2023-06-26T21:39:58,032 Created temporary directory: /tmp/pip-build-tracker-q0thhlk5
2023-06-26T21:39:58,035 Initialized build tracking at /tmp/pip-build-tracker-q0thhlk5
2023-06-26T21:39:58,036 Created build tracker: /tmp/pip-build-tracker-q0thhlk5
2023-06-26T21:39:58,036 Entered build tracker: /tmp/pip-build-tracker-q0thhlk5
2023-06-26T21:39:58,037 Created temporary directory: /tmp/pip-wheel-wk8g326w
2023-06-26T21:39:58,046 Created temporary directory: /tmp/pip-ephem-wheel-cache-9v_5if0j
2023-06-26T21:39:58,098 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-06-26T21:39:58,106 2 location(s) to search for versions of mgatk:
2023-06-26T21:39:58,106 * https://pypi.org/simple/mgatk/
2023-06-26T21:39:58,106 * https://www.piwheels.org/simple/mgatk/
2023-06-26T21:39:58,107 Fetching project page and analyzing links: https://pypi.org/simple/mgatk/
2023-06-26T21:39:58,108 Getting page https://pypi.org/simple/mgatk/
2023-06-26T21:39:58,112 Found index url https://pypi.org/simple/
2023-06-26T21:39:58,302 Fetched page https://pypi.org/simple/mgatk/ as application/vnd.pypi.simple.v1+json
2023-06-26T21:39:58,313   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
2023-06-26T21:39:58,314   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
2023-06-26T21:39:58,315   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
2023-06-26T21:39:58,315   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
2023-06-26T21:39:58,316   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
2023-06-26T21:39:58,317   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
2023-06-26T21:39:58,318   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
2023-06-26T21:39:58,318   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
2023-06-26T21:39:58,319   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
2023-06-26T21:39:58,320   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
2023-06-26T21:39:58,320   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
2023-06-26T21:39:58,321   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
2023-06-26T21:39:58,322   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
2023-06-26T21:39:58,322   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
2023-06-26T21:39:58,323   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
2023-06-26T21:39:58,324   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
2023-06-26T21:39:58,324   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
2023-06-26T21:39:58,325   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
2023-06-26T21:39:58,326   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
2023-06-26T21:39:58,327 Fetching project page and analyzing links: https://www.piwheels.org/simple/mgatk/
2023-06-26T21:39:58,327 Getting page https://www.piwheels.org/simple/mgatk/
2023-06-26T21:39:58,330 Found index url https://www.piwheels.org/simple/
2023-06-26T21:39:58,564 Fetched page https://www.piwheels.org/simple/mgatk/ as text/html
2023-06-26T21:39:58,578   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/)
2023-06-26T21:39:58,579   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/)
2023-06-26T21:39:58,580   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/)
2023-06-26T21:39:58,580   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/)
2023-06-26T21:39:58,581   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/)
2023-06-26T21:39:58,582   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/)
2023-06-26T21:39:58,582   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/)
2023-06-26T21:39:58,583   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/)
2023-06-26T21:39:58,583   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/)
2023-06-26T21:39:58,584   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/)
2023-06-26T21:39:58,585   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/)
2023-06-26T21:39:58,585   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/)
2023-06-26T21:39:58,586   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/)
2023-06-26T21:39:58,586   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/)
2023-06-26T21:39:58,587   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/)
2023-06-26T21:39:58,587   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/)
2023-06-26T21:39:58,588   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/)
2023-06-26T21:39:58,589   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/)
2023-06-26T21:39:58,589 Skipping link: not a file: https://www.piwheels.org/simple/mgatk/
2023-06-26T21:39:58,590 Skipping link: not a file: https://pypi.org/simple/mgatk/
2023-06-26T21:39:58,629 Given no hashes to check 1 links for project 'mgatk': discarding no candidates
2023-06-26T21:39:58,664 Collecting mgatk==0.6.8
2023-06-26T21:39:58,669   Created temporary directory: /tmp/pip-unpack-7s8_df6b
2023-06-26T21:39:58,855   Downloading mgatk-0.6.8.tar.gz (14.3 MB)
2023-06-26T21:40:03,761   Added mgatk==0.6.8 from https://files.pythonhosted.org/packages/3f/65/b0d2081526edf3cef5c0fbfee4ad477f6b3b9c14107ae5a41e45b1b0e169/mgatk-0.6.8.tar.gz to build tracker '/tmp/pip-build-tracker-q0thhlk5'
2023-06-26T21:40:03,765   Running setup.py (path:/tmp/pip-wheel-wk8g326w/mgatk_e588407f551f4ae6b33298c8e6a7b37a/setup.py) egg_info for package mgatk
2023-06-26T21:40:03,767   Created temporary directory: /tmp/pip-pip-egg-info-raa558tp
2023-06-26T21:40:03,767   Preparing metadata (setup.py): started
2023-06-26T21:40:03,769   Running command python setup.py egg_info
2023-06-26T21:40:05,322   running egg_info
2023-06-26T21:40:05,327   creating /tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info
2023-06-26T21:40:05,390   writing /tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info/PKG-INFO
2023-06-26T21:40:05,395   writing dependency_links to /tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info/dependency_links.txt
2023-06-26T21:40:05,399   writing entry points to /tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info/entry_points.txt
2023-06-26T21:40:05,402   writing requirements to /tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info/requires.txt
2023-06-26T21:40:05,404   writing top-level names to /tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info/top_level.txt
2023-06-26T21:40:05,407   writing manifest file '/tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info/SOURCES.txt'
2023-06-26T21:40:05,613   reading manifest file '/tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info/SOURCES.txt'
2023-06-26T21:40:05,617   reading manifest template 'MANIFEST.in'
2023-06-26T21:40:05,619   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
2023-06-26T21:40:05,620   !!

2023-06-26T21:40:05,621           ********************************************************************************
2023-06-26T21:40:05,621           Usage of dash-separated 'description-file' will not be supported in future
2023-06-26T21:40:05,621           versions. Please use the underscore name 'description_file' instead.

2023-06-26T21:40:05,622           By 2023-Sep-26, you need to update your project and remove deprecated calls
2023-06-26T21:40:05,622           or your builds will no longer be supported.

2023-06-26T21:40:05,623           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2023-06-26T21:40:05,624           ********************************************************************************

2023-06-26T21:40:05,625   !!
2023-06-26T21:40:05,625     opt = self.warn_dash_deprecation(opt, section)
2023-06-26T21:40:05,626   no previously-included directories found matching 'mgatk.egg-info/'
2023-06-26T21:40:05,626   no previously-included directories found matching 'tests/'
2023-06-26T21:40:05,627   no previously-included directories found matching '*.DS_Store'
2023-06-26T21:40:05,671   adding license file 'LICENSE.txt'
2023-06-26T21:40:05,679   writing manifest file '/tmp/pip-pip-egg-info-raa558tp/mgatk.egg-info/SOURCES.txt'
2023-06-26T21:40:05,800   Preparing metadata (setup.py): finished with status 'done'
2023-06-26T21:40:05,813   Source in /tmp/pip-wheel-wk8g326w/mgatk_e588407f551f4ae6b33298c8e6a7b37a has version 0.6.8, which satisfies requirement mgatk==0.6.8 from https://files.pythonhosted.org/packages/3f/65/b0d2081526edf3cef5c0fbfee4ad477f6b3b9c14107ae5a41e45b1b0e169/mgatk-0.6.8.tar.gz
2023-06-26T21:40:05,815   Removed mgatk==0.6.8 from https://files.pythonhosted.org/packages/3f/65/b0d2081526edf3cef5c0fbfee4ad477f6b3b9c14107ae5a41e45b1b0e169/mgatk-0.6.8.tar.gz from build tracker '/tmp/pip-build-tracker-q0thhlk5'
2023-06-26T21:40:05,827 Created temporary directory: /tmp/pip-unpack-0cabhtpj
2023-06-26T21:40:05,829 Building wheels for collected packages: mgatk
2023-06-26T21:40:05,838   Created temporary directory: /tmp/pip-wheel-8ac8asd6
2023-06-26T21:40:05,839   Building wheel for mgatk (setup.py): started
2023-06-26T21:40:05,841   Destination directory: /tmp/pip-wheel-8ac8asd6
2023-06-26T21:40:05,841   Running command python setup.py bdist_wheel
2023-06-26T21:40:07,024   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
2023-06-26T21:40:07,026   !!

2023-06-26T21:40:07,027           ********************************************************************************
2023-06-26T21:40:07,027           Usage of dash-separated 'description-file' will not be supported in future
2023-06-26T21:40:07,028           versions. Please use the underscore name 'description_file' instead.

2023-06-26T21:40:07,028           By 2023-Sep-26, you need to update your project and remove deprecated calls
2023-06-26T21:40:07,028           or your builds will no longer be supported.

2023-06-26T21:40:07,029           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2023-06-26T21:40:07,029           ********************************************************************************

2023-06-26T21:40:07,030   !!
2023-06-26T21:40:07,031     opt = self.warn_dash_deprecation(opt, section)
2023-06-26T21:40:07,457   running bdist_wheel
2023-06-26T21:40:08,179   running build
2023-06-26T21:40:08,180   running build_py
2023-06-26T21:40:08,251   creating build
2023-06-26T21:40:08,252   creating build/lib
2023-06-26T21:40:08,254   creating build/lib/mgatk
2023-06-26T21:40:08,256   copying mgatk/mgatkHelp.py -> build/lib/mgatk
2023-06-26T21:40:08,260   copying mgatk/cli.py -> build/lib/mgatk
2023-06-26T21:40:08,266   copying mgatk/__init__.py -> build/lib/mgatk
2023-06-26T21:40:08,269   running egg_info
2023-06-26T21:40:08,418   writing mgatk.egg-info/PKG-INFO
2023-06-26T21:40:08,423   writing dependency_links to mgatk.egg-info/dependency_links.txt
2023-06-26T21:40:08,427   writing entry points to mgatk.egg-info/entry_points.txt
2023-06-26T21:40:08,430   writing requirements to mgatk.egg-info/requires.txt
2023-06-26T21:40:08,432   writing top-level names to mgatk.egg-info/top_level.txt
2023-06-26T21:40:08,503   reading manifest file 'mgatk.egg-info/SOURCES.txt'
2023-06-26T21:40:08,509   reading manifest template 'MANIFEST.in'
2023-06-26T21:40:08,512   no previously-included directories found matching 'tests/'
2023-06-26T21:40:08,514   no previously-included directories found matching '*.DS_Store'
2023-06-26T21:40:08,558   adding license file 'LICENSE.txt'
2023-06-26T21:40:08,568   writing manifest file 'mgatk.egg-info/SOURCES.txt'
2023-06-26T21:40:08,573   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.__pycache__' is absent from the `packages` configuration.
2023-06-26T21:40:08,573   !!

2023-06-26T21:40:08,574           ********************************************************************************
2023-06-26T21:40:08,574           ############################
2023-06-26T21:40:08,574           # Package would be ignored #
2023-06-26T21:40:08,575           ############################
2023-06-26T21:40:08,575           Python recognizes 'mgatk.__pycache__' as an importable package[^1],
2023-06-26T21:40:08,575           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,576           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,577           package, please make sure that 'mgatk.__pycache__' is explicitly added
2023-06-26T21:40:08,577           to the `packages` configuration field.

2023-06-26T21:40:08,577           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,578           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,578           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,579           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,579           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,580           If you don't want 'mgatk.__pycache__' to be distributed and are
2023-06-26T21:40:08,580           already explicitly excluding 'mgatk.__pycache__' via
2023-06-26T21:40:08,580           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,581           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,581           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,582           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,582           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,583           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,583                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,584                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,584                 directory, all directories are treated like packages.
2023-06-26T21:40:08,584           ********************************************************************************

2023-06-26T21:40:08,585   !!
2023-06-26T21:40:08,585     check.warn(importable)
2023-06-26T21:40:08,586   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin' is absent from the `packages` configuration.
2023-06-26T21:40:08,586   !!

2023-06-26T21:40:08,587           ********************************************************************************
2023-06-26T21:40:08,587           ############################
2023-06-26T21:40:08,587           # Package would be ignored #
2023-06-26T21:40:08,588           ############################
2023-06-26T21:40:08,588           Python recognizes 'mgatk.bin' as an importable package[^1],
2023-06-26T21:40:08,588           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,589           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,589           package, please make sure that 'mgatk.bin' is explicitly added
2023-06-26T21:40:08,590           to the `packages` configuration field.

2023-06-26T21:40:08,590           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,590           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,591           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,591           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,592           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,593           If you don't want 'mgatk.bin' to be distributed and are
2023-06-26T21:40:08,593           already explicitly excluding 'mgatk.bin' via
2023-06-26T21:40:08,593           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,593           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,594           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,595           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,595           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,597           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,597                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,598                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,598                 directory, all directories are treated like packages.
2023-06-26T21:40:08,599           ********************************************************************************

2023-06-26T21:40:08,599   !!
2023-06-26T21:40:08,600     check.warn(importable)
2023-06-26T21:40:08,600   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin.R' is absent from the `packages` configuration.
2023-06-26T21:40:08,601   !!

2023-06-26T21:40:08,602           ********************************************************************************
2023-06-26T21:40:08,602           ############################
2023-06-26T21:40:08,602           # Package would be ignored #
2023-06-26T21:40:08,603           ############################
2023-06-26T21:40:08,603           Python recognizes 'mgatk.bin.R' as an importable package[^1],
2023-06-26T21:40:08,604           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,605           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,605           package, please make sure that 'mgatk.bin.R' is explicitly added
2023-06-26T21:40:08,605           to the `packages` configuration field.

2023-06-26T21:40:08,606           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,607           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,607           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,608           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,609           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,610           If you don't want 'mgatk.bin.R' to be distributed and are
2023-06-26T21:40:08,611           already explicitly excluding 'mgatk.bin.R' via
2023-06-26T21:40:08,611           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,611           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,612           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,613           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,614           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,615           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,616                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,616                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,617                 directory, all directories are treated like packages.
2023-06-26T21:40:08,617           ********************************************************************************

2023-06-26T21:40:08,618   !!
2023-06-26T21:40:08,618     check.warn(importable)
2023-06-26T21:40:08,619   /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.
2023-06-26T21:40:08,619   !!

2023-06-26T21:40:08,620           ********************************************************************************
2023-06-26T21:40:08,620           ############################
2023-06-26T21:40:08,621           # Package would be ignored #
2023-06-26T21:40:08,621           ############################
2023-06-26T21:40:08,621           Python recognizes 'mgatk.bin.anno.fasta' as an importable package[^1],
2023-06-26T21:40:08,622           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,622           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,622           package, please make sure that 'mgatk.bin.anno.fasta' is explicitly added
2023-06-26T21:40:08,623           to the `packages` configuration field.

2023-06-26T21:40:08,623           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,624           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,624           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,625           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,625           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,626           If you don't want 'mgatk.bin.anno.fasta' to be distributed and are
2023-06-26T21:40:08,626           already explicitly excluding 'mgatk.bin.anno.fasta' via
2023-06-26T21:40:08,626           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,627           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,627           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,628           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,628           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,629           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,629                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,630                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,630                 directory, all directories are treated like packages.
2023-06-26T21:40:08,630           ********************************************************************************

2023-06-26T21:40:08,631   !!
2023-06-26T21:40:08,631     check.warn(importable)
2023-06-26T21:40:08,631   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin.python' is absent from the `packages` configuration.
2023-06-26T21:40:08,632   !!

2023-06-26T21:40:08,632           ********************************************************************************
2023-06-26T21:40:08,633           ############################
2023-06-26T21:40:08,633           # Package would be ignored #
2023-06-26T21:40:08,633           ############################
2023-06-26T21:40:08,633           Python recognizes 'mgatk.bin.python' as an importable package[^1],
2023-06-26T21:40:08,634           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,634           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,635           package, please make sure that 'mgatk.bin.python' is explicitly added
2023-06-26T21:40:08,635           to the `packages` configuration field.

2023-06-26T21:40:08,636           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,636           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,636           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,637           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,637           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,638           If you don't want 'mgatk.bin.python' to be distributed and are
2023-06-26T21:40:08,638           already explicitly excluding 'mgatk.bin.python' via
2023-06-26T21:40:08,639           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,639           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,639           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,640           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,640           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,641           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,642                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,642                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,642                 directory, all directories are treated like packages.
2023-06-26T21:40:08,642           ********************************************************************************

2023-06-26T21:40:08,643   !!
2023-06-26T21:40:08,643     check.warn(importable)
2023-06-26T21:40:08,644   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.bin.snake' is absent from the `packages` configuration.
2023-06-26T21:40:08,644   !!

2023-06-26T21:40:08,645           ********************************************************************************
2023-06-26T21:40:08,645           ############################
2023-06-26T21:40:08,645           # Package would be ignored #
2023-06-26T21:40:08,646           ############################
2023-06-26T21:40:08,646           Python recognizes 'mgatk.bin.snake' as an importable package[^1],
2023-06-26T21:40:08,646           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,647           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,647           package, please make sure that 'mgatk.bin.snake' is explicitly added
2023-06-26T21:40:08,648           to the `packages` configuration field.

2023-06-26T21:40:08,648           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,648           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,649           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,649           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,650           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,651           If you don't want 'mgatk.bin.snake' to be distributed and are
2023-06-26T21:40:08,651           already explicitly excluding 'mgatk.bin.snake' via
2023-06-26T21:40:08,651           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,651           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,652           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,652           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,653           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,654           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,654                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,654                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,655                 directory, all directories are treated like packages.
2023-06-26T21:40:08,655           ********************************************************************************

2023-06-26T21:40:08,656   !!
2023-06-26T21:40:08,656     check.warn(importable)
2023-06-26T21:40:08,656   /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:201: _Warning: Package 'mgatk.deletioncalling' is absent from the `packages` configuration.
2023-06-26T21:40:08,657   !!

2023-06-26T21:40:08,657           ********************************************************************************
2023-06-26T21:40:08,658           ############################
2023-06-26T21:40:08,658           # Package would be ignored #
2023-06-26T21:40:08,658           ############################
2023-06-26T21:40:08,658           Python recognizes 'mgatk.deletioncalling' as an importable package[^1],
2023-06-26T21:40:08,659           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,659           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,660           package, please make sure that 'mgatk.deletioncalling' is explicitly added
2023-06-26T21:40:08,660           to the `packages` configuration field.

2023-06-26T21:40:08,660           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,661           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,661           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,662           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,662           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,663           If you don't want 'mgatk.deletioncalling' to be distributed and are
2023-06-26T21:40:08,663           already explicitly excluding 'mgatk.deletioncalling' via
2023-06-26T21:40:08,663           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,664           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,664           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,665           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,665           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,666           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,667                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,667                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,667                 directory, all directories are treated like packages.
2023-06-26T21:40:08,668           ********************************************************************************

2023-06-26T21:40:08,668   !!
2023-06-26T21:40:08,669     check.warn(importable)
2023-06-26T21:40:08,669   /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.
2023-06-26T21:40:08,669   !!

2023-06-26T21:40:08,670           ********************************************************************************
2023-06-26T21:40:08,670           ############################
2023-06-26T21:40:08,670           # Package would be ignored #
2023-06-26T21:40:08,671           ############################
2023-06-26T21:40:08,671           Python recognizes 'mgatk.deletioncalling.bulk_del' as an importable package[^1],
2023-06-26T21:40:08,671           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,672           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,672           package, please make sure that 'mgatk.deletioncalling.bulk_del' is explicitly added
2023-06-26T21:40:08,672           to the `packages` configuration field.

2023-06-26T21:40:08,673           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,673           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,674           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,674           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,675           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,675           If you don't want 'mgatk.deletioncalling.bulk_del' to be distributed and are
2023-06-26T21:40:08,676           already explicitly excluding 'mgatk.deletioncalling.bulk_del' via
2023-06-26T21:40:08,676           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,676           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,677           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,677           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,678           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,679           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,679                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,679                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,680                 directory, all directories are treated like packages.
2023-06-26T21:40:08,680           ********************************************************************************

2023-06-26T21:40:08,680   !!
2023-06-26T21:40:08,681     check.warn(importable)
2023-06-26T21:40:08,681   /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.
2023-06-26T21:40:08,681   !!

2023-06-26T21:40:08,682           ********************************************************************************
2023-06-26T21:40:08,682           ############################
2023-06-26T21:40:08,683           # Package would be ignored #
2023-06-26T21:40:08,683           ############################
2023-06-26T21:40:08,683           Python recognizes 'mgatk.deletioncalling.singles_del' as an importable package[^1],
2023-06-26T21:40:08,683           but it is absent from setuptools' `packages` configuration.

2023-06-26T21:40:08,684           This leads to an ambiguous overall configuration. If you want to distribute this
2023-06-26T21:40:08,684           package, please make sure that 'mgatk.deletioncalling.singles_del' is explicitly added
2023-06-26T21:40:08,685           to the `packages` configuration field.

2023-06-26T21:40:08,685           Alternatively, you can also rely on setuptools' discovery methods
2023-06-26T21:40:08,686           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2023-06-26T21:40:08,686           instead of `find_packages(...)`/`find:`).

2023-06-26T21:40:08,686           You can read more about "package discovery" on setuptools documentation page:

2023-06-26T21:40:08,687           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2023-06-26T21:40:08,688           If you don't want 'mgatk.deletioncalling.singles_del' to be distributed and are
2023-06-26T21:40:08,688           already explicitly excluding 'mgatk.deletioncalling.singles_del' via
2023-06-26T21:40:08,688           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2023-06-26T21:40:08,689           you can try to use `exclude_package_data`, or `include-package-data=False` in
2023-06-26T21:40:08,689           combination with a more fine grained `package-data` configuration.

2023-06-26T21:40:08,689           You can read more about "package data files" on setuptools documentation page:

2023-06-26T21:40:08,690           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2023-06-26T21:40:08,691           [^1]: For Python, any directory (with suitable naming) can be imported,
2023-06-26T21:40:08,691                 even if it does not contain any `.py` files.
2023-06-26T21:40:08,691                 On the other hand, currently there is no concept of package data
2023-06-26T21:40:08,692                 directory, all directories are treated like packages.
2023-06-26T21:40:08,692           ********************************************************************************

2023-06-26T21:40:08,693   !!
2023-06-26T21:40:08,693     check.warn(importable)
2023-06-26T21:40:08,693   copying mgatk/devnotes.md -> build/lib/mgatk
2023-06-26T21:40:08,694   creating build/lib/mgatk/__pycache__
2023-06-26T21:40:08,694   copying mgatk/__pycache__/__init__.cpython-38.pyc -> build/lib/mgatk/__pycache__
2023-06-26T21:40:08,694   copying mgatk/__pycache__/cli.cpython-38.pyc -> build/lib/mgatk/__pycache__
2023-06-26T21:40:08,695   copying mgatk/__pycache__/mgatkHelp.cpython-38.pyc -> build/lib/mgatk/__pycache__
2023-06-26T21:40:08,695   creating build/lib/mgatk/bin
2023-06-26T21:40:08,695   copying mgatk/bin/picard.jar -> build/lib/mgatk/bin
2023-06-26T21:40:09,214   creating build/lib/mgatk/bin/R
2023-06-26T21:40:09,216   copying mgatk/bin/R/convert_cellbender_output.R -> build/lib/mgatk/bin/R
2023-06-26T21:40:09,222   copying mgatk/bin/R/prepare_cellbender.R -> build/lib/mgatk/bin/R
2023-06-26T21:40:09,228   copying mgatk/bin/R/toRDS.R -> build/lib/mgatk/bin/R
2023-06-26T21:40:09,233   creating build/lib/mgatk/bin/anno
2023-06-26T21:40:09,234   creating build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,237   copying mgatk/bin/anno/fasta/GRCh37.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,243   copying mgatk/bin/anno/fasta/GRCh38.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,249   copying mgatk/bin/anno/fasta/GRCm38.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,255   copying mgatk/bin/anno/fasta/GRCz10.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,261   copying mgatk/bin/anno/fasta/NC_012920.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,267   copying mgatk/bin/anno/fasta/hg19.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,273   copying mgatk/bin/anno/fasta/hg19_chrM.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,279   copying mgatk/bin/anno/fasta/hg38.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,284   copying mgatk/bin/anno/fasta/mm10.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,290   copying mgatk/bin/anno/fasta/mm9.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,296   copying mgatk/bin/anno/fasta/rCRS.fasta -> build/lib/mgatk/bin/anno/fasta
2023-06-26T21:40:09,302   creating build/lib/mgatk/bin/python
2023-06-26T21:40:09,304   copying mgatk/bin/python/chunk_barcoded_bam.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,308   copying mgatk/bin/python/filterClipBam.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,312   copying mgatk/bin/python/find_barcodes.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,316   copying mgatk/bin/python/oneSample.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,321   copying mgatk/bin/python/split_barcoded_bam.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,324   copying mgatk/bin/python/sumstatsBP.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,329   copying mgatk/bin/python/sumstatsBP_overlap.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,333   copying mgatk/bin/python/sumstatsBPtenx.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,337   copying mgatk/bin/python/sumstatsBPtenx_overlap.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,342   copying mgatk/bin/python/variant_calling.py -> build/lib/mgatk/bin/python
2023-06-26T21:40:09,347   creating build/lib/mgatk/bin/snake
2023-06-26T21:40:09,349   copying mgatk/bin/snake/Snakefile.Gather -> build/lib/mgatk/bin/snake
2023-06-26T21:40:09,353   copying mgatk/bin/snake/Snakefile.Scatter -> build/lib/mgatk/bin/snake
2023-06-26T21:40:09,357   copying mgatk/bin/snake/Snakefile.tenx -> build/lib/mgatk/bin/snake
2023-06-26T21:40:09,362   creating build/lib/mgatk/deletioncalling
2023-06-26T21:40:09,363   copying mgatk/deletioncalling/clidel.py -> build/lib/mgatk/deletioncalling
2023-06-26T21:40:09,368   copying mgatk/deletioncalling/clifind.py -> build/lib/mgatk/deletioncalling
2023-06-26T21:40:09,372   creating build/lib/mgatk/deletioncalling/bulk_del
2023-06-26T21:40:09,374   copying mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R -> build/lib/mgatk/deletioncalling/bulk_del
2023-06-26T21:40:09,379   creating build/lib/mgatk/deletioncalling/singles_del
2023-06-26T21:40:09,380   copying mgatk/deletioncalling/singles_del/01_process_cell_reads.py -> build/lib/mgatk/deletioncalling/singles_del
2023-06-26T21:40:09,385   copying mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R -> build/lib/mgatk/deletioncalling/singles_del
2023-06-26T21:40:09,389   copying mgatk/deletioncalling/singles_del/Snakefile.delSingles -> build/lib/mgatk/deletioncalling/singles_del
2023-06-26T21:40:09,467   /usr/local/lib/python3.7/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-06-26T21:40:09,468   !!

2023-06-26T21:40:09,468           ********************************************************************************
2023-06-26T21:40:09,469           Please avoid running ``setup.py`` directly.
2023-06-26T21:40:09,469           Instead, use pypa/build, pypa/installer, pypa/build or
2023-06-26T21:40:09,470           other standards-based tools.

2023-06-26T21:40:09,470           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-06-26T21:40:09,471           ********************************************************************************

2023-06-26T21:40:09,471   !!
2023-06-26T21:40:09,472     self.initialize_options()
2023-06-26T21:40:09,532   installing to build/bdist.linux-armv7l/wheel
2023-06-26T21:40:09,533   running install
2023-06-26T21:40:09,592   running install_lib
2023-06-26T21:40:09,661   creating build/bdist.linux-armv7l
2023-06-26T21:40:09,662   creating build/bdist.linux-armv7l/wheel
2023-06-26T21:40:09,665   creating build/bdist.linux-armv7l/wheel/mgatk
2023-06-26T21:40:09,667   copying build/lib/mgatk/mgatkHelp.py -> build/bdist.linux-armv7l/wheel/mgatk
2023-06-26T21:40:09,673   creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling
2023-06-26T21:40:09,676   creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del
2023-06-26T21:40:09,678   copying build/lib/mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del
2023-06-26T21:40:09,682   copying build/lib/mgatk/deletioncalling/singles_del/Snakefile.delSingles -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del
2023-06-26T21:40:09,686   copying build/lib/mgatk/deletioncalling/singles_del/01_process_cell_reads.py -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del
2023-06-26T21:40:09,689   copying build/lib/mgatk/deletioncalling/clifind.py -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling
2023-06-26T21:40:09,693   copying build/lib/mgatk/deletioncalling/clidel.py -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling
2023-06-26T21:40:09,698   creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/bulk_del
2023-06-26T21:40:09,700   copying build/lib/mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R -> build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/bulk_del
2023-06-26T21:40:09,705   copying build/lib/mgatk/cli.py -> build/bdist.linux-armv7l/wheel/mgatk
2023-06-26T21:40:09,710   copying build/lib/mgatk/__init__.py -> build/bdist.linux-armv7l/wheel/mgatk
2023-06-26T21:40:09,715   creating build/bdist.linux-armv7l/wheel/mgatk/__pycache__
2023-06-26T21:40:09,716   copying build/lib/mgatk/__pycache__/__init__.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__
2023-06-26T21:40:09,720   copying build/lib/mgatk/__pycache__/mgatkHelp.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__
2023-06-26T21:40:09,725   copying build/lib/mgatk/__pycache__/cli.cpython-38.pyc -> build/bdist.linux-armv7l/wheel/mgatk/__pycache__
2023-06-26T21:40:09,731   creating build/bdist.linux-armv7l/wheel/mgatk/bin
2023-06-26T21:40:09,732   copying build/lib/mgatk/bin/picard.jar -> build/bdist.linux-armv7l/wheel/mgatk/bin
2023-06-26T21:40:10,363   creating build/bdist.linux-armv7l/wheel/mgatk/bin/snake
2023-06-26T21:40:10,364   copying build/lib/mgatk/bin/snake/Snakefile.Scatter -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake
2023-06-26T21:40:10,369   copying build/lib/mgatk/bin/snake/Snakefile.tenx -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake
2023-06-26T21:40:10,373   copying build/lib/mgatk/bin/snake/Snakefile.Gather -> build/bdist.linux-armv7l/wheel/mgatk/bin/snake
2023-06-26T21:40:10,377   creating build/bdist.linux-armv7l/wheel/mgatk/bin/anno
2023-06-26T21:40:10,380   creating build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,382   copying build/lib/mgatk/bin/anno/fasta/hg19.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,387   copying build/lib/mgatk/bin/anno/fasta/GRCz10.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,392   copying build/lib/mgatk/bin/anno/fasta/GRCh37.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,397   copying build/lib/mgatk/bin/anno/fasta/GRCh38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,402   copying build/lib/mgatk/bin/anno/fasta/mm10.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,407   copying build/lib/mgatk/bin/anno/fasta/GRCm38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,412   copying build/lib/mgatk/bin/anno/fasta/rCRS.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,417   copying build/lib/mgatk/bin/anno/fasta/mm9.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,422   copying build/lib/mgatk/bin/anno/fasta/NC_012920.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,426   copying build/lib/mgatk/bin/anno/fasta/hg38.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,432   copying build/lib/mgatk/bin/anno/fasta/hg19_chrM.fasta -> build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2023-06-26T21:40:10,438   creating build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,440   copying build/lib/mgatk/bin/python/oneSample.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,444   copying build/lib/mgatk/bin/python/sumstatsBPtenx.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,447   copying build/lib/mgatk/bin/python/sumstatsBP.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,451   copying build/lib/mgatk/bin/python/chunk_barcoded_bam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,455   copying build/lib/mgatk/bin/python/split_barcoded_bam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,459   copying build/lib/mgatk/bin/python/variant_calling.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,463   copying build/lib/mgatk/bin/python/sumstatsBP_overlap.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,467   copying build/lib/mgatk/bin/python/find_barcodes.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,471   copying build/lib/mgatk/bin/python/sumstatsBPtenx_overlap.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,475   copying build/lib/mgatk/bin/python/filterClipBam.py -> build/bdist.linux-armv7l/wheel/mgatk/bin/python
2023-06-26T21:40:10,479   creating build/bdist.linux-armv7l/wheel/mgatk/bin/R
2023-06-26T21:40:10,481   copying build/lib/mgatk/bin/R/prepare_cellbender.R -> build/bdist.linux-armv7l/wheel/mgatk/bin/R
2023-06-26T21:40:10,486   copying build/lib/mgatk/bin/R/convert_cellbender_output.R -> build/bdist.linux-armv7l/wheel/mgatk/bin/R
2023-06-26T21:40:10,490   copying build/lib/mgatk/bin/R/toRDS.R -> build/bdist.linux-armv7l/wheel/mgatk/bin/R
2023-06-26T21:40:10,494   copying build/lib/mgatk/devnotes.md -> build/bdist.linux-armv7l/wheel/mgatk
2023-06-26T21:40:10,498   running install_egg_info
2023-06-26T21:40:10,574   Copying mgatk.egg-info to build/bdist.linux-armv7l/wheel/mgatk-0.6.8-py3.7.egg-info
2023-06-26T21:40:10,600   running install_scripts
2023-06-26T21:40:10,637   creating build/bdist.linux-armv7l/wheel/mgatk-0.6.8.dist-info/WHEEL
2023-06-26T21:40:10,642   creating '/tmp/pip-wheel-8ac8asd6/mgatk-0.6.8-py2.py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-06-26T21:40:10,647   adding 'mgatk/__init__.py'
2023-06-26T21:40:10,654   adding 'mgatk/cli.py'
2023-06-26T21:40:10,658   adding 'mgatk/devnotes.md'
2023-06-26T21:40:10,662   adding 'mgatk/mgatkHelp.py'
2023-06-26T21:40:10,665   adding 'mgatk/__pycache__/__init__.cpython-38.pyc'
2023-06-26T21:40:10,671   adding 'mgatk/__pycache__/cli.cpython-38.pyc'
2023-06-26T21:40:10,676   adding 'mgatk/__pycache__/mgatkHelp.cpython-38.pyc'
2023-06-26T21:40:15,126   adding 'mgatk/bin/picard.jar'
2023-06-26T21:40:15,440   adding 'mgatk/bin/R/convert_cellbender_output.R'
2023-06-26T21:40:15,445   adding 'mgatk/bin/R/prepare_cellbender.R'
2023-06-26T21:40:15,449   adding 'mgatk/bin/R/toRDS.R'
2023-06-26T21:40:15,471   adding 'mgatk/bin/anno/fasta/GRCh37.fasta'
2023-06-26T21:40:15,491   adding 'mgatk/bin/anno/fasta/GRCh38.fasta'
2023-06-26T21:40:15,510   adding 'mgatk/bin/anno/fasta/GRCm38.fasta'
2023-06-26T21:40:15,530   adding 'mgatk/bin/anno/fasta/GRCz10.fasta'
2023-06-26T21:40:15,550   adding 'mgatk/bin/anno/fasta/NC_012920.fasta'
2023-06-26T21:40:15,570   adding 'mgatk/bin/anno/fasta/hg19.fasta'
2023-06-26T21:40:15,591   adding 'mgatk/bin/anno/fasta/hg19_chrM.fasta'
2023-06-26T21:40:15,610   adding 'mgatk/bin/anno/fasta/hg38.fasta'
2023-06-26T21:40:15,629   adding 'mgatk/bin/anno/fasta/mm10.fasta'
2023-06-26T21:40:15,648   adding 'mgatk/bin/anno/fasta/mm9.fasta'
2023-06-26T21:40:15,668   adding 'mgatk/bin/anno/fasta/rCRS.fasta'
2023-06-26T21:40:15,673   adding 'mgatk/bin/python/chunk_barcoded_bam.py'
2023-06-26T21:40:15,675   adding 'mgatk/bin/python/filterClipBam.py'
2023-06-26T21:40:15,678   adding 'mgatk/bin/python/find_barcodes.py'
2023-06-26T21:40:15,681   adding 'mgatk/bin/python/oneSample.py'
2023-06-26T21:40:15,684   adding 'mgatk/bin/python/split_barcoded_bam.py'
2023-06-26T21:40:15,687   adding 'mgatk/bin/python/sumstatsBP.py'
2023-06-26T21:40:15,691   adding 'mgatk/bin/python/sumstatsBP_overlap.py'
2023-06-26T21:40:15,694   adding 'mgatk/bin/python/sumstatsBPtenx.py'
2023-06-26T21:40:15,698   adding 'mgatk/bin/python/sumstatsBPtenx_overlap.py'
2023-06-26T21:40:15,701   adding 'mgatk/bin/python/variant_calling.py'
2023-06-26T21:40:15,705   adding 'mgatk/bin/snake/Snakefile.Gather'
2023-06-26T21:40:15,708   adding 'mgatk/bin/snake/Snakefile.Scatter'
2023-06-26T21:40:15,712   adding 'mgatk/bin/snake/Snakefile.tenx'
2023-06-26T21:40:15,717   adding 'mgatk/deletioncalling/clidel.py'
2023-06-26T21:40:15,720   adding 'mgatk/deletioncalling/clifind.py'
2023-06-26T21:40:15,724   adding 'mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R'
2023-06-26T21:40:15,729   adding 'mgatk/deletioncalling/singles_del/01_process_cell_reads.py'
2023-06-26T21:40:15,732   adding 'mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R'
2023-06-26T21:40:15,735   adding 'mgatk/deletioncalling/singles_del/Snakefile.delSingles'
2023-06-26T21:40:15,739   adding 'mgatk-0.6.8.dist-info/LICENSE.txt'
2023-06-26T21:40:15,742   adding 'mgatk-0.6.8.dist-info/METADATA'
2023-06-26T21:40:15,744   adding 'mgatk-0.6.8.dist-info/WHEEL'
2023-06-26T21:40:15,746   adding 'mgatk-0.6.8.dist-info/entry_points.txt'
2023-06-26T21:40:15,748   adding 'mgatk-0.6.8.dist-info/top_level.txt'
2023-06-26T21:40:15,750   adding 'mgatk-0.6.8.dist-info/RECORD'
2023-06-26T21:40:16,281   removing build/bdist.linux-armv7l/wheel
2023-06-26T21:40:16,487   Building wheel for mgatk (setup.py): finished with status 'done'
2023-06-26T21:40:16,918   Created wheel for mgatk: filename=mgatk-0.6.8-py2.py3-none-any.whl size=14325441 sha256=ee01a0d2c63bbec27ac1c2ab8e29aa90ebe118a13dc3113c74dabb1e233256eb
2023-06-26T21:40:16,921   Stored in directory: /tmp/pip-ephem-wheel-cache-9v_5if0j/wheels/a7/e8/77/49a359ee9c2d9c24ea804819082d014ac2e2b81159d91225e8
2023-06-26T21:40:16,966 Successfully built mgatk
2023-06-26T21:40:18,065 Removed build tracker: '/tmp/pip-build-tracker-q0thhlk5'