39:10,200 copying gtdbtk/model/__init__.py -> build/lib/gtdbtk/model 2025-09-17T00:39:10,202 copying gtdbtk/model/enum.py -> build/lib/gtdbtk/model 2025-09-17T00:39:10,205 creating build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,207 copying gtdbtk/biolib_lite/taxonomy.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,210 copying gtdbtk/biolib_lite/common.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,212 copying gtdbtk/biolib_lite/exceptions.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,215 copying gtdbtk/biolib_lite/custom_help_formatter.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,217 copying gtdbtk/biolib_lite/newick.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,219 copying gtdbtk/biolib_lite/execute.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,222 copying gtdbtk/biolib_lite/__init__.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,224 copying gtdbtk/biolib_lite/seq_io.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,226 copying gtdbtk/biolib_lite/logger.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,229 copying gtdbtk/biolib_lite/parallel.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,232 copying gtdbtk/biolib_lite/prodigal_biolib.py -> build/lib/gtdbtk/biolib_lite 2025-09-17T00:39:10,238 creating build/lib/gtdbtk/files/prodigal 2025-09-17T00:39:10,240 copying gtdbtk/files/prodigal/tln_table.py -> build/lib/gtdbtk/files/prodigal 2025-09-17T00:39:10,244 copying gtdbtk/files/prodigal/__init__.py -> build/lib/gtdbtk/files/prodigal 2025-09-17T00:39:10,246 copying gtdbtk/files/prodigal/tln_table_summary.py -> build/lib/gtdbtk/files/prodigal 2025-09-17T00:39:10,248 creating build/lib/gtdbtk/files/marker 2025-09-17T00:39:10,249 copying gtdbtk/files/marker/tophit.py -> build/lib/gtdbtk/files/marker 2025-09-17T00:39:10,251 copying gtdbtk/files/marker/copy_number.py -> build/lib/gtdbtk/files/marker 2025-09-17T00:39:10,254 copying gtdbtk/files/marker/__init__.py -> build/lib/gtdbtk/files/marker 2025-09-17T00:39:10,256 creating build/lib/gtdbtk/external/pypfam 2025-09-17T00:39:10,257 copying gtdbtk/external/pypfam/__init__.py -> build/lib/gtdbtk/external/pypfam 2025-09-17T00:39:10,259 creating build/lib/gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,260 copying gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,262 copying gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,264 copying gtdbtk/external/pypfam/HMM/__init__.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,265 copying gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,268 copying gtdbtk/external/pypfam/HMM/HMMResults.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,270 copying gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/lib/gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,272 creating build/lib/gtdbtk/external/pypfam/Scan 2025-09-17T00:39:10,273 copying gtdbtk/external/pypfam/Scan/__init__.py -> build/lib/gtdbtk/external/pypfam/Scan 2025-09-17T00:39:10,275 copying gtdbtk/external/pypfam/Scan/PfamScan.py -> build/lib/gtdbtk/external/pypfam/Scan 2025-09-17T00:39:10,286 creating build/lib/gtdbtk/tests/data/genomes 2025-09-17T00:39:10,288 copying gtdbtk/tests/data/genomes/genome_1.fna -> build/lib/gtdbtk/tests/data/genomes 2025-09-17T00:39:10,342 copying gtdbtk/tests/data/genomes/genome_2.fna -> build/lib/gtdbtk/tests/data/genomes 2025-09-17T00:39:10,364 copying gtdbtk/tests/data/genomes/genome_3.fna -> build/lib/gtdbtk/tests/data/genomes 2025-09-17T00:39:10,399 running build_scripts 2025-09-17T00:39:10,401 creating build/scripts-3.11 2025-09-17T00:39:10,402 copying and adjusting scripts/gtdb_to_ncbi_majority_vote.py -> build/scripts-3.11 2025-09-17T00:39:10,406 changing mode of build/scripts-3.11/gtdb_to_ncbi_majority_vote.py from 644 to 755 2025-09-17T00:39:10,434 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-17T00:39:10,435 !! 2025-09-17T00:39:10,435 ******************************************************************************** 2025-09-17T00:39:10,436 Please avoid running ``setup.py`` directly. 2025-09-17T00:39:10,436 Instead, use pypa/build, pypa/installer or other 2025-09-17T00:39:10,437 standards-based tools. 2025-09-17T00:39:10,438 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-17T00:39:10,438 or your builds will no longer be supported. 2025-09-17T00:39:10,439 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-17T00:39:10,440 ******************************************************************************** 2025-09-17T00:39:10,441 !! 2025-09-17T00:39:10,441 self.initialize_options() 2025-09-17T00:39:10,468 installing to build/bdist.linux-armv7l/wheel 2025-09-17T00:39:10,468 running install 2025-09-17T00:39:10,492 running install_lib 2025-09-17T00:39:10,520 creating build/bdist.linux-armv7l/wheel 2025-09-17T00:39:10,523 creating build/bdist.linux-armv7l/wheel/tests 2025-09-17T00:39:10,524 copying build/lib/tests/common.py -> build/bdist.linux-armv7l/wheel/./tests 2025-09-17T00:39:10,527 copying build/lib/tests/test_classify.py -> build/bdist.linux-armv7l/wheel/./tests 2025-09-17T00:39:10,529 copying build/lib/tests/test_cli.py -> build/bdist.linux-armv7l/wheel/./tests 2025-09-17T00:39:10,532 copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests 2025-09-17T00:39:10,535 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk 2025-09-17T00:39:10,536 copying build/lib/tests/test_gtdbtk/test_main.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-17T00:39:10,539 copying build/lib/tests/test_gtdbtk/test_trim_msa.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-17T00:39:10,541 copying build/lib/tests/test_gtdbtk/test_tools.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-17T00:39:10,543 copying build/lib/tests/test_gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-17T00:39:10,546 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files 2025-09-17T00:39:10,548 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_marker 2025-09-17T00:39:10,549 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 2025-09-17T00:39:10,552 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 2025-09-17T00:39:10,554 copying build/lib/tests/test_gtdbtk/test_files/test_marker/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_files/test_marker 2025-09-17T00:39:10,557 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_files/test_prodigal 2025-09-17T00:39:10,558 copying build/lib/tests/test_gtdbtk/test_files/test_prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_files/test_prodigal 2025-09-17T00:39:10,560 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 2025-09-17T00:39:10,562 copying build/lib/tests/test_gtdbtk/test_files/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_files 2025-09-17T00:39:10,565 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,566 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,569 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_seq_io.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,571 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_newick.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,573 copying build/lib/tests/test_gtdbtk/test_biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,575 copying build/lib/tests/test_gtdbtk/test_biolib_lite/test_common.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_biolib_lite 2025-09-17T00:39:10,577 creating build/bdist.linux-armv7l/wheel/tests/test_gtdbtk/test_external 2025-09-17T00:39:10,578 copying build/lib/tests/test_gtdbtk/test_external/test_fasttree.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_external 2025-09-17T00:39:10,580 copying build/lib/tests/test_gtdbtk/test_external/test_skani.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_external 2025-09-17T00:39:10,582 copying build/lib/tests/test_gtdbtk/test_external/test_fastani.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_external 2025-09-17T00:39:10,584 copying build/lib/tests/test_gtdbtk/test_external/__init__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk/test_external 2025-09-17T00:39:10,586 copying build/lib/tests/test_gtdbtk/test_markers.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-17T00:39:10,588 copying build/lib/tests/test_gtdbtk/test__main__.py -> build/bdist.linux-armv7l/wheel/./tests/test_gtdbtk 2025-09-17T00:39:10,591 creating build/bdist.linux-armv7l/wheel/gtdbtk 2025-09-17T00:39:10,593 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests 2025-09-17T00:39:10,595 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data 2025-09-17T00:39:10,596 creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes 2025-09-17T00:39:10,597 copying build/lib/gtdbtk/tests/data/genomes/genome_1.fna -> build/bdist.linux-armv7l/wheel/./gtdbtk/tests/data/genomes 2025-09-17T00:39:10,644 copying build/lib/gtdbtk/tests/data/genomes/genome_2.fna -> build/bdist.linux-armv7l/wheel/./gtdbtk/tests/data/genomes 2025-09-17T00:39:10,664 copying build/lib/gtdbtk/tests/data/genomes/genome_3.fna -> build/bdist.linux-armv7l/wheel/./gtdbtk/tests/data/genomes 2025-09-17T00:39:10,685 copying build/lib/gtdbtk/classify.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,689 creating build/bdist.linux-armv7l/wheel/gtdbtk/config 2025-09-17T00:39:10,690 copying build/lib/gtdbtk/config/common.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/config 2025-09-17T00:39:10,693 copying build/lib/gtdbtk/config/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/config 2025-09-17T00:39:10,694 copying build/lib/gtdbtk/config/output.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/config 2025-09-17T00:39:10,696 copying build/lib/gtdbtk/exceptions.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,699 copying build/lib/gtdbtk/relative_distance.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,701 copying build/lib/gtdbtk/__main__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,703 copying build/lib/gtdbtk/trim_msa.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,705 copying build/lib/gtdbtk/markers.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,709 creating build/bdist.linux-armv7l/wheel/gtdbtk/files 2025-09-17T00:39:10,710 copying build/lib/gtdbtk/files/tree_mapping.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,712 copying build/lib/gtdbtk/files/missing_genomes.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,714 copying build/lib/gtdbtk/files/classify_summary.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,716 copying build/lib/gtdbtk/files/red_dict.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,718 copying build/lib/gtdbtk/files/pplacer_classification.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,720 copying build/lib/gtdbtk/files/stage_logger.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,722 copying build/lib/gtdbtk/files/gtdb_radii.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,725 copying build/lib/gtdbtk/files/batchfile.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,726 copying build/lib/gtdbtk/files/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,728 copying build/lib/gtdbtk/files/marker_info.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files 2025-09-17T00:39:10,730 creating build/bdist.linux-armv7l/wheel/gtdbtk/files/prodigal 2025-09-17T00:39:10,731 copying build/lib/gtdbtk/files/prodigal/tln_table.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/prodigal 2025-09-17T00:39:10,733 copying build/lib/gtdbtk/files/prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/prodigal 2025-09-17T00:39:10,735 copying build/lib/gtdbtk/files/prodigal/tln_table_summary.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/prodigal 2025-09-17T00:39:10,737 creating build/bdist.linux-armv7l/wheel/gtdbtk/files/marker 2025-09-17T00:39:10,739 copying build/lib/gtdbtk/files/marker/tophit.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/marker 2025-09-17T00:39:10,741 copying build/lib/gtdbtk/files/marker/copy_number.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/marker 2025-09-17T00:39:10,743 copying build/lib/gtdbtk/files/marker/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/files/marker 2025-09-17T00:39:10,745 copying build/lib/gtdbtk/tools.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,748 creating build/bdist.linux-armv7l/wheel/gtdbtk/pipeline 2025-09-17T00:39:10,749 copying build/lib/gtdbtk/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/pipeline 2025-09-17T00:39:10,750 copying build/lib/gtdbtk/pipeline/align.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/pipeline 2025-09-17T00:39:10,752 copying build/lib/gtdbtk/pipeline/export_msa.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/pipeline 2025-09-17T00:39:10,754 copying build/lib/gtdbtk/cli.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,757 copying build/lib/gtdbtk/ani_rep.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,759 creating build/bdist.linux-armv7l/wheel/gtdbtk/external 2025-09-17T00:39:10,760 copying build/lib/gtdbtk/external/hmm_aligner.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,763 copying build/lib/gtdbtk/external/pfam_search.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,765 copying build/lib/gtdbtk/external/pplacer.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,767 copying build/lib/gtdbtk/external/tigrfam_search.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,769 copying build/lib/gtdbtk/external/prodigal.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,772 copying build/lib/gtdbtk/external/fastani.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,774 copying build/lib/gtdbtk/external/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,775 copying build/lib/gtdbtk/external/fasttree.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,778 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam 2025-09-17T00:39:10,779 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,780 copying build/lib/gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,782 copying build/lib/gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,784 copying build/lib/gtdbtk/external/pypfam/HMM/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,786 copying build/lib/gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,788 copying build/lib/gtdbtk/external/pypfam/HMM/HMMResults.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,790 copying build/lib/gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/HMM 2025-09-17T00:39:10,793 creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan 2025-09-17T00:39:10,794 copying build/lib/gtdbtk/external/pypfam/Scan/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/Scan 2025-09-17T00:39:10,795 copying build/lib/gtdbtk/external/pypfam/Scan/PfamScan.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam/Scan 2025-09-17T00:39:10,798 copying build/lib/gtdbtk/external/pypfam/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external/pypfam 2025-09-17T00:39:10,799 copying build/lib/gtdbtk/external/skani.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/external 2025-09-17T00:39:10,802 copying build/lib/gtdbtk/split.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,804 copying build/lib/gtdbtk/main.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,808 creating build/bdist.linux-armv7l/wheel/gtdbtk/model 2025-09-17T00:39:10,809 copying build/lib/gtdbtk/model/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/model 2025-09-17T00:39:10,811 copying build/lib/gtdbtk/model/enum.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/model 2025-09-17T00:39:10,813 copying build/lib/gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,815 creating build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite 2025-09-17T00:39:10,816 copying build/lib/gtdbtk/biolib_lite/taxonomy.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,819 copying build/lib/gtdbtk/biolib_lite/common.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,821 copying build/lib/gtdbtk/biolib_lite/exceptions.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,823 copying build/lib/gtdbtk/biolib_lite/custom_help_formatter.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,825 copying build/lib/gtdbtk/biolib_lite/newick.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,827 copying build/lib/gtdbtk/biolib_lite/execute.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,829 copying build/lib/gtdbtk/biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,830 copying build/lib/gtdbtk/biolib_lite/seq_io.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,832 copying build/lib/gtdbtk/biolib_lite/logger.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,835 copying build/lib/gtdbtk/biolib_lite/parallel.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,837 copying build/lib/gtdbtk/biolib_lite/prodigal_biolib.py -> build/bdist.linux-armv7l/wheel/./gtdbtk/biolib_lite 2025-09-17T00:39:10,839 copying build/lib/gtdbtk/infer_ranks.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,842 copying build/lib/gtdbtk/ani_screen.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,844 copying build/lib/gtdbtk/reroot_tree.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,846 copying build/lib/gtdbtk/misc.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,848 copying build/lib/gtdbtk/decorate.py -> build/bdist.linux-armv7l/wheel/./gtdbtk 2025-09-17T00:39:10,851 running install_data 2025-09-17T00:39:10,879 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.5.2.data/data 2025-09-17T00:39:10,881 copying LICENSE -> build/bdist.linux-armv7l/wheel/gtdbtk-2.5.2.data/data/. 2025-09-17T00:39:10,883 running install_egg_info 2025-09-17T00:39:10,919 running egg_info 2025-09-17T00:39:10,946 writing gtdbtk.egg-info/PKG-INFO 2025-09-17T00:39:10,950 writing dependency_links to gtdbtk.egg-info/dependency_links.txt 2025-09-17T00:39:10,951 writing entry points to gtdbtk.egg-info/entry_points.txt 2025-09-17T00:39:10,953 writing requirements to gtdbtk.egg-info/requires.txt 2025-09-17T00:39:10,954 writing top-level names to gtdbtk.egg-info/top_level.txt 2025-09-17T00:39:11,001 reading manifest file 'gtdbtk.egg-info/SOURCES.txt' 2025-09-17T00:39:11,008 adding license file 'LICENSE' 2025-09-17T00:39:11,014 writing manifest file 'gtdbtk.egg-info/SOURCES.txt' 2025-09-17T00:39:11,016 Copying gtdbtk.egg-info to build/bdist.linux-armv7l/wheel/./gtdbtk-2.5.2-py3.11.egg-info 2025-09-17T00:39:11,028 running install_scripts 2025-09-17T00:39:11,029 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.5.2.data/scripts 2025-09-17T00:39:11,030 copying build/scripts-3.11/gtdb_to_ncbi_majority_vote.py -> build/bdist.linux-armv7l/wheel/gtdbtk-2.5.2.data/scripts 2025-09-17T00:39:11,032 changing mode of build/bdist.linux-armv7l/wheel/gtdbtk-2.5.2.data/scripts/gtdb_to_ncbi_majority_vote.py to 755 2025-09-17T00:39:11,046 creating build/bdist.linux-armv7l/wheel/gtdbtk-2.5.2.dist-info/WHEEL 2025-09-17T00:39:11,048 creating '/tmp/pip-wheel-x869ic2y/gtdbtk-2.5.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-17T00:39:11,051 adding 'gtdbtk/__init__.py' 2025-09-17T00:39:11,053 adding 'gtdbtk/__main__.py' 2025-09-17T00:39:11,055 adding 'gtdbtk/ani_rep.py' 2025-09-17T00:39:11,056 adding 'gtdbtk/ani_screen.py' 2025-09-17T00:39:11,068 adding 'gtdbtk/classify.py' 2025-09-17T00:39:11,071 adding 'gtdbtk/cli.py' 2025-09-17T00:39:11,073 adding 'gtdbtk/decorate.py' 2025-09-17T00:39:11,075 adding 'gtdbtk/exceptions.py' 2025-09-17T00:39:11,076 adding 'gtdbtk/infer_ranks.py' 2025-09-17T00:39:11,081 adding 'gtdbtk/main.py' 2025-09-17T00:39:11,085 adding 'gtdbtk/markers.py' 2025-09-17T00:39:11,087 adding 'gtdbtk/misc.py' 2025-09-17T00:39:11,090 adding 'gtdbtk/relative_distance.py' 2025-09-17T00:39:11,091 adding 'gtdbtk/reroot_tree.py' 2025-09-17T00:39:11,094 adding 'gtdbtk/split.py' 2025-09-17T00:39:11,096 adding 'gtdbtk/tools.py' 2025-09-17T00:39:11,098 adding 'gtdbtk/trim_msa.py' 2025-09-17T00:39:11,100 adding 'gtdbtk/biolib_lite/__init__.py' 2025-09-17T00:39:11,102 adding 'gtdbtk/biolib_lite/common.py' 2025-09-17T00:39:11,103 adding 'gtdbtk/biolib_lite/custom_help_formatter.py' 2025-09-17T00:39:11,105 adding 'gtdbtk/biolib_lite/exceptions.py' 2025-09-17T00:39:11,106 adding 'gtdbtk/biolib_lite/execute.py' 2025-09-17T00:39:11,108 adding 'gtdbtk/biolib_lite/logger.py' 2025-09-17T00:39:11,109 adding 'gtdbtk/biolib_lite/newick.py' 2025-09-17T00:39:11,111 adding 'gtdbtk/biolib_lite/parallel.py' 2025-09-17T00:39:11,113 adding 'gtdbtk/biolib_lite/prodigal_biolib.py' 2025-09-17T00:39:11,115 adding 'gtdbtk/biolib_lite/seq_io.py' 2025-09-17T00:39:11,118 adding 'gtdbtk/biolib_lite/taxonomy.py' 2025-09-17T00:39:11,120 adding 'gtdbtk/config/__init__.py' 2025-09-17T00:39:11,122 adding 'gtdbtk/config/common.py' 2025-09-17T00:39:11,123 adding 'gtdbtk/config/output.py' 2025-09-17T00:39:11,125 adding 'gtdbtk/external/__init__.py' 2025-09-17T00:39:11,127 adding 'gtdbtk/external/fastani.py' 2025-09-17T00:39:11,129 adding 'gtdbtk/external/fasttree.py' 2025-09-17T00:39:11,131 adding 'gtdbtk/external/hmm_aligner.py' 2025-09-17T00:39:11,132 adding 'gtdbtk/external/pfam_search.py' 2025-09-17T00:39:11,134 adding 'gtdbtk/external/pplacer.py' 2025-09-17T00:39:11,136 adding 'gtdbtk/external/prodigal.py' 2025-09-17T00:39:11,139 adding 'gtdbtk/external/skani.py' 2025-09-17T00:39:11,140 adding 'gtdbtk/external/tigrfam_search.py' 2025-09-17T00:39:11,142 adding 'gtdbtk/external/pypfam/__init__.py' 2025-09-17T00:39:11,144 adding 'gtdbtk/external/pypfam/HMM/HMMMatch.py' 2025-09-17T00:39:11,145 adding 'gtdbtk/external/pypfam/HMM/HMMResults.py' 2025-09-17T00:39:11,148 adding 'gtdbtk/external/pypfam/HMM/HMMResultsIO.py' 2025-09-17T00:39:11,149 adding 'gtdbtk/external/pypfam/HMM/HMMSequence.py' 2025-09-17T00:39:11,150 adding 'gtdbtk/external/pypfam/HMM/HMMUnit.py' 2025-09-17T00:39:11,152 adding 'gtdbtk/external/pypfam/HMM/__init__.py' 2025-09-17T00:39:11,155 adding 'gtdbtk/external/pypfam/Scan/PfamScan.py' 2025-09-17T00:39:11,156 adding 'gtdbtk/external/pypfam/Scan/__init__.py' 2025-09-17T00:39:11,157 adding 'gtdbtk/files/__init__.py' 2025-09-17T00:39:11,159 adding 'gtdbtk/files/batchfile.py' 2025-09-17T00:39:11,160 adding 'gtdbtk/files/classify_summary.py' 2025-09-17T00:39:11,162 adding 'gtdbtk/files/gtdb_radii.py' 2025-09-17T00:39:11,163 adding 'gtdbtk/files/marker_info.py' 2025-09-17T00:39:11,164 adding 'gtdbtk/files/missing_genomes.py' 2025-09-17T00:39:11,166 adding 'gtdbtk/files/pplacer_classification.py' 2025-09-17T00:39:11,167 adding 'gtdbtk/files/red_dict.py' 2025-09-17T00:39:11,169 adding 'gtdbtk/files/stage_logger.py' 2025-09-17T00:39:11,171 adding 'gtdbtk/files/tree_mapping.py' 2025-09-17T00:39:11,173 adding 'gtdbtk/files/marker/__init__.py' 2025-09-17T00:39:11,174 adding 'gtdbtk/files/marker/copy_number.py' 2025-09-17T00:39:11,176 adding 'gtdbtk/files/marker/tophit.py' 2025-09-17T00:39:11,178 adding 'gtdbtk/files/prodigal/__init__.py' 2025-09-17T00:39:11,179 adding 'gtdbtk/files/prodigal/tln_table.py' 2025-09-17T00:39:11,181 adding 'gtdbtk/files/prodigal/tln_table_summary.py' 2025-09-17T00:39:11,182 adding 'gtdbtk/model/__init__.py' 2025-09-17T00:39:11,183 adding 'gtdbtk/model/enum.py' 2025-09-17T00:39:11,185 adding 'gtdbtk/pipeline/__init__.py' 2025-09-17T00:39:11,187 adding 'gtdbtk/pipeline/align.py' 2025-09-17T00:39:11,188 adding 'gtdbtk/pipeline/export_msa.py' 2025-09-17T00:39:12,832 adding 'gtdbtk/tests/data/genomes/genome_1.fna' 2025-09-17T00:39:13,597 adding 'gtdbtk/tests/data/genomes/genome_2.fna' 2025-09-17T00:39:14,296 adding 'gtdbtk/tests/data/genomes/genome_3.fna' 2025-09-17T00:39:14,311 adding 'gtdbtk-2.5.2.data/data/LICENSE' 2025-09-17T00:39:14,315 adding 'gtdbtk-2.5.2.data/scripts/gtdb_to_ncbi_majority_vote.py' 2025-09-17T00:39:14,322 adding 'gtdbtk-2.5.2.dist-info/licenses/LICENSE' 2025-09-17T00:39:14,323 adding 'tests/__init__.py' 2025-09-17T00:39:14,324 adding 'tests/common.py' 2025-09-17T00:39:14,326 adding 'tests/test_classify.py' 2025-09-17T00:39:14,328 adding 'tests/test_cli.py' 2025-09-17T00:39:14,329 adding 'tests/test_gtdbtk/__init__.py' 2025-09-17T00:39:14,331 adding 'tests/test_gtdbtk/test__main__.py' 2025-09-17T00:39:14,333 adding 'tests/test_gtdbtk/test_main.py' 2025-09-17T00:39:14,334 adding 'tests/test_gtdbtk/test_markers.py' 2025-09-17T00:39:14,335 adding 'tests/test_gtdbtk/test_tools.py' 2025-09-17T00:39:14,337 adding 'tests/test_gtdbtk/test_trim_msa.py' 2025-09-17T00:39:14,338 adding 'tests/test_gtdbtk/test_biolib_lite/__init__.py' 2025-09-17T00:39:14,340 adding 'tests/test_gtdbtk/test_biolib_lite/test_common.py' 2025-09-17T00:39:14,341 adding 'tests/test_gtdbtk/test_biolib_lite/test_newick.py' 2025-09-17T00:39:14,342 adding 'tests/test_gtdbtk/test_biolib_lite/test_seq_io.py' 2025-09-17T00:39:14,344 adding 'tests/test_gtdbtk/test_biolib_lite/test_taxonomy.py' 2025-09-17T00:39:14,345 adding 'tests/test_gtdbtk/test_external/__init__.py' 2025-09-17T00:39:14,347 adding 'tests/test_gtdbtk/test_external/test_fastani.py' 2025-09-17T00:39:14,348 adding 'tests/test_gtdbtk/test_external/test_fasttree.py' 2025-09-17T00:39:14,349 adding 'tests/test_gtdbtk/test_external/test_skani.py' 2025-09-17T00:39:14,351 adding 'tests/test_gtdbtk/test_files/__init__.py' 2025-09-17T00:39:14,353 adding 'tests/test_gtdbtk/test_files/test_marker/__init__.py' 2025-09-17T00:39:14,354 adding 'tests/test_gtdbtk/test_files/test_marker/test_copy_number.py' 2025-09-17T00:39:14,356 adding 'tests/test_gtdbtk/test_files/test_marker/test_tophit.py' 2025-09-17T00:39:14,358 adding 'tests/test_gtdbtk/test_files/test_prodigal/__init__.py' 2025-09-17T00:39:14,359 adding 'tests/test_gtdbtk/test_files/test_prodigal/test_tln_table_summary.py' 2025-09-17T00:39:14,361 adding 'gtdbtk-2.5.2.dist-info/METADATA' 2025-09-17T00:39:14,362 adding 'gtdbtk-2.5.2.dist-info/WHEEL' 2025-09-17T00:39:14,363 adding 'gtdbtk-2.5.2.dist-info/entry_points.txt' 2025-09-17T00:39:14,364 adding 'gtdbtk-2.5.2.dist-info/top_level.txt' 2025-09-17T00:39:14,365 adding 'gtdbtk-2.5.2.dist-info/RECORD' 2025-09-17T00:39:14,386 removing build/bdist.linux-armv7l/wheel 2025-09-17T00:39:14,528 Building wheel for gtdbtk (setup.py): finished with status 'done' 2025-09-17T00:39:14,585 Created wheel for gtdbtk: filename=gtdbtk-2.5.2-py3-none-any.whl size=1840234 sha256=7d6c217e5aab099e5a1e709b11c1e3e2390da4d37ae0ff7d5631e78d4da981a2 2025-09-17T00:39:14,586 Stored in directory: /tmp/pip-ephem-wheel-cache-tg9g5jog/wheels/48/a0/80/130ae9218d60542345c3faf6f0fbe2e8e9f04084fb5af801c9 2025-09-17T00:39:14,617 Successfully built gtdbtk 2025-09-17T00:39:14,659 Removed build tracker: '/tmp/pip-build-tracker-oxogx523'