2023-12-07T10:08:48,370 Created temporary directory: /tmp/pip-build-tracker-bvm66ogb 2023-12-07T10:08:48,372 Initialized build tracking at /tmp/pip-build-tracker-bvm66ogb 2023-12-07T10:08:48,372 Created build tracker: /tmp/pip-build-tracker-bvm66ogb 2023-12-07T10:08:48,373 Entered build tracker: /tmp/pip-build-tracker-bvm66ogb 2023-12-07T10:08:48,373 Created temporary directory: /tmp/pip-wheel-zvqf1dao 2023-12-07T10:08:48,377 Created temporary directory: /tmp/pip-ephem-wheel-cache-61rgt80o 2023-12-07T10:08:48,400 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-12-07T10:08:48,403 2 location(s) to search for versions of kage-genotyper: 2023-12-07T10:08:48,403 * https://pypi.org/simple/kage-genotyper/ 2023-12-07T10:08:48,403 * https://www.piwheels.org/simple/kage-genotyper/ 2023-12-07T10:08:48,404 Fetching project page and analyzing links: https://pypi.org/simple/kage-genotyper/ 2023-12-07T10:08:48,405 Getting page https://pypi.org/simple/kage-genotyper/ 2023-12-07T10:08:48,406 Found index url https://pypi.org/simple/ 2023-12-07T10:08:48,627 Fetched page https://pypi.org/simple/kage-genotyper/ as application/vnd.pypi.simple.v1+json 2023-12-07T10:08:48,635 Found link https://files.pythonhosted.org/packages/e7/66/016860668992a70bab9c872c5032fbc34e2f9ecc6936b95b4e9a0b0c812b/kage-genotyper-0.0.2.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.0.2 2023-12-07T10:08:48,636 Found link https://files.pythonhosted.org/packages/80/ee/e08c95ccb0c401cfb2049e7271acdcb455196900f035e0700f6229d6c25d/kage-genotyper-0.0.3.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.0.3 2023-12-07T10:08:48,637 Found link https://files.pythonhosted.org/packages/47/5d/a155072db4e4e73f1a7b0f115f4641172458ef39411234990de2601e453a/kage-genotyper-0.0.4.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.0.4 2023-12-07T10:08:48,637 Found link 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https://files.pythonhosted.org/packages/34/29/5624612fbd8ecc4fa9fa120a2c98a6b03990db6d0bd8b949450c31a0607a/kage-genotyper-0.0.30.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.0.30 2023-12-07T10:08:48,654 Found link https://files.pythonhosted.org/packages/e2/20/58431b71a41936744a457814111b46939b67bc9f5a8c5aa3286e97eeb370/kage-genotyper-0.1.0.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.0 2023-12-07T10:08:48,655 Found link https://files.pythonhosted.org/packages/60/02/88cd3521d06f167af9773608ac2db840bb7f90943fb8d9463436a2406baa/kage-genotyper-0.1.1.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.1 2023-12-07T10:08:48,656 Found link https://files.pythonhosted.org/packages/9d/11/2de2b62db1ed40a897bf2c8b31399ca3b3c774d5ad8732f69a08a3702261/kage-genotyper-0.1.2.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.2 2023-12-07T10:08:48,656 Found link https://files.pythonhosted.org/packages/a0/05/f5534cac773ba893d3c93012a0150dbf9f8cb535a3b33f1f03957d3dbd69/kage-genotyper-0.1.3.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.3 2023-12-07T10:08:48,657 Found link https://files.pythonhosted.org/packages/82/aa/9aced1ac4cc86f4bee19188f607e13563fb10b00353cf2dd43468ecf53b8/kage-genotyper-0.1.4.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.4 2023-12-07T10:08:48,658 Found link https://files.pythonhosted.org/packages/c7/e3/b7c4d3b74ba8925070ce4a3bf43649f3c2307e16f410784948827d60121a/kage-genotyper-0.1.5.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.5 2023-12-07T10:08:48,658 Found link https://files.pythonhosted.org/packages/03/2a/60bf909f494aa560ab360d944e5a8d50fb3c49e0b8234c66a8707450c700/kage-genotyper-0.1.6.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.6 2023-12-07T10:08:48,659 Found link https://files.pythonhosted.org/packages/92/a7/16ea375bfd0cedabe9ff3e3de05dac0200e29b8e10da32ca14fa2a08618a/kage-genotyper-0.1.7.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.7 2023-12-07T10:08:48,659 Found link https://files.pythonhosted.org/packages/38/17/f0baef7183ba4438de06bc31f1b8f2c0ff2d74d4c4722c3eb03b6775a1db/kage-genotyper-0.1.9.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.9 2023-12-07T10:08:48,660 Found link https://files.pythonhosted.org/packages/ea/65/6603d0188274d337bf016d69e92d70c0346b18cf82aee13e9636fb8a98ea/kage-genotyper-0.1.11.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.11 2023-12-07T10:08:48,660 Found link https://files.pythonhosted.org/packages/83/51/4614c411c210988f58596f9dd2074d917ba9e5434f0da4887dd7c1df7737/kage-genotyper-0.1.12.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.12 2023-12-07T10:08:48,661 Found link https://files.pythonhosted.org/packages/39/09/58efe36d13073b7e4e1d0a34ac7d4e5a30c05c6fb99a2e0723b4c7882285/kage-genotyper-0.1.13.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.13 2023-12-07T10:08:48,662 Found link https://files.pythonhosted.org/packages/77/c4/2bc34acb31ab5175cdb7a195a9fe1f59c7795cc859f869c5d5efd5dad759/kage-genotyper-0.1.14.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.1.14 2023-12-07T10:08:48,662 Found link https://files.pythonhosted.org/packages/77/e5/892007364823bbc1ff487614d77afcd1b738dadf40009ee9a7c4baf3dc41/kage-genotyper-0.2.0.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.2.0 2023-12-07T10:08:48,663 Found link https://files.pythonhosted.org/packages/c0/22/2af38d12dc8622e10ea42e304ba06fe3655398885f043098ff22a0725652/kage-genotyper-0.2.1.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.2.1 2023-12-07T10:08:48,664 Found link https://files.pythonhosted.org/packages/bd/65/426b8d4ed8b16fa400bd19959a26592979c02947830463d8da779476a20c/kage-genotyper-0.2.2.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.2.2 2023-12-07T10:08:48,664 Found link https://files.pythonhosted.org/packages/c3/8f/95df6d19af07be70be24557f51402a59aa7ce7e2e6ffa6fb041070c41582/kage-genotyper-0.2.3.tar.gz (from https://pypi.org/simple/kage-genotyper/), version: 0.2.3 2023-12-07T10:08:48,665 Fetching project page and analyzing links: https://www.piwheels.org/simple/kage-genotyper/ 2023-12-07T10:08:48,666 Getting page https://www.piwheels.org/simple/kage-genotyper/ 2023-12-07T10:08:48,667 Found index url https://www.piwheels.org/simple/ 2023-12-07T10:08:48,855 Fetched page https://www.piwheels.org/simple/kage-genotyper/ as text/html 2023-12-07T10:08:48,866 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.2.1-py3-none-any.whl#sha256=787bcfd15fdadab85ee28dd29967a3f92c4302cb16549911d93f7b95ac14c50d (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,867 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.2.0-py3-none-any.whl#sha256=c6f295d7ee07f206eb458327d59668b39e20994daa63a92c41f5eea2b751c768 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,868 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.14-py3-none-any.whl#sha256=89aa46552e9ebf050aee9b3e46e89416d8f1aea98bd1b612338c3fda037644ac (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,868 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.13-py3-none-any.whl#sha256=9bab52d5e6efcb201a0c5e79e1e7137c1edb5fbe54012b27da2e1ecec3430b40 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,868 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.12-py3-none-any.whl#sha256=cd646570f0e14c8ab99fcc6d060f5fd865d19cf26c182b9496dbd5036ef8474f (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,869 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.11-py3-none-any.whl#sha256=712cbb5cdf0871b3e86a1bfe294160b9dd2f5e975cbeb0b069608b05e61c2e63 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,869 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.9-py3-none-any.whl#sha256=abd4c09ec1c0e4e768343edc00f128ef5051e536f64ea1cf8574bc4189560df4 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,870 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.7-py3-none-any.whl#sha256=8f43fee2c6e410f98da126e538c321be6635f13c4117ae655b5903f85ba61a37 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,870 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.6-py3-none-any.whl#sha256=9a7614ebd0f8fbe1f2ffd60e6026cca8df99304e7df1a63f9a12e083dd8783c9 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,871 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.5-py3-none-any.whl#sha256=863ff32767fc3a5a4edf2d12a875bdb5282e1d7585f5cccadd07e34291bace14 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,871 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.4-py3-none-any.whl#sha256=1e408f1ed6d4777d59ddd7a160fb14c4c1f41d5c812a10b71d15c6691a376ba9 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,872 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.1.3-py3-none-any.whl#sha256=019dc5797ec7e2f674c903aec8ffec4e6144d072983bc357b84210d089c2aa00 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,872 Skipping link: No binaries permitted for kage-genotyper: 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https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.21-py3-none-any.whl#sha256=986ef6dc08553b37b5f45a3f5d4fab3fe7b7533b66c46d61d0ccd7e1805808e9 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,880 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.20-py3-none-any.whl#sha256=52ce4e67bf082e0c52c1e017279afb7f816d91a56ba7b84f05da7b2f90c5f773 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,880 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.19-py3-none-any.whl#sha256=1e722fb7bd2ba87c1876b357e13c266b42cac5fe7a90181bdf470c0adf294a8b (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,881 Skipping link: No binaries permitted for kage-genotyper: 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https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.8-py3-none-any.whl#sha256=17c38eb9469806ae1d16028b61450a754b7a2e9607b63cf4cb2c1bc4cd19f562 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,886 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.7-py3-none-any.whl#sha256=6c45550e73562e3543e4dedf63f5e42897169f62a701603f2c4a460ac1e0b5fa (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,887 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.6-py3-none-any.whl#sha256=7f26289022b49cd9611615aa9f542bea798b0827f5df45e23c5d65148fb2f169 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,887 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.5-py3-none-any.whl#sha256=dbca21ae8964d1bf38306442e517c6b17b688a29519f7675082be82135c4c98f (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,888 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.4-py3-none-any.whl#sha256=a279c71d67ea133f1cf0818eb5c559c97e5f2460cc45aba044dd17abf30d6446 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,888 Skipping link: No binaries permitted for kage-genotyper: https://www.piwheels.org/simple/kage-genotyper/kage_genotyper-0.0.3-py3-none-any.whl#sha256=7d52b7bdc251d8fa41b2627126137f9c9d6b34e76dcc9d8c85de8d0d42f6bf33 (from https://www.piwheels.org/simple/kage-genotyper/) 2023-12-07T10:08:48,889 Skipping link: not a file: https://www.piwheels.org/simple/kage-genotyper/ 2023-12-07T10:08:48,890 Skipping link: not a file: https://pypi.org/simple/kage-genotyper/ 2023-12-07T10:08:48,913 Given no hashes to check 1 links for project 'kage-genotyper': discarding no candidates 2023-12-07T10:08:48,931 Collecting kage-genotyper==0.2.2 2023-12-07T10:08:48,933 Created temporary directory: /tmp/pip-unpack-r47h1sye 2023-12-07T10:08:49,154 Downloading kage-genotyper-0.2.2.tar.gz (12.8 MB) 2023-12-07T10:08:51,597 Added kage-genotyper==0.2.2 from https://files.pythonhosted.org/packages/bd/65/426b8d4ed8b16fa400bd19959a26592979c02947830463d8da779476a20c/kage-genotyper-0.2.2.tar.gz to build tracker '/tmp/pip-build-tracker-bvm66ogb' 2023-12-07T10:08:51,599 Running setup.py (path:/tmp/pip-wheel-zvqf1dao/kage-genotyper_76f2f25465194600b08ad53626a018e5/setup.py) egg_info for package kage-genotyper 2023-12-07T10:08:51,599 Created temporary directory: /tmp/pip-pip-egg-info-gpuue8pc 2023-12-07T10:08:51,600 Preparing metadata (setup.py): started 2023-12-07T10:08:51,601 Running command python setup.py egg_info 2023-12-07T10:08:52,631 running egg_info 2023-12-07T10:08:52,632 creating /tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info 2023-12-07T10:08:52,656 writing /tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info/PKG-INFO 2023-12-07T10:08:52,660 writing dependency_links to /tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info/dependency_links.txt 2023-12-07T10:08:52,661 writing entry points to /tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info/entry_points.txt 2023-12-07T10:08:52,663 writing requirements to /tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info/requires.txt 2023-12-07T10:08:52,663 writing top-level names to /tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info/top_level.txt 2023-12-07T10:08:52,665 writing manifest file '/tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info/SOURCES.txt' 2023-12-07T10:08:52,750 reading manifest file '/tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info/SOURCES.txt' 2023-12-07T10:08:52,752 adding license file 'LICENSE' 2023-12-07T10:08:52,756 writing manifest file '/tmp/pip-pip-egg-info-gpuue8pc/kage_genotyper.egg-info/SOURCES.txt' 2023-12-07T10:08:52,860 Preparing metadata (setup.py): finished with status 'done' 2023-12-07T10:08:52,864 Source in /tmp/pip-wheel-zvqf1dao/kage-genotyper_76f2f25465194600b08ad53626a018e5 has version 0.2.2, which satisfies requirement kage-genotyper==0.2.2 from https://files.pythonhosted.org/packages/bd/65/426b8d4ed8b16fa400bd19959a26592979c02947830463d8da779476a20c/kage-genotyper-0.2.2.tar.gz 2023-12-07T10:08:52,865 Removed kage-genotyper==0.2.2 from https://files.pythonhosted.org/packages/bd/65/426b8d4ed8b16fa400bd19959a26592979c02947830463d8da779476a20c/kage-genotyper-0.2.2.tar.gz from build tracker '/tmp/pip-build-tracker-bvm66ogb' 2023-12-07T10:08:52,870 Created temporary directory: /tmp/pip-unpack-tuvp1uvs 2023-12-07T10:08:52,871 Created temporary directory: /tmp/pip-unpack-yff711ik 2023-12-07T10:08:52,892 Building wheels for collected packages: kage-genotyper 2023-12-07T10:08:52,896 Created temporary directory: /tmp/pip-wheel-b6koz_pr 2023-12-07T10:08:52,896 Building wheel for kage-genotyper (setup.py): started 2023-12-07T10:08:52,898 Destination directory: /tmp/pip-wheel-b6koz_pr 2023-12-07T10:08:52,898 Running command python setup.py bdist_wheel 2023-12-07T10:08:53,882 running bdist_wheel 2023-12-07T10:08:53,978 running build 2023-12-07T10:08:53,979 running build_py 2023-12-07T10:08:54,007 creating build 2023-12-07T10:08:54,007 creating build/lib 2023-12-07T10:08:54,008 creating build/lib/kage 2023-12-07T10:08:54,009 copying kage/io.py -> build/lib/kage 2023-12-07T10:08:54,012 copying kage/util.py -> build/lib/kage 2023-12-07T10:08:54,014 copying kage/__init__.py -> build/lib/kage 2023-12-07T10:08:54,016 copying kage/variant_filtering.py -> build/lib/kage 2023-12-07T10:08:54,017 copying kage/node_counts.py -> build/lib/kage 2023-12-07T10:08:54,019 copying kage/command_line_interface.py -> build/lib/kage 2023-12-07T10:08:54,022 copying kage/configuration.py -> build/lib/kage 2023-12-07T10:08:54,024 creating build/lib/kage/models 2023-12-07T10:08:54,025 copying kage/models/sampling_combo_model.py -> build/lib/kage/models 2023-12-07T10:08:54,028 copying kage/models/helper_model.py -> build/lib/kage/models 2023-12-07T10:08:54,030 copying kage/models/models.py -> build/lib/kage/models 2023-12-07T10:08:54,032 copying kage/models/helper_index_using_duplicate_counts.py -> build/lib/kage/models 2023-12-07T10:08:54,034 copying kage/models/joint_distribution.py -> build/lib/kage/models 2023-12-07T10:08:54,035 copying kage/models/__init__.py -> build/lib/kage/models 2023-12-07T10:08:54,037 copying kage/models/helper_index.py -> build/lib/kage/models 2023-12-07T10:08:54,039 copying kage/models/mapping_model.py -> build/lib/kage/models 2023-12-07T10:08:54,041 creating build/lib/kage/genotyping 2023-12-07T10:08:54,042 copying kage/genotyping/multiallelic.py -> build/lib/kage/genotyping 2023-12-07T10:08:54,044 copying kage/genotyping/__init__.py -> build/lib/kage/genotyping 2023-12-07T10:08:54,045 copying kage/genotyping/combination_model_genotyper.py -> build/lib/kage/genotyping 2023-12-07T10:08:54,048 creating build/lib/kage/benchmarking 2023-12-07T10:08:54,049 copying kage/benchmarking/__init__.py -> build/lib/kage/benchmarking 2023-12-07T10:08:54,050 copying kage/benchmarking/vcf_preprocessing.py -> build/lib/kage/benchmarking 2023-12-07T10:08:54,053 creating build/lib/kage/modles 2023-12-07T10:08:54,054 copying kage/modles/__init__.py -> build/lib/kage/modles 2023-12-07T10:08:54,056 creating build/lib/kage/indexing 2023-12-07T10:08:54,057 copying kage/indexing/kmer_scoring.py -> build/lib/kage/indexing 2023-12-07T10:08:54,059 copying kage/indexing/main.py -> build/lib/kage/indexing 2023-12-07T10:08:54,062 copying kage/indexing/path_based_count_model.py -> build/lib/kage/indexing 2023-12-07T10:08:54,064 copying kage/indexing/tricky_variants.py -> build/lib/kage/indexing 2023-12-07T10:08:54,066 copying kage/indexing/sparse_haplotype_matrix.py -> build/lib/kage/indexing 2023-12-07T10:08:54,068 copying kage/indexing/graph.py -> build/lib/kage/indexing 2023-12-07T10:08:54,071 copying kage/indexing/__init__.py -> build/lib/kage/indexing 2023-12-07T10:08:54,072 copying kage/indexing/index_bundle.py -> build/lib/kage/indexing 2023-12-07T10:08:54,074 copying kage/indexing/modulo_filter.py -> build/lib/kage/indexing 2023-12-07T10:08:54,075 copying kage/indexing/div.py -> build/lib/kage/indexing 2023-12-07T10:08:54,077 copying kage/indexing/paths.py -> build/lib/kage/indexing 2023-12-07T10:08:54,080 copying kage/indexing/path_variant_indexing.py -> build/lib/kage/indexing 2023-12-07T10:08:54,084 copying kage/indexing/signatures.py -> build/lib/kage/indexing 2023-12-07T10:08:54,087 creating build/lib/kage/simulation 2023-12-07T10:08:54,088 copying kage/simulation/read_simulation.py -> build/lib/kage/simulation 2023-12-07T10:08:54,090 copying kage/simulation/__init__.py -> build/lib/kage/simulation 2023-12-07T10:08:54,092 copying kage/simulation/simulation.py -> build/lib/kage/simulation 2023-12-07T10:08:54,095 creating build/lib/kage/analysis 2023-12-07T10:08:54,096 copying kage/analysis/debugging.py -> build/lib/kage/analysis 2023-12-07T10:08:54,098 copying kage/analysis/analysis.py -> build/lib/kage/analysis 2023-12-07T10:08:54,101 copying kage/analysis/__init__.py -> build/lib/kage/analysis 2023-12-07T10:08:54,102 copying kage/analysis/variant_kmer_analyser.py -> build/lib/kage/analysis 2023-12-07T10:08:54,104 copying kage/analysis/genotype_accuracy.py -> build/lib/kage/analysis 2023-12-07T10:08:54,107 creating build/lib/kage/preprocessing 2023-12-07T10:08:54,108 copying kage/preprocessing/__init__.py -> build/lib/kage/preprocessing 2023-12-07T10:08:54,110 copying kage/preprocessing/variants.py -> build/lib/kage/preprocessing 2023-12-07T10:08:54,146 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-12-07T10:08:54,147 !! 2023-12-07T10:08:54,148 ******************************************************************************** 2023-12-07T10:08:54,149 Please avoid running ``setup.py`` directly. 2023-12-07T10:08:54,149 Instead, use pypa/build, pypa/installer or other 2023-12-07T10:08:54,149 standards-based tools. 2023-12-07T10:08:54,150 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-12-07T10:08:54,151 ******************************************************************************** 2023-12-07T10:08:54,151 !! 2023-12-07T10:08:54,152 self.initialize_options() 2023-12-07T10:08:54,173 installing to build/bdist.linux-armv7l/wheel 2023-12-07T10:08:54,174 running install 2023-12-07T10:08:54,198 running install_lib 2023-12-07T10:08:54,224 creating build/bdist.linux-armv7l 2023-12-07T10:08:54,224 creating build/bdist.linux-armv7l/wheel 2023-12-07T10:08:54,226 creating build/bdist.linux-armv7l/wheel/kage 2023-12-07T10:08:54,227 creating build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,228 copying build/lib/kage/models/sampling_combo_model.py -> build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,231 copying build/lib/kage/models/helper_model.py -> build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,233 copying build/lib/kage/models/models.py -> build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,235 copying build/lib/kage/models/helper_index_using_duplicate_counts.py -> build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,237 copying build/lib/kage/models/joint_distribution.py -> build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,239 copying build/lib/kage/models/__init__.py -> build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,240 copying build/lib/kage/models/helper_index.py -> build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,242 copying build/lib/kage/models/mapping_model.py -> build/bdist.linux-armv7l/wheel/kage/models 2023-12-07T10:08:54,245 creating build/bdist.linux-armv7l/wheel/kage/genotyping 2023-12-07T10:08:54,246 copying build/lib/kage/genotyping/multiallelic.py -> build/bdist.linux-armv7l/wheel/kage/genotyping 2023-12-07T10:08:54,248 copying build/lib/kage/genotyping/__init__.py -> build/bdist.linux-armv7l/wheel/kage/genotyping 2023-12-07T10:08:54,249 copying build/lib/kage/genotyping/combination_model_genotyper.py -> build/bdist.linux-armv7l/wheel/kage/genotyping 2023-12-07T10:08:54,252 creating build/bdist.linux-armv7l/wheel/kage/benchmarking 2023-12-07T10:08:54,253 copying build/lib/kage/benchmarking/__init__.py -> build/bdist.linux-armv7l/wheel/kage/benchmarking 2023-12-07T10:08:54,255 copying build/lib/kage/benchmarking/vcf_preprocessing.py -> build/bdist.linux-armv7l/wheel/kage/benchmarking 2023-12-07T10:08:54,257 copying build/lib/kage/io.py -> build/bdist.linux-armv7l/wheel/kage 2023-12-07T10:08:54,260 creating build/bdist.linux-armv7l/wheel/kage/modles 2023-12-07T10:08:54,260 copying build/lib/kage/modles/__init__.py -> build/bdist.linux-armv7l/wheel/kage/modles 2023-12-07T10:08:54,262 copying build/lib/kage/util.py -> build/bdist.linux-armv7l/wheel/kage 2023-12-07T10:08:54,264 copying build/lib/kage/__init__.py -> build/bdist.linux-armv7l/wheel/kage 2023-12-07T10:08:54,266 copying build/lib/kage/variant_filtering.py -> build/bdist.linux-armv7l/wheel/kage 2023-12-07T10:08:54,269 creating build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,269 copying build/lib/kage/indexing/kmer_scoring.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,272 copying build/lib/kage/indexing/main.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,275 copying build/lib/kage/indexing/path_based_count_model.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,277 copying build/lib/kage/indexing/tricky_variants.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,280 copying build/lib/kage/indexing/sparse_haplotype_matrix.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,282 copying build/lib/kage/indexing/graph.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,284 copying build/lib/kage/indexing/__init__.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,286 copying build/lib/kage/indexing/index_bundle.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,288 copying build/lib/kage/indexing/modulo_filter.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,289 copying build/lib/kage/indexing/div.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,291 copying build/lib/kage/indexing/paths.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,294 copying build/lib/kage/indexing/path_variant_indexing.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,296 copying build/lib/kage/indexing/signatures.py -> build/bdist.linux-armv7l/wheel/kage/indexing 2023-12-07T10:08:54,300 copying build/lib/kage/node_counts.py -> build/bdist.linux-armv7l/wheel/kage 2023-12-07T10:08:54,302 creating build/bdist.linux-armv7l/wheel/kage/simulation 2023-12-07T10:08:54,303 copying build/lib/kage/simulation/read_simulation.py -> build/bdist.linux-armv7l/wheel/kage/simulation 2023-12-07T10:08:54,305 copying build/lib/kage/simulation/__init__.py -> build/bdist.linux-armv7l/wheel/kage/simulation 2023-12-07T10:08:54,307 copying build/lib/kage/simulation/simulation.py -> build/bdist.linux-armv7l/wheel/kage/simulation 2023-12-07T10:08:54,309 copying build/lib/kage/command_line_interface.py -> build/bdist.linux-armv7l/wheel/kage 2023-12-07T10:08:54,312 creating build/bdist.linux-armv7l/wheel/kage/analysis 2023-12-07T10:08:54,313 copying build/lib/kage/analysis/debugging.py -> build/bdist.linux-armv7l/wheel/kage/analysis 2023-12-07T10:08:54,316 copying build/lib/kage/analysis/analysis.py -> build/bdist.linux-armv7l/wheel/kage/analysis 2023-12-07T10:08:54,320 copying build/lib/kage/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/kage/analysis 2023-12-07T10:08:54,322 copying build/lib/kage/analysis/variant_kmer_analyser.py -> build/bdist.linux-armv7l/wheel/kage/analysis 2023-12-07T10:08:54,323 copying build/lib/kage/analysis/genotype_accuracy.py -> build/bdist.linux-armv7l/wheel/kage/analysis 2023-12-07T10:08:54,326 copying build/lib/kage/configuration.py -> build/bdist.linux-armv7l/wheel/kage 2023-12-07T10:08:54,329 creating build/bdist.linux-armv7l/wheel/kage/preprocessing 2023-12-07T10:08:54,329 copying build/lib/kage/preprocessing/__init__.py -> build/bdist.linux-armv7l/wheel/kage/preprocessing 2023-12-07T10:08:54,331 copying build/lib/kage/preprocessing/variants.py -> build/bdist.linux-armv7l/wheel/kage/preprocessing 2023-12-07T10:08:54,334 running install_egg_info 2023-12-07T10:08:54,395 running egg_info 2023-12-07T10:08:54,420 writing kage_genotyper.egg-info/PKG-INFO 2023-12-07T10:08:54,423 writing dependency_links to kage_genotyper.egg-info/dependency_links.txt 2023-12-07T10:08:54,425 writing entry points to kage_genotyper.egg-info/entry_points.txt 2023-12-07T10:08:54,427 writing requirements to kage_genotyper.egg-info/requires.txt 2023-12-07T10:08:54,428 writing top-level names to kage_genotyper.egg-info/top_level.txt 2023-12-07T10:08:54,462 reading manifest file 'kage_genotyper.egg-info/SOURCES.txt' 2023-12-07T10:08:54,468 adding license file 'LICENSE' 2023-12-07T10:08:54,473 writing manifest file 'kage_genotyper.egg-info/SOURCES.txt' 2023-12-07T10:08:54,475 Copying kage_genotyper.egg-info to build/bdist.linux-armv7l/wheel/kage_genotyper-0.2.2-py3.11.egg-info 2023-12-07T10:08:54,489 running install_scripts 2023-12-07T10:08:54,508 creating build/bdist.linux-armv7l/wheel/kage_genotyper-0.2.2.dist-info/WHEEL 2023-12-07T10:08:54,511 creating '/tmp/pip-wheel-b6koz_pr/kage_genotyper-0.2.2-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-12-07T10:08:54,513 adding 'kage/__init__.py' 2023-12-07T10:08:54,516 adding 'kage/command_line_interface.py' 2023-12-07T10:08:54,518 adding 'kage/configuration.py' 2023-12-07T10:08:54,520 adding 'kage/io.py' 2023-12-07T10:08:54,521 adding 'kage/node_counts.py' 2023-12-07T10:08:54,523 adding 'kage/util.py' 2023-12-07T10:08:54,524 adding 'kage/variant_filtering.py' 2023-12-07T10:08:54,526 adding 'kage/analysis/__init__.py' 2023-12-07T10:08:54,528 adding 'kage/analysis/analysis.py' 2023-12-07T10:08:54,530 adding 'kage/analysis/debugging.py' 2023-12-07T10:08:54,533 adding 'kage/analysis/genotype_accuracy.py' 2023-12-07T10:08:54,535 adding 'kage/analysis/variant_kmer_analyser.py' 2023-12-07T10:08:54,536 adding 'kage/benchmarking/__init__.py' 2023-12-07T10:08:54,538 adding 'kage/benchmarking/vcf_preprocessing.py' 2023-12-07T10:08:54,540 adding 'kage/genotyping/__init__.py' 2023-12-07T10:08:54,541 adding 'kage/genotyping/combination_model_genotyper.py' 2023-12-07T10:08:54,543 adding 'kage/genotyping/multiallelic.py' 2023-12-07T10:08:54,545 adding 'kage/indexing/__init__.py' 2023-12-07T10:08:54,546 adding 'kage/indexing/div.py' 2023-12-07T10:08:54,548 adding 'kage/indexing/graph.py' 2023-12-07T10:08:54,549 adding 'kage/indexing/index_bundle.py' 2023-12-07T10:08:54,551 adding 'kage/indexing/kmer_scoring.py' 2023-12-07T10:08:54,554 adding 'kage/indexing/main.py' 2023-12-07T10:08:54,555 adding 'kage/indexing/modulo_filter.py' 2023-12-07T10:08:54,558 adding 'kage/indexing/path_based_count_model.py' 2023-12-07T10:08:54,560 adding 'kage/indexing/path_variant_indexing.py' 2023-12-07T10:08:54,563 adding 'kage/indexing/paths.py' 2023-12-07T10:08:54,569 adding 'kage/indexing/signatures.py' 2023-12-07T10:08:54,572 adding 'kage/indexing/sparse_haplotype_matrix.py' 2023-12-07T10:08:54,573 adding 'kage/indexing/tricky_variants.py' 2023-12-07T10:08:54,575 adding 'kage/models/__init__.py' 2023-12-07T10:08:54,576 adding 'kage/models/helper_index.py' 2023-12-07T10:08:54,578 adding 'kage/models/helper_index_using_duplicate_counts.py' 2023-12-07T10:08:54,580 adding 'kage/models/helper_model.py' 2023-12-07T10:08:54,581 adding 'kage/models/joint_distribution.py' 2023-12-07T10:08:54,583 adding 'kage/models/mapping_model.py' 2023-12-07T10:08:54,585 adding 'kage/models/models.py' 2023-12-07T10:08:54,588 adding 'kage/models/sampling_combo_model.py' 2023-12-07T10:08:54,589 adding 'kage/modles/__init__.py' 2023-12-07T10:08:54,591 adding 'kage/preprocessing/__init__.py' 2023-12-07T10:08:54,595 adding 'kage/preprocessing/variants.py' 2023-12-07T10:08:54,597 adding 'kage/simulation/__init__.py' 2023-12-07T10:08:54,599 adding 'kage/simulation/read_simulation.py' 2023-12-07T10:08:54,600 adding 'kage/simulation/simulation.py' 2023-12-07T10:08:54,607 adding 'kage_genotyper-0.2.2.dist-info/LICENSE' 2023-12-07T10:08:54,609 adding 'kage_genotyper-0.2.2.dist-info/METADATA' 2023-12-07T10:08:54,610 adding 'kage_genotyper-0.2.2.dist-info/WHEEL' 2023-12-07T10:08:54,611 adding 'kage_genotyper-0.2.2.dist-info/entry_points.txt' 2023-12-07T10:08:54,612 adding 'kage_genotyper-0.2.2.dist-info/top_level.txt' 2023-12-07T10:08:54,613 adding 'kage_genotyper-0.2.2.dist-info/RECORD' 2023-12-07T10:08:54,617 removing build/bdist.linux-armv7l/wheel 2023-12-07T10:08:54,738 Building wheel for kage-genotyper (setup.py): finished with status 'done' 2023-12-07T10:08:54,742 Created wheel for kage-genotyper: filename=kage_genotyper-0.2.2-py3-none-any.whl size=117282 sha256=88d2948dca9541da3d416e6931026b4f4cf80b78c15c58a58b9ce9ae1665e343 2023-12-07T10:08:54,744 Stored in directory: /tmp/pip-ephem-wheel-cache-61rgt80o/wheels/ab/a9/e0/733a02a8852587957df70d38aea83cad40400f7a66c4fa4803 2023-12-07T10:08:54,756 Successfully built kage-genotyper 2023-12-07T10:08:54,763 Removed build tracker: '/tmp/pip-build-tracker-bvm66ogb'