2023-07-17T16:58:49,883 Created temporary directory: /tmp/pip-build-tracker-2vjnzvus 2023-07-17T16:58:49,887 Initialized build tracking at /tmp/pip-build-tracker-2vjnzvus 2023-07-17T16:58:49,887 Created build tracker: /tmp/pip-build-tracker-2vjnzvus 2023-07-17T16:58:49,887 Entered build tracker: /tmp/pip-build-tracker-2vjnzvus 2023-07-17T16:58:49,889 Created temporary directory: /tmp/pip-wheel-nt8hsn1b 2023-07-17T16:58:49,897 Created temporary directory: /tmp/pip-ephem-wheel-cache-smmovb_8 2023-07-17T16:58:49,951 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-07-17T16:58:49,959 2 location(s) to search for versions of mgatk: 2023-07-17T16:58:49,959 * https://pypi.org/simple/mgatk/ 2023-07-17T16:58:49,959 * https://www.piwheels.org/simple/mgatk/ 2023-07-17T16:58:49,960 Fetching project page and analyzing links: https://pypi.org/simple/mgatk/ 2023-07-17T16:58:49,961 Getting page https://pypi.org/simple/mgatk/ 2023-07-17T16:58:49,965 Found index url https://pypi.org/simple/ 2023-07-17T16:58:50,155 Fetched page https://pypi.org/simple/mgatk/ as application/vnd.pypi.simple.v1+json 2023-07-17T16:58:50,166 Found link https://files.pythonhosted.org/packages/8f/0c/47da433403828d2e53de436d7689af32d8ee5130dc1c748ce0175d0f2eb1/mgatk-0.0.1.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.0.1 2023-07-17T16:58:50,167 Found link https://files.pythonhosted.org/packages/f7/7f/f09842055b19e670fbc309415123b423d30cc0fd1a8c430785bd1754827f/mgatk-0.1.0.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.1.0 2023-07-17T16:58:50,168 Found link https://files.pythonhosted.org/packages/b7/8e/ac9ab509199f852d88097608e3fb60fc85232c87a36a062a041043ea869d/mgatk-0.2.5.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.2.5 2023-07-17T16:58:50,169 Found link https://files.pythonhosted.org/packages/74/28/da183d0b56f401dec7f3bded24c50a02396e56c4f995fd50a3cf21c4381d/mgatk-0.5.0.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.5.0 2023-07-17T16:58:50,169 Found link https://files.pythonhosted.org/packages/96/e8/e35c039eac8d418ca9213b1db69c4176b59783ca43638a75e824b475197d/mgatk-0.5.1.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.5.1 2023-07-17T16:58:50,170 Found link https://files.pythonhosted.org/packages/b6/16/d11afe05a803f23995d04af8fd832473fa1d21f73f242340f6086eb97183/mgatk-0.5.3.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.5.3 2023-07-17T16:58:50,171 Found link https://files.pythonhosted.org/packages/be/5f/896adc0419fad47b3434866dd68deb7b93a1328916be0eb1f0827393633e/mgatk-0.5.5.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.5.5 2023-07-17T16:58:50,171 Found link https://files.pythonhosted.org/packages/d0/3d/4a67edbf2648ab25ee6b2361e454638ecd5de6753a0c5f3de21975a7c5bd/mgatk-0.5.6.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.5.6 2023-07-17T16:58:50,172 Found link https://files.pythonhosted.org/packages/64/fa/87883d229672ffb048510fb9eade72ad77fb6ea787e82631311fdf2099c9/mgatk-0.5.7.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.5.7 2023-07-17T16:58:50,173 Found link https://files.pythonhosted.org/packages/9e/e3/9ff8a48cac72aaaea4c5c9bdbe71925be6763d6d71ce032905f23c2bc4b6/mgatk-0.5.8.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.5.8 2023-07-17T16:58:50,173 Found link https://files.pythonhosted.org/packages/f1/06/47716f2b5fec77a4a48fb5f3722ec27da0ce98d2219cb2eceb113fc72d8b/mgatk-0.5.9.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.5.9 2023-07-17T16:58:50,174 Found link https://files.pythonhosted.org/packages/e6/73/33c2bdc77eead0a8d9b81a38adb54b75f804b189adabad25795edb5bdc60/mgatk-0.6.0.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.0 2023-07-17T16:58:50,175 Found link https://files.pythonhosted.org/packages/20/57/9e2171535e864b06353f2ef16f9bcbc8308f92406c9909e65fe2a7aa39a6/mgatk-0.6.1.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.1 2023-07-17T16:58:50,175 Found link https://files.pythonhosted.org/packages/0c/20/8b326bdf214a7a05c0cf4f9469bb42ba3005cb3b749af130ff8d7a3dbef2/mgatk-0.6.2.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.2 2023-07-17T16:58:50,176 Found link https://files.pythonhosted.org/packages/c0/c5/7b13208a566f6860899245bf07beabfefa7af72c6abb7f2ef1afaa3b76fe/mgatk-0.6.3.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.3 2023-07-17T16:58:50,177 Found link https://files.pythonhosted.org/packages/57/ab/d3cb224a9845960e129904adcfa09d4c59725c9a6abf8a7f6842765530b9/mgatk-0.6.4.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.4 2023-07-17T16:58:50,178 Found link https://files.pythonhosted.org/packages/21/1f/a19a9984313d6cc4243c7b3bd0c1b1a811f55c369a44222c74fac075e6db/mgatk-0.6.6.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.6 2023-07-17T16:58:50,178 Found link https://files.pythonhosted.org/packages/c5/e9/c9ca2e20b08b9d5c16c56598bff3ef3d77b93dfd39552d07e374de43d069/mgatk-0.6.7.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.7 2023-07-17T16:58:50,179 Found link https://files.pythonhosted.org/packages/3f/65/b0d2081526edf3cef5c0fbfee4ad477f6b3b9c14107ae5a41e45b1b0e169/mgatk-0.6.8.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.8 2023-07-17T16:58:50,180 Found link https://files.pythonhosted.org/packages/26/77/fc56d5e66786658de94f3154901b739d32c6d6bef6680a62ef1dc19e40fa/mgatk-0.6.9.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.6.9 2023-07-17T16:58:50,181 Fetching project page and analyzing links: https://www.piwheels.org/simple/mgatk/ 2023-07-17T16:58:50,181 Getting page https://www.piwheels.org/simple/mgatk/ 2023-07-17T16:58:50,184 Found index url https://www.piwheels.org/simple/ 2023-07-17T16:58:50,408 Fetched page https://www.piwheels.org/simple/mgatk/ as text/html 2023-07-17T16:58:50,424 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.6.8-py2.py3-none-any.whl#sha256=ee01a0d2c63bbec27ac1c2ab8e29aa90ebe118a13dc3113c74dabb1e233256eb (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,425 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.6.7-py2.py3-none-any.whl#sha256=79fed343da0db4117616398f89d660c2fbd8e79fe68fb94ec1aefc118d87648a (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,425 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.6.6-py2.py3-none-any.whl#sha256=db1b17b9efe2010d5474e233eb127e3b9ebbaa04eaebe474d461622e040bc634 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,426 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.6.4-py2.py3-none-any.whl#sha256=58b5484ca92bb15aac4a8f9063b494c87022e986d856ae9c5e4fc15002965db7 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,427 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.6.3-py2.py3-none-any.whl#sha256=360fb6d8cb87a3d76ecd2ac7a4b94e1f13cdcd515050c8926af8309672d0c0d2 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,427 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.6.2-py2.py3-none-any.whl#sha256=ad87bf28d8140677cd9328a5b9582470aedc1867c3a9b307d9420c2712454009 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,428 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.6.1-py2.py3-none-any.whl#sha256=751c5ba1854115dc6815f5c3b6fcaa4860c66dc8970dfcf7449b18cd4306395e (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,429 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.6.0-py2.py3-none-any.whl#sha256=36135d81a973357f7125fb1ff898ef3590364d14ee64ee4f9c6a25b1340d78ca (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,429 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.5.9-py2.py3-none-any.whl#sha256=7078b4d3d77e2260f01ca68bb7f6707cb4a2c852ed2c7a5e4f7a6c68cc1c50e2 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,430 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.5.8-py2.py3-none-any.whl#sha256=6e2875d8620ce7ed459c23ad983c0413adef335eabc99b82aedd074c181592d0 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,430 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.5.7-py2.py3-none-any.whl#sha256=95b59ea0189b6f7d87453823792ba21b9f45deaaeb5a205ccb173694fd16c43d (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,431 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.5.6-py2.py3-none-any.whl#sha256=a199b8ec80e8f6581d33504f49229ef908c215936379d77f622394cf1ab2b558 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,432 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.5.5-py2.py3-none-any.whl#sha256=ff9f09e518b7936a8a6923a2d095fa02bb30822361e426c072ea2018006d5f96 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,432 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.5.3-py2.py3-none-any.whl#sha256=f7709526d1c046488d849a38c4b85838814c2db9a8e9b140f8f706febe4bed36 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,433 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.5.1-py2.py3-none-any.whl#sha256=886bbaef1900c90d54489c15e59b0f38125d0aca802a551b958af8e9b34c8101 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,433 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.5.0-py2.py3-none-any.whl#sha256=906c45dd6c1ccb708de36350b787e0dfbda0a4d49a08f02c211deec0c5d19da9 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,434 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.2.5-py2.py3-none-any.whl#sha256=9c0333783e998b2493f6bbd8d93e2a5ce9f332bd53d83e3ff3fe0ce921182b3a (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,435 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.1.0-py2.py3-none-any.whl#sha256=cef81c26f6eb16952e9f8d05c24dc85d491f400645c82c478dddfd64b785d487 (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,435 Skipping link: No binaries permitted for mgatk: https://www.piwheels.org/simple/mgatk/mgatk-0.0.1-py2.py3-none-any.whl#sha256=7e7d06dc92473d5d2f2c99cc022aaf64ab8d0301f1a1bd06edb2b37e8a17efbc (from https://www.piwheels.org/simple/mgatk/) 2023-07-17T16:58:50,436 Skipping link: not a file: https://www.piwheels.org/simple/mgatk/ 2023-07-17T16:58:50,437 Skipping link: not a file: https://pypi.org/simple/mgatk/ 2023-07-17T16:58:50,476 Given no hashes to check 1 links for project 'mgatk': discarding no candidates 2023-07-17T16:58:50,511 Collecting mgatk==0.6.9 2023-07-17T16:58:50,516 Created temporary directory: /tmp/pip-unpack-1573x4_a 2023-07-17T16:58:50,794 Downloading mgatk-0.6.9.tar.gz (14.3 MB) 2023-07-17T16:58:56,310 Added mgatk==0.6.9 from https://files.pythonhosted.org/packages/26/77/fc56d5e66786658de94f3154901b739d32c6d6bef6680a62ef1dc19e40fa/mgatk-0.6.9.tar.gz to build tracker '/tmp/pip-build-tracker-2vjnzvus' 2023-07-17T16:58:56,316 Running setup.py (path:/tmp/pip-wheel-nt8hsn1b/mgatk_774917b4556940fbba98cf81e3abdabe/setup.py) egg_info for package mgatk 2023-07-17T16:58:56,317 Created temporary directory: /tmp/pip-pip-egg-info-m1ig0heh 2023-07-17T16:58:56,318 Preparing metadata (setup.py): started 2023-07-17T16:58:56,320 Running command python setup.py egg_info 2023-07-17T16:58:57,907 running egg_info 2023-07-17T16:58:57,912 creating /tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info 2023-07-17T16:58:57,977 writing /tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info/PKG-INFO 2023-07-17T16:58:57,982 writing dependency_links to /tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info/dependency_links.txt 2023-07-17T16:58:57,986 writing entry points to /tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info/entry_points.txt 2023-07-17T16:58:57,989 writing requirements to /tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info/requires.txt 2023-07-17T16:58:57,991 writing top-level names to /tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info/top_level.txt 2023-07-17T16:58:57,994 writing manifest file '/tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info/SOURCES.txt' 2023-07-17T16:58:58,196 reading manifest file '/tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info/SOURCES.txt' 2023-07-17T16:58:58,200 reading manifest template 'MANIFEST.in' 2023-07-17T16:58:58,203 /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-07-17T16:58:58,203 !! 2023-07-17T16:58:58,204 ******************************************************************************** 2023-07-17T16:58:58,204 Usage of dash-separated 'description-file' will not be supported in future 2023-07-17T16:58:58,205 versions. Please use the underscore name 'description_file' instead. 2023-07-17T16:58:58,205 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-07-17T16:58:58,206 or your builds will no longer be supported. 2023-07-17T16:58:58,206 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-07-17T16:58:58,207 ******************************************************************************** 2023-07-17T16:58:58,208 !! 2023-07-17T16:58:58,208 opt = self.warn_dash_deprecation(opt, section) 2023-07-17T16:58:58,209 no previously-included directories found matching 'mgatk.egg-info/' 2023-07-17T16:58:58,209 no previously-included directories found matching 'tests/' 2023-07-17T16:58:58,209 no previously-included directories found matching '*.DS_Store' 2023-07-17T16:58:58,258 adding license file 'LICENSE.txt' 2023-07-17T16:58:58,267 writing manifest file '/tmp/pip-pip-egg-info-m1ig0heh/mgatk.egg-info/SOURCES.txt' 2023-07-17T16:58:58,388 Preparing metadata (setup.py): finished with status 'done' 2023-07-17T16:58:58,402 Source in /tmp/pip-wheel-nt8hsn1b/mgatk_774917b4556940fbba98cf81e3abdabe has version 0.6.9, which satisfies requirement mgatk==0.6.9 from https://files.pythonhosted.org/packages/26/77/fc56d5e66786658de94f3154901b739d32c6d6bef6680a62ef1dc19e40fa/mgatk-0.6.9.tar.gz 2023-07-17T16:58:58,404 Removed mgatk==0.6.9 from https://files.pythonhosted.org/packages/26/77/fc56d5e66786658de94f3154901b739d32c6d6bef6680a62ef1dc19e40fa/mgatk-0.6.9.tar.gz from build tracker '/tmp/pip-build-tracker-2vjnzvus' 2023-07-17T16:58:58,415 Created temporary directory: /tmp/pip-unpack-15hf07kd 2023-07-17T16:58:58,416 Building wheels for collected packages: mgatk 2023-07-17T16:58:58,426 Created temporary directory: /tmp/pip-wheel-8u0xyx3b 2023-07-17T16:58:58,427 Building wheel for mgatk (setup.py): started 2023-07-17T16:58:58,429 Destination directory: /tmp/pip-wheel-8u0xyx3b 2023-07-17T16:58:58,429 Running command python setup.py bdist_wheel 2023-07-17T16:58:59,597 /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options 2023-07-17T16:58:59,598 !! 2023-07-17T16:58:59,599 ******************************************************************************** 2023-07-17T16:58:59,600 Usage of dash-separated 'description-file' will not be supported in future 2023-07-17T16:58:59,600 versions. Please use the underscore name 'description_file' instead. 2023-07-17T16:58:59,601 By 2023-Sep-26, you need to update your project and remove deprecated calls 2023-07-17T16:58:59,601 or your builds will no longer be supported. 2023-07-17T16:58:59,602 See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details. 2023-07-17T16:58:59,602 ******************************************************************************** 2023-07-17T16:58:59,603 !! 2023-07-17T16:58:59,603 opt = self.warn_dash_deprecation(opt, section) 2023-07-17T16:59:00,021 running bdist_wheel 2023-07-17T16:59:00,728 running build 2023-07-17T16:59:00,729 running build_py 2023-07-17T16:59:00,801 creating build 2023-07-17T16:59:00,802 creating build/lib 2023-07-17T16:59:00,804 creating build/lib/mgatk 2023-07-17T16:59:00,806 copying mgatk/mgatkHelp.py -> build/lib/mgatk 2023-07-17T16:59:00,811 copying mgatk/cli.py -> build/lib/mgatk 2023-07-17T16:59:00,816 copying mgatk/__init__.py -> build/lib/mgatk 2023-07-17T16:59:00,819 running egg_info 2023-07-17T16:59:00,972 writing mgatk.egg-info/PKG-INFO 2023-07-17T16:59:00,976 writing dependency_links to mgatk.egg-info/dependency_links.txt 2023-07-17T16:59:00,980 writing entry points to mgatk.egg-info/entry_points.txt 2023-07-17T16:59:00,983 writing requirements to mgatk.egg-info/requires.txt 2023-07-17T16:59:00,985 writing top-level names to mgatk.egg-info/top_level.txt 2023-07-17T16:59:01,055 reading manifest file 'mgatk.egg-info/SOURCES.txt' 2023-07-17T16:59:01,062 reading manifest template 'MANIFEST.in' 2023-07-17T16:59:01,065 no previously-included directories found matching 'tests/' 2023-07-17T16:59:01,067 no previously-included directories found matching '*.DS_Store' 2023-07-17T16:59:01,113 adding license file 'LICENSE.txt' 2023-07-17T16:59:01,123 writing manifest file 'mgatk.egg-info/SOURCES.txt' 2023-07-17T16:59:01,128 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.__pycache__' is absent from the `packages` configuration. 2023-07-17T16:59:01,129 !! 2023-07-17T16:59:01,129 ******************************************************************************** 2023-07-17T16:59:01,129 ############################ 2023-07-17T16:59:01,130 # Package would be ignored # 2023-07-17T16:59:01,130 ############################ 2023-07-17T16:59:01,130 Python recognizes 'mgatk.__pycache__' as an importable package[^1], 2023-07-17T16:59:01,131 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,131 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,132 package, please make sure that 'mgatk.__pycache__' is explicitly added 2023-07-17T16:59:01,132 to the `packages` configuration field. 2023-07-17T16:59:01,133 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,133 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,133 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,134 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,134 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,135 If you don't want 'mgatk.__pycache__' to be distributed and are 2023-07-17T16:59:01,135 already explicitly excluding 'mgatk.__pycache__' via 2023-07-17T16:59:01,136 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,136 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,136 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,137 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,137 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,138 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,139 even if it does not contain any `.py` files. 2023-07-17T16:59:01,139 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,139 directory, all directories are treated like packages. 2023-07-17T16:59:01,139 ******************************************************************************** 2023-07-17T16:59:01,140 !! 2023-07-17T16:59:01,140 check.warn(importable) 2023-07-17T16:59:01,141 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin' is absent from the `packages` configuration. 2023-07-17T16:59:01,141 !! 2023-07-17T16:59:01,142 ******************************************************************************** 2023-07-17T16:59:01,142 ############################ 2023-07-17T16:59:01,142 # Package would be ignored # 2023-07-17T16:59:01,143 ############################ 2023-07-17T16:59:01,143 Python recognizes 'mgatk.bin' as an importable package[^1], 2023-07-17T16:59:01,143 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,144 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,144 package, please make sure that 'mgatk.bin' is explicitly added 2023-07-17T16:59:01,145 to the `packages` configuration field. 2023-07-17T16:59:01,145 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,146 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,146 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,147 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,147 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,148 If you don't want 'mgatk.bin' to be distributed and are 2023-07-17T16:59:01,148 already explicitly excluding 'mgatk.bin' via 2023-07-17T16:59:01,148 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,149 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,149 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,149 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,150 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,151 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,152 even if it does not contain any `.py` files. 2023-07-17T16:59:01,152 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,153 directory, all directories are treated like packages. 2023-07-17T16:59:01,153 ******************************************************************************** 2023-07-17T16:59:01,154 !! 2023-07-17T16:59:01,155 check.warn(importable) 2023-07-17T16:59:01,155 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin.R' is absent from the `packages` configuration. 2023-07-17T16:59:01,156 !! 2023-07-17T16:59:01,156 ******************************************************************************** 2023-07-17T16:59:01,157 ############################ 2023-07-17T16:59:01,157 # Package would be ignored # 2023-07-17T16:59:01,158 ############################ 2023-07-17T16:59:01,158 Python recognizes 'mgatk.bin.R' as an importable package[^1], 2023-07-17T16:59:01,158 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,159 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,160 package, please make sure that 'mgatk.bin.R' is explicitly added 2023-07-17T16:59:01,160 to the `packages` configuration field. 2023-07-17T16:59:01,161 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,161 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,162 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,163 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,164 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,164 If you don't want 'mgatk.bin.R' to be distributed and are 2023-07-17T16:59:01,165 already explicitly excluding 'mgatk.bin.R' via 2023-07-17T16:59:01,165 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,166 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,166 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,167 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,168 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,170 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,170 even if it does not contain any `.py` files. 2023-07-17T16:59:01,171 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,171 directory, all directories are treated like packages. 2023-07-17T16:59:01,171 ******************************************************************************** 2023-07-17T16:59:01,172 !! 2023-07-17T16:59:01,173 check.warn(importable) 2023-07-17T16:59:01,173 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin.anno.fasta' is absent from the `packages` configuration. 2023-07-17T16:59:01,174 !! 2023-07-17T16:59:01,175 ******************************************************************************** 2023-07-17T16:59:01,176 ############################ 2023-07-17T16:59:01,177 # Package would be ignored # 2023-07-17T16:59:01,177 ############################ 2023-07-17T16:59:01,178 Python recognizes 'mgatk.bin.anno.fasta' as an importable package[^1], 2023-07-17T16:59:01,178 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,179 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,179 package, please make sure that 'mgatk.bin.anno.fasta' is explicitly added 2023-07-17T16:59:01,180 to the `packages` configuration field. 2023-07-17T16:59:01,181 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,181 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,182 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,183 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,183 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,184 If you don't want 'mgatk.bin.anno.fasta' to be distributed and are 2023-07-17T16:59:01,185 already explicitly excluding 'mgatk.bin.anno.fasta' via 2023-07-17T16:59:01,185 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,186 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,186 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,186 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,187 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,188 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,188 even if it does not contain any `.py` files. 2023-07-17T16:59:01,189 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,189 directory, all directories are treated like packages. 2023-07-17T16:59:01,189 ******************************************************************************** 2023-07-17T16:59:01,190 !! 2023-07-17T16:59:01,190 check.warn(importable) 2023-07-17T16:59:01,190 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin.python' is absent from the `packages` configuration. 2023-07-17T16:59:01,191 !! 2023-07-17T16:59:01,191 ******************************************************************************** 2023-07-17T16:59:01,191 ############################ 2023-07-17T16:59:01,192 # Package would be ignored # 2023-07-17T16:59:01,192 ############################ 2023-07-17T16:59:01,192 Python recognizes 'mgatk.bin.python' as an importable package[^1], 2023-07-17T16:59:01,193 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,193 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,194 package, please make sure that 'mgatk.bin.python' is explicitly added 2023-07-17T16:59:01,194 to the `packages` configuration field. 2023-07-17T16:59:01,194 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,195 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,195 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,196 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,196 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,197 If you don't want 'mgatk.bin.python' to be distributed and are 2023-07-17T16:59:01,197 already explicitly excluding 'mgatk.bin.python' via 2023-07-17T16:59:01,197 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,198 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,198 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,199 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,199 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,200 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,200 even if it does not contain any `.py` files. 2023-07-17T16:59:01,201 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,201 directory, all directories are treated like packages. 2023-07-17T16:59:01,201 ******************************************************************************** 2023-07-17T16:59:01,202 !! 2023-07-17T16:59:01,202 check.warn(importable) 2023-07-17T16:59:01,203 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin.snake' is absent from the `packages` configuration. 2023-07-17T16:59:01,203 !! 2023-07-17T16:59:01,203 ******************************************************************************** 2023-07-17T16:59:01,204 ############################ 2023-07-17T16:59:01,204 # Package would be ignored # 2023-07-17T16:59:01,204 ############################ 2023-07-17T16:59:01,205 Python recognizes 'mgatk.bin.snake' as an importable package[^1], 2023-07-17T16:59:01,205 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,206 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,206 package, please make sure that 'mgatk.bin.snake' is explicitly added 2023-07-17T16:59:01,206 to the `packages` configuration field. 2023-07-17T16:59:01,207 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,207 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,207 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,208 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,209 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,209 If you don't want 'mgatk.bin.snake' to be distributed and are 2023-07-17T16:59:01,209 already explicitly excluding 'mgatk.bin.snake' via 2023-07-17T16:59:01,210 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,210 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,210 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,211 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,211 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,212 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,213 even if it does not contain any `.py` files. 2023-07-17T16:59:01,213 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,213 directory, all directories are treated like packages. 2023-07-17T16:59:01,214 ******************************************************************************** 2023-07-17T16:59:01,214 !! 2023-07-17T16:59:01,215 check.warn(importable) 2023-07-17T16:59:01,215 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.deletioncalling' is absent from the `packages` configuration. 2023-07-17T16:59:01,215 !! 2023-07-17T16:59:01,216 ******************************************************************************** 2023-07-17T16:59:01,216 ############################ 2023-07-17T16:59:01,216 # Package would be ignored # 2023-07-17T16:59:01,217 ############################ 2023-07-17T16:59:01,217 Python recognizes 'mgatk.deletioncalling' as an importable package[^1], 2023-07-17T16:59:01,217 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,218 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,218 package, please make sure that 'mgatk.deletioncalling' is explicitly added 2023-07-17T16:59:01,218 to the `packages` configuration field. 2023-07-17T16:59:01,219 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,219 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,220 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,220 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,221 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,221 If you don't want 'mgatk.deletioncalling' to be distributed and are 2023-07-17T16:59:01,222 already explicitly excluding 'mgatk.deletioncalling' via 2023-07-17T16:59:01,222 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,222 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,222 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,223 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,224 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,224 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,225 even if it does not contain any `.py` files. 2023-07-17T16:59:01,225 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,225 directory, all directories are treated like packages. 2023-07-17T16:59:01,226 ******************************************************************************** 2023-07-17T16:59:01,226 !! 2023-07-17T16:59:01,227 check.warn(importable) 2023-07-17T16:59:01,227 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.deletioncalling.bulk_del' is absent from the `packages` configuration. 2023-07-17T16:59:01,227 !! 2023-07-17T16:59:01,228 ******************************************************************************** 2023-07-17T16:59:01,228 ############################ 2023-07-17T16:59:01,229 # Package would be ignored # 2023-07-17T16:59:01,229 ############################ 2023-07-17T16:59:01,229 Python recognizes 'mgatk.deletioncalling.bulk_del' as an importable package[^1], 2023-07-17T16:59:01,229 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,230 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,230 package, please make sure that 'mgatk.deletioncalling.bulk_del' is explicitly added 2023-07-17T16:59:01,231 to the `packages` configuration field. 2023-07-17T16:59:01,231 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,231 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,232 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,232 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,233 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,233 If you don't want 'mgatk.deletioncalling.bulk_del' to be distributed and are 2023-07-17T16:59:01,234 already explicitly excluding 'mgatk.deletioncalling.bulk_del' via 2023-07-17T16:59:01,234 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,234 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,235 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,235 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,236 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,237 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,237 even if it does not contain any `.py` files. 2023-07-17T16:59:01,237 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,238 directory, all directories are treated like packages. 2023-07-17T16:59:01,238 ******************************************************************************** 2023-07-17T16:59:01,238 !! 2023-07-17T16:59:01,239 check.warn(importable) 2023-07-17T16:59:01,239 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.deletioncalling.singles_del' is absent from the `packages` configuration. 2023-07-17T16:59:01,239 !! 2023-07-17T16:59:01,240 ******************************************************************************** 2023-07-17T16:59:01,240 ############################ 2023-07-17T16:59:01,240 # Package would be ignored # 2023-07-17T16:59:01,241 ############################ 2023-07-17T16:59:01,241 Python recognizes 'mgatk.deletioncalling.singles_del' as an importable package[^1], 2023-07-17T16:59:01,241 but it is absent from setuptools' `packages` configuration. 2023-07-17T16:59:01,242 This leads to an ambiguous overall configuration. If you want to distribute this 2023-07-17T16:59:01,242 package, please make sure that 'mgatk.deletioncalling.singles_del' is explicitly added 2023-07-17T16:59:01,243 to the `packages` configuration field. 2023-07-17T16:59:01,243 Alternatively, you can also rely on setuptools' discovery methods 2023-07-17T16:59:01,243 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-07-17T16:59:01,244 instead of `find_packages(...)`/`find:`). 2023-07-17T16:59:01,244 You can read more about "package discovery" on setuptools documentation page: 2023-07-17T16:59:01,245 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2023-07-17T16:59:01,246 If you don't want 'mgatk.deletioncalling.singles_del' to be distributed and are 2023-07-17T16:59:01,246 already explicitly excluding 'mgatk.deletioncalling.singles_del' via 2023-07-17T16:59:01,246 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2023-07-17T16:59:01,246 you can try to use `exclude_package_data`, or `include-package-data=False` in 2023-07-17T16:59:01,247 combination with a more fine grained `package-data` configuration. 2023-07-17T16:59:01,247 You can read more about "package data files" on setuptools documentation page: 2023-07-17T16:59:01,248 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2023-07-17T16:59:01,249 [^1]: For Python, any directory (with suitable naming) can be imported, 2023-07-17T16:59:01,249 even if it does not contain any `.py` files. 2023-07-17T16:59:01,249 On the other hand, currently there is no concept of package data 2023-07-17T16:59:01,250 directory, all directories are treated like packages. 2023-07-17T16:59:01,250 ******************************************************************************** 2023-07-17T16:59:01,251 !! 2023-07-17T16:59:01,251 check.warn(importable) 2023-07-17T16:59:01,251 copying mgatk/.DS_Store -> build/lib/mgatk 2023-07-17T16:59:01,252 copying mgatk/devnotes.md -> build/lib/mgatk 2023-07-17T16:59:01,252 creating build/lib/mgatk/__pycache__ 2023-07-17T16:59:01,252 copying mgatk/__pycache__/__init__.cpython-38.pyc -> build/lib/mgatk/__pycache__ 2023-07-17T16:59:01,252 copying mgatk/__pycache__/cli.cpython-38.pyc -> build/lib/mgatk/__pycache__ 2023-07-17T16:59:01,253 copying mgatk/__pycache__/mgatkHelp.cpython-38.pyc -> build/lib/mgatk/__pycache__ 2023-07-17T16:59:01,253 creating build/lib/mgatk/bin 2023-07-17T16:59:01,253 copying mgatk/bin/.DS_Store -> build/lib/mgatk/bin 2023-07-17T16:59:01,254 copying mgatk/bin/picard.jar -> build/lib/mgatk/bin 2023-07-17T16:59:01,945 creating build/lib/mgatk/bin/R 2023-07-17T16:59:01,947 copying mgatk/bin/R/convert_cellbender_output.R -> build/lib/mgatk/bin/R 2023-07-17T16:59:01,952 copying mgatk/bin/R/prepare_cellbender.R -> build/lib/mgatk/bin/R 2023-07-17T16:59:01,958 copying mgatk/bin/R/toRDS.R -> build/lib/mgatk/bin/R 2023-07-17T16:59:01,963 creating build/lib/mgatk/bin/anno 2023-07-17T16:59:01,964 creating build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:01,968 copying mgatk/bin/anno/fasta/GRCh37.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:01,973 copying mgatk/bin/anno/fasta/GRCh38.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:01,979 copying mgatk/bin/anno/fasta/GRCm38.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:01,986 copying mgatk/bin/anno/fasta/GRCz10.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:01,992 copying mgatk/bin/anno/fasta/NC_012920.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:01,997 copying mgatk/bin/anno/fasta/hg19.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:02,003 copying mgatk/bin/anno/fasta/hg19_chrM.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:02,008 copying mgatk/bin/anno/fasta/hg38.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:02,013 copying mgatk/bin/anno/fasta/mm10.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:02,018 copying mgatk/bin/anno/fasta/mm9.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:02,024 copying mgatk/bin/anno/fasta/rCRS.fasta -> build/lib/mgatk/bin/anno/fasta 2023-07-17T16:59:02,030 creating build/lib/mgatk/bin/python 2023-07-17T16:59:02,032 copying mgatk/bin/python/chunk_barcoded_bam.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,037 copying mgatk/bin/python/filterClipBam.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,042 copying mgatk/bin/python/find_barcodes.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,047 copying mgatk/bin/python/oneSample.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,052 copying mgatk/bin/python/split_barcoded_bam.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,056 copying mgatk/bin/python/sumstatsBP.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,061 copying mgatk/bin/python/sumstatsBP_overlap.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,067 copying mgatk/bin/python/sumstatsBPtenx.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,072 copying mgatk/bin/python/sumstatsBPtenx_overlap.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,077 copying mgatk/bin/python/variant_calling.py -> build/lib/mgatk/bin/python 2023-07-17T16:59:02,082 creating build/lib/mgatk/bin/snake 2023-07-17T16:59:02,084 copying mgatk/bin/snake/Snakefile.Gather -> build/lib/mgatk/bin/snake 2023-07-17T16:59:02,090 copying mgatk/bin/snake/Snakefile.Scatter -> build/lib/mgatk/bin/snake 2023-07-17T16:59:02,094 copying mgatk/bin/snake/Snakefile.tenx -> build/lib/mgatk/bin/snake 2023-07-17T16:59:02,100 creating build/lib/mgatk/deletioncalling 2023-07-17T16:59:02,102 copying mgatk/deletioncalling/clidel.py -> build/lib/mgatk/deletioncalling 2023-07-17T16:59:02,108 copying mgatk/deletioncalling/clifind.py -> build/lib/mgatk/deletioncalling 2023-07-17T16:59:02,113 creating build/lib/mgatk/deletioncalling/bulk_del 2023-07-17T16:59:02,115 copying mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R -> build/lib/mgatk/deletioncalling/bulk_del 2023-07-17T16:59:02,120 creating build/lib/mgatk/deletioncalling/singles_del 2023-07-17T16:59:02,123 copying mgatk/deletioncalling/singles_del/01_process_cell_reads.py -> build/lib/mgatk/deletioncalling/singles_del 2023-07-17T16:59:02,128 copying mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R -> build/lib/mgatk/deletioncalling/singles_del 2023-07-17T16:59:02,133 copying mgatk/deletioncalling/singles_del/Snakefile.delSingles -> build/lib/mgatk/deletioncalling/singles_del 2023-07-17T16:59:02,213 /usr/local/lib/python3.7/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2023-07-17T16:59:02,213 !! 2023-07-17T16:59:02,214 ******************************************************************************** 2023-07-17T16:59:02,214 Please avoid running ``setup.py`` directly. 2023-07-17T16:59:02,214 Instead, use pypa/build, pypa/installer, pypa/build or 2023-07-17T16:59:02,215 other standards-based tools. 2023-07-17T16:59:02,215 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2023-07-17T16:59:02,216 ******************************************************************************** 2023-07-17T16:59:02,216 !! 2023-07-17T16:59:02,217 self.initialize_options() 2023-07-17T16:59:02,281 installing to build/bdist.linux-armv7l/wheel 2023-07-17T16:59:02,282 running install 2023-07-17T16:59:02,343 running install_lib 2023-07-17T16:59:02,414 creating build/bdist.linux-armv7l 2023-07-17T16:59:02,414 creating build/bdist.linux-armv7l/wheel 2023-07-17T16:59:02,418 creating build/bdist.linux-armv7l/wheel/mgatk 2023-07-17T16:59:02,420 copying build/lib/mgatk/mgatkHelp.py -> build/bdist.linux-armv7l/wheel/mgatk 2023-07-17T16:59:02,427 creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling 2023-07-17T16:59:02,430 creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del 2023-07-17T16:59:02,432 copying build/lib/mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del 2023-07-17T16:59:02,436 copying build/lib/mgatk/deletioncalling/singles_del/Snakefile.delSingles -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del 2023-07-17T16:59:02,440 copying build/lib/mgatk/deletioncalling/singles_del/01_process_cell_reads.py -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del 2023-07-17T16:59:02,444 copying build/lib/mgatk/deletioncalling/clifind.py -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling 2023-07-17T16:59:02,448 copying build/lib/mgatk/deletioncalling/clidel.py -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling 2023-07-17T16:59:02,453 creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/bulk_del 2023-07-17T16:59:02,455 copying build/lib/mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/bulk_del 2023-07-17T16:59:02,460 copying build/lib/mgatk/cli.py -> build/bdist.linux-armv7l/wheel/mgatk 2023-07-17T16:59:02,465 copying build/lib/mgatk/.DS_Store -> build/bdist.linux-armv7l/wheel/mgatk 2023-07-17T16:59:02,469 copying build/lib/mgatk/__init__.py -> build/bdist.linux-armv7l/wheel/mgatk 2023-07-17T16:59:02,474 creating build/bdist.linux-armv7l/wheel/mgatk/__pycache__ 2023-07-17T16:59:02,476 copying build/lib/mgatk/__pycache__/__init__.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__ 2023-07-17T16:59:02,480 copying build/lib/mgatk/__pycache__/mgatkHelp.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__ 2023-07-17T16:59:02,485 copying build/lib/mgatk/__pycache__/cli.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__ 2023-07-17T16:59:02,491 creating build/bdist.linux-armv7l/wheel/mgatk/bin 2023-07-17T16:59:02,493 copying build/lib/mgatk/bin/picard.jar -> build/bdist.linux-armv7l/wheel/mgatk/bin 2023-07-17T16:59:03,122 copying build/lib/mgatk/bin/.DS_Store -> build/bdist.linux-armv7l/wheel/mgatk/bin 2023-07-17T16:59:03,127 creating build/bdist.linux-armv7l/wheel/mgatk/bin/snake 2023-07-17T16:59:03,129 copying build/lib/mgatk/bin/snake/Snakefile.Scatter -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake 2023-07-17T16:59:03,133 copying build/lib/mgatk/bin/snake/Snakefile.tenx -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake 2023-07-17T16:59:03,137 copying build/lib/mgatk/bin/snake/Snakefile.Gather -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake 2023-07-17T16:59:03,142 creating build/bdist.linux-armv7l/wheel/mgatk/bin/anno 2023-07-17T16:59:03,145 creating build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,148 copying build/lib/mgatk/bin/anno/fasta/hg19.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,153 copying build/lib/mgatk/bin/anno/fasta/GRCz10.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,158 copying build/lib/mgatk/bin/anno/fasta/GRCh37.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,163 copying build/lib/mgatk/bin/anno/fasta/GRCh38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,168 copying build/lib/mgatk/bin/anno/fasta/mm10.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,173 copying build/lib/mgatk/bin/anno/fasta/GRCm38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,178 copying build/lib/mgatk/bin/anno/fasta/rCRS.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,183 copying build/lib/mgatk/bin/anno/fasta/mm9.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,187 copying build/lib/mgatk/bin/anno/fasta/NC_012920.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,192 copying build/lib/mgatk/bin/anno/fasta/hg38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,197 copying build/lib/mgatk/bin/anno/fasta/hg19_chrM.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta 2023-07-17T16:59:03,203 creating build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,205 copying build/lib/mgatk/bin/python/oneSample.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,209 copying build/lib/mgatk/bin/python/sumstatsBPtenx.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,213 copying build/lib/mgatk/bin/python/sumstatsBP.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,217 copying build/lib/mgatk/bin/python/chunk_barcoded_bam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,221 copying build/lib/mgatk/bin/python/split_barcoded_bam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,224 copying build/lib/mgatk/bin/python/variant_calling.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,229 copying build/lib/mgatk/bin/python/sumstatsBP_overlap.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,233 copying build/lib/mgatk/bin/python/find_barcodes.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,238 copying build/lib/mgatk/bin/python/sumstatsBPtenx_overlap.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,241 copying build/lib/mgatk/bin/python/filterClipBam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python 2023-07-17T16:59:03,246 creating build/bdist.linux-armv7l/wheel/mgatk/bin/R 2023-07-17T16:59:03,247 copying build/lib/mgatk/bin/R/prepare_cellbender.R -> build/bdist.linux-armv7l/wheel/mgatk/bin/R 2023-07-17T16:59:03,252 copying build/lib/mgatk/bin/R/convert_cellbender_output.R -> build/bdist.linux-armv7l/wheel/mgatk/bin/R 2023-07-17T16:59:03,256 copying build/lib/mgatk/bin/R/toRDS.R -> build/bdist.linux-armv7l/wheel/mgatk/bin/R 2023-07-17T16:59:03,261 copying build/lib/mgatk/devnotes.md -> build/bdist.linux-armv7l/wheel/mgatk 2023-07-17T16:59:03,264 running install_egg_info 2023-07-17T16:59:03,340 Copying mgatk.egg-info to build/bdist.linux-armv7l/wheel/mgatk-0.6.9-py3.7.egg-info 2023-07-17T16:59:03,366 running install_scripts 2023-07-17T16:59:03,402 creating build/bdist.linux-armv7l/wheel/mgatk-0.6.9.dist-info/WHEEL 2023-07-17T16:59:03,407 creating '/tmp/pip-wheel-8u0xyx3b/mgatk-0.6.9-py2.py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-07-17T16:59:03,413 adding 'mgatk/.DS_Store' 2023-07-17T16:59:03,415 adding 'mgatk/__init__.py' 2023-07-17T16:59:03,423 adding 'mgatk/cli.py' 2023-07-17T16:59:03,426 adding 'mgatk/devnotes.md' 2023-07-17T16:59:03,430 adding 'mgatk/mgatkHelp.py' 2023-07-17T16:59:03,433 adding 'mgatk/__pycache__/__init__.cpython-38.pyc' 2023-07-17T16:59:03,439 adding 'mgatk/__pycache__/cli.cpython-38.pyc' 2023-07-17T16:59:03,444 adding 'mgatk/__pycache__/mgatkHelp.cpython-38.pyc' 2023-07-17T16:59:03,449 adding 'mgatk/bin/.DS_Store' 2023-07-17T16:59:07,890 adding 'mgatk/bin/picard.jar' 2023-07-17T16:59:08,203 adding 'mgatk/bin/R/convert_cellbender_output.R' 2023-07-17T16:59:08,208 adding 'mgatk/bin/R/prepare_cellbender.R' 2023-07-17T16:59:08,212 adding 'mgatk/bin/R/toRDS.R' 2023-07-17T16:59:08,234 adding 'mgatk/bin/anno/fasta/GRCh37.fasta' 2023-07-17T16:59:08,254 adding 'mgatk/bin/anno/fasta/GRCh38.fasta' 2023-07-17T16:59:08,273 adding 'mgatk/bin/anno/fasta/GRCm38.fasta' 2023-07-17T16:59:08,293 adding 'mgatk/bin/anno/fasta/GRCz10.fasta' 2023-07-17T16:59:08,314 adding 'mgatk/bin/anno/fasta/NC_012920.fasta' 2023-07-17T16:59:08,333 adding 'mgatk/bin/anno/fasta/hg19.fasta' 2023-07-17T16:59:08,353 adding 'mgatk/bin/anno/fasta/hg19_chrM.fasta' 2023-07-17T16:59:08,373 adding 'mgatk/bin/anno/fasta/hg38.fasta' 2023-07-17T16:59:08,392 adding 'mgatk/bin/anno/fasta/mm10.fasta' 2023-07-17T16:59:08,411 adding 'mgatk/bin/anno/fasta/mm9.fasta' 2023-07-17T16:59:08,430 adding 'mgatk/bin/anno/fasta/rCRS.fasta' 2023-07-17T16:59:08,435 adding 'mgatk/bin/python/chunk_barcoded_bam.py' 2023-07-17T16:59:08,438 adding 'mgatk/bin/python/filterClipBam.py' 2023-07-17T16:59:08,441 adding 'mgatk/bin/python/find_barcodes.py' 2023-07-17T16:59:08,444 adding 'mgatk/bin/python/oneSample.py' 2023-07-17T16:59:08,447 adding 'mgatk/bin/python/split_barcoded_bam.py' 2023-07-17T16:59:08,450 adding 'mgatk/bin/python/sumstatsBP.py' 2023-07-17T16:59:08,454 adding 'mgatk/bin/python/sumstatsBP_overlap.py' 2023-07-17T16:59:08,457 adding 'mgatk/bin/python/sumstatsBPtenx.py' 2023-07-17T16:59:08,460 adding 'mgatk/bin/python/sumstatsBPtenx_overlap.py' 2023-07-17T16:59:08,464 adding 'mgatk/bin/python/variant_calling.py' 2023-07-17T16:59:08,469 adding 'mgatk/bin/snake/Snakefile.Gather' 2023-07-17T16:59:08,471 adding 'mgatk/bin/snake/Snakefile.Scatter' 2023-07-17T16:59:08,475 adding 'mgatk/bin/snake/Snakefile.tenx' 2023-07-17T16:59:08,480 adding 'mgatk/deletioncalling/clidel.py' 2023-07-17T16:59:08,483 adding 'mgatk/deletioncalling/clifind.py' 2023-07-17T16:59:08,488 adding 'mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R' 2023-07-17T16:59:08,492 adding 'mgatk/deletioncalling/singles_del/01_process_cell_reads.py' 2023-07-17T16:59:08,495 adding 'mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R' 2023-07-17T16:59:08,498 adding 'mgatk/deletioncalling/singles_del/Snakefile.delSingles' 2023-07-17T16:59:08,503 adding 'mgatk-0.6.9.dist-info/LICENSE.txt' 2023-07-17T16:59:08,506 adding 'mgatk-0.6.9.dist-info/METADATA' 2023-07-17T16:59:08,508 adding 'mgatk-0.6.9.dist-info/WHEEL' 2023-07-17T16:59:08,510 adding 'mgatk-0.6.9.dist-info/entry_points.txt' 2023-07-17T16:59:08,512 adding 'mgatk-0.6.9.dist-info/top_level.txt' 2023-07-17T16:59:08,515 adding 'mgatk-0.6.9.dist-info/RECORD' 2023-07-17T16:59:08,910 removing build/bdist.linux-armv7l/wheel 2023-07-17T16:59:09,110 Building wheel for mgatk (setup.py): finished with status 'done' 2023-07-17T16:59:09,538 Created wheel for mgatk: filename=mgatk-0.6.9-py2.py3-none-any.whl size=14326476 sha256=3d7e110966e8ec8ca672b880356fbf86596208ef2aefb3fef7fd1200b1c90db9 2023-07-17T16:59:09,541 Stored in directory: /tmp/pip-ephem-wheel-cache-smmovb_8/wheels/13/2e/a2/eb30e5ffc74db05b1ac1a7b7c61b1a1ee0bed27b3d696ca77a 2023-07-17T16:59:09,587 Successfully built mgatk 2023-07-17T16:59:10,690 Removed build tracker: '/tmp/pip-build-tracker-2vjnzvus'