2026-07-09T10:07:40,012 Created temporary directory: /tmp/pip-ephem-wheel-cache-oxorb1oj
2026-07-09T10:07:40,014 Created temporary directory: /tmp/pip-build-tracker-6chduk98
2026-07-09T10:07:40,015 Initialized build tracking at /tmp/pip-build-tracker-6chduk98
2026-07-09T10:07:40,015 Created build tracker: /tmp/pip-build-tracker-6chduk98
2026-07-09T10:07:40,015 Entered build tracker: /tmp/pip-build-tracker-6chduk98
2026-07-09T10:07:40,016 Created temporary directory: /tmp/pip-wheel-7anv3sl4
2026-07-09T10:07:40,019 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453
2026-07-09T10:07:40,021 Created temporary directory: /tmp/pip-ephem-wheel-cache-8l5rsvqy
2026-07-09T10:07:40,043 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2026-07-09T10:07:40,047 2 location(s) to search for versions of mgatk:
2026-07-09T10:07:40,047 * https://pypi.org/simple/mgatk/
2026-07-09T10:07:40,047 * https://www.piwheels.org/simple/mgatk/
2026-07-09T10:07:40,047 Fetching project page and analyzing links: https://pypi.org/simple/mgatk/
2026-07-09T10:07:40,048 Getting page https://pypi.org/simple/mgatk/
2026-07-09T10:07:40,050 Found index url https://pypi.org/simple
2026-07-09T10:07:40,379 Fetched page https://pypi.org/simple/mgatk/ as application/vnd.pypi.simple.v1+json
2026-07-09T10:07:40,387   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
2026-07-09T10:07:40,388   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
2026-07-09T10:07:40,388   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
2026-07-09T10:07:40,389   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
2026-07-09T10:07:40,390   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
2026-07-09T10:07:40,391   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
2026-07-09T10:07:40,392   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
2026-07-09T10:07:40,393   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
2026-07-09T10:07:40,394   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
2026-07-09T10:07:40,395   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
2026-07-09T10:07:40,396   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
2026-07-09T10:07:40,397   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
2026-07-09T10:07:40,398   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
2026-07-09T10:07:40,399   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
2026-07-09T10:07:40,399   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
2026-07-09T10:07:40,400   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
2026-07-09T10:07:40,401   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
2026-07-09T10:07:40,402   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
2026-07-09T10:07:40,402   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
2026-07-09T10:07:40,403   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
2026-07-09T10:07:40,404   Found link https://files.pythonhosted.org/packages/8f/ad/de6a0dc7c3c8606f257a12491b0f0d22f84bb6b1ceff779df262b38d9fb8/mgatk-0.7.0.tar.gz (from https://pypi.org/simple/mgatk/), version: 0.7.0
2026-07-09T10:07:40,405   Found link https://files.pythonhosted.org/packages/f6/a9/8d27851daf475b8b264f94f4170555b3745d33e9db949d8a5e85b73254dd/mgatk-0.9.0.tar.gz (from https://pypi.org/simple/mgatk/) (requires-python:>=3.11), version: 0.9.0
2026-07-09T10:07:40,406 Fetching project page and analyzing links: https://www.piwheels.org/simple/mgatk/
2026-07-09T10:07:40,407 Getting page https://www.piwheels.org/simple/mgatk/
2026-07-09T10:07:40,409 Found index url https://www.piwheels.org/simple
2026-07-09T10:07:40,734 Fetched page https://www.piwheels.org/simple/mgatk/ as text/html
2026-07-09T10:07:40,742   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.7.0-py2.py3-none-any.whl#sha256=15579f7b257ef133c497de588a15bbe11c6c9dd06ce4dcfe3447f2f073c140c4 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,743   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.9-py2.py3-none-any.whl#sha256=3d7e110966e8ec8ca672b880356fbf86596208ef2aefb3fef7fd1200b1c90db9 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,744   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.8-py2.py3-none-any.whl#sha256=ee01a0d2c63bbec27ac1c2ab8e29aa90ebe118a13dc3113c74dabb1e233256eb (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,745   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.7-py2.py3-none-any.whl#sha256=79fed343da0db4117616398f89d660c2fbd8e79fe68fb94ec1aefc118d87648a (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,745   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.6-py2.py3-none-any.whl#sha256=db1b17b9efe2010d5474e233eb127e3b9ebbaa04eaebe474d461622e040bc634 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,746   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.4-py2.py3-none-any.whl#sha256=58b5484ca92bb15aac4a8f9063b494c87022e986d856ae9c5e4fc15002965db7 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,747   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.3-py2.py3-none-any.whl#sha256=360fb6d8cb87a3d76ecd2ac7a4b94e1f13cdcd515050c8926af8309672d0c0d2 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,748   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.2-py2.py3-none-any.whl#sha256=ad87bf28d8140677cd9328a5b9582470aedc1867c3a9b307d9420c2712454009 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,748   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.1-py2.py3-none-any.whl#sha256=751c5ba1854115dc6815f5c3b6fcaa4860c66dc8970dfcf7449b18cd4306395e (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,748   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.6.0-py2.py3-none-any.whl#sha256=36135d81a973357f7125fb1ff898ef3590364d14ee64ee4f9c6a25b1340d78ca (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,749   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.5.9-py2.py3-none-any.whl#sha256=7078b4d3d77e2260f01ca68bb7f6707cb4a2c852ed2c7a5e4f7a6c68cc1c50e2 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,749   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.5.8-py2.py3-none-any.whl#sha256=6e2875d8620ce7ed459c23ad983c0413adef335eabc99b82aedd074c181592d0 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,750   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.5.7-py2.py3-none-any.whl#sha256=95b59ea0189b6f7d87453823792ba21b9f45deaaeb5a205ccb173694fd16c43d (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,750   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.5.6-py2.py3-none-any.whl#sha256=a199b8ec80e8f6581d33504f49229ef908c215936379d77f622394cf1ab2b558 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,751   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.5.5-py2.py3-none-any.whl#sha256=ff9f09e518b7936a8a6923a2d095fa02bb30822361e426c072ea2018006d5f96 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,752   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.5.3-py2.py3-none-any.whl#sha256=f7709526d1c046488d849a38c4b85838814c2db9a8e9b140f8f706febe4bed36 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,752   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.5.1-py2.py3-none-any.whl#sha256=886bbaef1900c90d54489c15e59b0f38125d0aca802a551b958af8e9b34c8101 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,753   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.5.0-py2.py3-none-any.whl#sha256=906c45dd6c1ccb708de36350b787e0dfbda0a4d49a08f02c211deec0c5d19da9 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,753   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.2.5-py2.py3-none-any.whl#sha256=9c0333783e998b2493f6bbd8d93e2a5ce9f332bd53d83e3ff3fe0ce921182b3a (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,754   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.1.0-py2.py3-none-any.whl#sha256=cef81c26f6eb16952e9f8d05c24dc85d491f400645c82c478dddfd64b785d487 (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,754   Skipping link: No binaries permitted for mgatk: https://archive1.piwheels.org/simple/mgatk/mgatk-0.0.1-py2.py3-none-any.whl#sha256=7e7d06dc92473d5d2f2c99cc022aaf64ab8d0301f1a1bd06edb2b37e8a17efbc (from https://www.piwheels.org/simple/mgatk/)
2026-07-09T10:07:40,755 Skipping link: not a file: https://www.piwheels.org/simple/mgatk/
2026-07-09T10:07:40,756 Skipping link: not a file: https://pypi.org/simple/mgatk/
2026-07-09T10:07:40,779 Given no hashes to check 1 links for project 'mgatk': discarding no candidates
2026-07-09T10:07:40,800 Collecting mgatk==0.9.0
2026-07-09T10:07:40,802   Created temporary directory: /tmp/pip-unpack-fmoq9c0q
2026-07-09T10:07:41,128   Downloading mgatk-0.9.0.tar.gz (128 kB)
2026-07-09T10:07:41,397   Added mgatk==0.9.0 from https://files.pythonhosted.org/packages/f6/a9/8d27851daf475b8b264f94f4170555b3745d33e9db949d8a5e85b73254dd/mgatk-0.9.0.tar.gz to build tracker '/tmp/pip-build-tracker-6chduk98'
2026-07-09T10:07:41,399   Running setup.py (path:/tmp/pip-wheel-7anv3sl4/mgatk_23f91b8ae7324c24843f22a8fe00b730/setup.py) egg_info for package mgatk
2026-07-09T10:07:41,399   Created temporary directory: /tmp/pip-pip-egg-info-0obt4_97
2026-07-09T10:07:41,400   Preparing metadata (setup.py): started
2026-07-09T10:07:41,401   Running command python setup.py egg_info
2026-07-09T10:07:41,935   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead.
2026-07-09T10:07:41,935   !!

2026-07-09T10:07:41,936           ********************************************************************************
2026-07-09T10:07:41,937           Usage of dash-separated 'description-file' will not be supported in future
2026-07-09T10:07:41,937           versions. Please use the underscore name 'description_file' instead.


2026-07-09T10:07:41,939           Available configuration options are listed in:
2026-07-09T10:07:41,940           https://setuptools.pypa.io/en/latest/userguide/declarative_config.html

2026-07-09T10:07:41,941           This deprecation is overdue, please update your project and remove deprecated
2026-07-09T10:07:41,942           calls to avoid build errors in the future.

2026-07-09T10:07:41,944           See https://github.com/pypa/setuptools/discussions/5011 for details.
2026-07-09T10:07:41,945           ********************************************************************************

2026-07-09T10:07:41,946   !!
2026-07-09T10:07:41,947     opt = self._enforce_underscore(opt, section)
2026-07-09T10:07:42,282   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead.
2026-07-09T10:07:42,283   !!

2026-07-09T10:07:42,284           ********************************************************************************
2026-07-09T10:07:42,285           Usage of dash-separated 'description-file' will not be supported in future
2026-07-09T10:07:42,286           versions. Please use the underscore name 'description_file' instead.
2026-07-09T10:07:42,286           (Affected: mgatk).

2026-07-09T10:07:42,287           Available configuration options are listed in:
2026-07-09T10:07:42,288           https://setuptools.pypa.io/en/latest/userguide/declarative_config.html

2026-07-09T10:07:42,289           This deprecation is overdue, please update your project and remove deprecated
2026-07-09T10:07:42,290           calls to avoid build errors in the future.

2026-07-09T10:07:42,291           See https://github.com/pypa/setuptools/discussions/5011 for details.
2026-07-09T10:07:42,292           ********************************************************************************

2026-07-09T10:07:42,293   !!
2026-07-09T10:07:42,293     opt = self._enforce_underscore(opt, section)
2026-07-09T10:07:42,294   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-07-09T10:07:42,294   !!

2026-07-09T10:07:42,296           ********************************************************************************
2026-07-09T10:07:42,296           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-07-09T10:07:42,297           License :: OSI Approved :: MIT License

2026-07-09T10:07:42,298           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-07-09T10:07:42,299           ********************************************************************************

2026-07-09T10:07:42,300   !!
2026-07-09T10:07:42,300     self._finalize_license_expression()
2026-07-09T10:07:42,316   running egg_info
2026-07-09T10:07:42,343   creating /tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info
2026-07-09T10:07:42,344   writing /tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info/PKG-INFO
2026-07-09T10:07:42,348   writing dependency_links to /tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info/dependency_links.txt
2026-07-09T10:07:42,350   writing entry points to /tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info/entry_points.txt
2026-07-09T10:07:42,351   writing requirements to /tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info/requires.txt
2026-07-09T10:07:42,352   writing top-level names to /tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info/top_level.txt
2026-07-09T10:07:42,354   writing manifest file '/tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info/SOURCES.txt'
2026-07-09T10:07:42,445   reading manifest file '/tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info/SOURCES.txt'
2026-07-09T10:07:42,447   reading manifest template 'MANIFEST.in'
2026-07-09T10:07:42,448   no previously-included directories found matching 'mgatk.egg-info'
2026-07-09T10:07:42,448   no previously-included directories found matching 'tests'
2026-07-09T10:07:42,449   no previously-included directories found matching '*.DS_Store'
2026-07-09T10:07:42,475   adding license file 'LICENSE.txt'
2026-07-09T10:07:42,480   writing manifest file '/tmp/pip-pip-egg-info-0obt4_97/mgatk.egg-info/SOURCES.txt'
2026-07-09T10:07:42,588   Preparing metadata (setup.py): finished with status 'done'
2026-07-09T10:07:42,592   Source in /tmp/pip-wheel-7anv3sl4/mgatk_23f91b8ae7324c24843f22a8fe00b730 has version 0.9.0, which satisfies requirement mgatk==0.9.0 from https://files.pythonhosted.org/packages/f6/a9/8d27851daf475b8b264f94f4170555b3745d33e9db949d8a5e85b73254dd/mgatk-0.9.0.tar.gz
2026-07-09T10:07:42,593   Removed mgatk==0.9.0 from https://files.pythonhosted.org/packages/f6/a9/8d27851daf475b8b264f94f4170555b3745d33e9db949d8a5e85b73254dd/mgatk-0.9.0.tar.gz from build tracker '/tmp/pip-build-tracker-6chduk98'
2026-07-09T10:07:42,599 Created temporary directory: /tmp/pip-unpack-ozmurq9o
2026-07-09T10:07:42,599 Building wheels for collected packages: mgatk
2026-07-09T10:07:42,604   Created temporary directory: /tmp/pip-wheel-9va8wf00
2026-07-09T10:07:42,605   Building wheel for mgatk (setup.py): started
2026-07-09T10:07:42,606   Destination directory: /tmp/pip-wheel-9va8wf00
2026-07-09T10:07:42,606   Running command python setup.py bdist_wheel
2026-07-09T10:07:43,121   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead.
2026-07-09T10:07:43,121   !!

2026-07-09T10:07:43,122           ********************************************************************************
2026-07-09T10:07:43,123           Usage of dash-separated 'description-file' will not be supported in future
2026-07-09T10:07:43,124           versions. Please use the underscore name 'description_file' instead.


2026-07-09T10:07:43,126           Available configuration options are listed in:
2026-07-09T10:07:43,126           https://setuptools.pypa.io/en/latest/userguide/declarative_config.html

2026-07-09T10:07:43,128           This deprecation is overdue, please update your project and remove deprecated
2026-07-09T10:07:43,128           calls to avoid build errors in the future.

2026-07-09T10:07:43,129           See https://github.com/pypa/setuptools/discussions/5011 for details.
2026-07-09T10:07:43,130           ********************************************************************************

2026-07-09T10:07:43,131   !!
2026-07-09T10:07:43,132     opt = self._enforce_underscore(opt, section)
2026-07-09T10:07:43,459   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:599: SetuptoolsDeprecationWarning: Invalid dash-separated key 'description-file' in 'metadata' (setup.cfg), please use the underscore name 'description_file' instead.
2026-07-09T10:07:43,460   !!

2026-07-09T10:07:43,461           ********************************************************************************
2026-07-09T10:07:43,462           Usage of dash-separated 'description-file' will not be supported in future
2026-07-09T10:07:43,462           versions. Please use the underscore name 'description_file' instead.
2026-07-09T10:07:43,463           (Affected: mgatk).

2026-07-09T10:07:43,464           Available configuration options are listed in:
2026-07-09T10:07:43,464           https://setuptools.pypa.io/en/latest/userguide/declarative_config.html

2026-07-09T10:07:43,465           This deprecation is overdue, please update your project and remove deprecated
2026-07-09T10:07:43,466           calls to avoid build errors in the future.

2026-07-09T10:07:43,467           See https://github.com/pypa/setuptools/discussions/5011 for details.
2026-07-09T10:07:43,467           ********************************************************************************

2026-07-09T10:07:43,468   !!
2026-07-09T10:07:43,469     opt = self._enforce_underscore(opt, section)
2026-07-09T10:07:43,469   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:765: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2026-07-09T10:07:43,470   !!

2026-07-09T10:07:43,471           ********************************************************************************
2026-07-09T10:07:43,472           Please consider removing the following classifiers in favor of a SPDX license expression:

2026-07-09T10:07:43,473           License :: OSI Approved :: MIT License

2026-07-09T10:07:43,474           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2026-07-09T10:07:43,475           ********************************************************************************

2026-07-09T10:07:43,476   !!
2026-07-09T10:07:43,476     self._finalize_license_expression()
2026-07-09T10:07:43,477   running bdist_wheel
2026-07-09T10:07:43,599   running build
2026-07-09T10:07:43,600   running build_py
2026-07-09T10:07:43,630   creating build/lib/mgatk
2026-07-09T10:07:43,632   copying mgatk/cli.py -> build/lib/mgatk
2026-07-09T10:07:43,635   copying mgatk/mgatkHelp.py -> build/lib/mgatk
2026-07-09T10:07:43,638   copying mgatk/__init__.py -> build/lib/mgatk
2026-07-09T10:07:43,641   creating build/lib/mgatk/processing
2026-07-09T10:07:43,642   copying mgatk/processing/allele_counts.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,644   copying mgatk/processing/variant_calling.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,647   copying mgatk/processing/filtering.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,649   copying mgatk/processing/__init__.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,651   copying mgatk/processing/barcodes.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,653   copying mgatk/processing/allele_counts_tenx.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,656   copying mgatk/processing/dedup.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,657   copying mgatk/processing/one_slice_tenx.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,659   copying mgatk/processing/one_sample.py -> build/lib/mgatk/processing
2026-07-09T10:07:43,661   running egg_info
2026-07-09T10:07:43,690   writing mgatk.egg-info/PKG-INFO
2026-07-09T10:07:43,694   writing dependency_links to mgatk.egg-info/dependency_links.txt
2026-07-09T10:07:43,696   writing entry points to mgatk.egg-info/entry_points.txt
2026-07-09T10:07:43,698   writing requirements to mgatk.egg-info/requires.txt
2026-07-09T10:07:43,699   writing top-level names to mgatk.egg-info/top_level.txt
2026-07-09T10:07:43,732   reading manifest file 'mgatk.egg-info/SOURCES.txt'
2026-07-09T10:07:43,737   reading manifest template 'MANIFEST.in'
2026-07-09T10:07:43,738   no previously-included directories found matching 'tests'
2026-07-09T10:07:43,739   no previously-included directories found matching '*.DS_Store'
2026-07-09T10:07:43,763   adding license file 'LICENSE.txt'
2026-07-09T10:07:43,768   writing manifest file 'mgatk.egg-info/SOURCES.txt'
2026-07-09T10:07:43,770   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.__pycache__' is absent from the `packages` configuration.
2026-07-09T10:07:43,771   !!

2026-07-09T10:07:43,772           ********************************************************************************
2026-07-09T10:07:43,772           ############################
2026-07-09T10:07:43,772           # Package would be ignored #
2026-07-09T10:07:43,773           ############################
2026-07-09T10:07:43,774           Python recognizes 'mgatk.__pycache__' as an importable package[^1],
2026-07-09T10:07:43,774           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,775           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,776           package, please make sure that 'mgatk.__pycache__' is explicitly added
2026-07-09T10:07:43,776           to the `packages` configuration field.

2026-07-09T10:07:43,777           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,778           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,778           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,779           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,780           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,782           If you don't want 'mgatk.__pycache__' to be distributed and are
2026-07-09T10:07:43,782           already explicitly excluding 'mgatk.__pycache__' via
2026-07-09T10:07:43,783           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,783           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,784           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,785           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,786           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,788           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,788                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,789                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,790                 directory, all directories are treated like packages.
2026-07-09T10:07:43,790           ********************************************************************************

2026-07-09T10:07:43,791   !!
2026-07-09T10:07:43,792     check.warn(importable)
2026-07-09T10:07:43,793   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.bin.R' is absent from the `packages` configuration.
2026-07-09T10:07:43,794   !!

2026-07-09T10:07:43,795           ********************************************************************************
2026-07-09T10:07:43,795           ############################
2026-07-09T10:07:43,796           # Package would be ignored #
2026-07-09T10:07:43,796           ############################
2026-07-09T10:07:43,797           Python recognizes 'mgatk.bin.R' as an importable package[^1],
2026-07-09T10:07:43,798           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,799           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,800           package, please make sure that 'mgatk.bin.R' is explicitly added
2026-07-09T10:07:43,800           to the `packages` configuration field.

2026-07-09T10:07:43,801           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,802           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,802           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,803           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,804           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,805           If you don't want 'mgatk.bin.R' to be distributed and are
2026-07-09T10:07:43,806           already explicitly excluding 'mgatk.bin.R' via
2026-07-09T10:07:43,806           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,807           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,807           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,808           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,809           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,811           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,811                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,812                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,812                 directory, all directories are treated like packages.
2026-07-09T10:07:43,813           ********************************************************************************

2026-07-09T10:07:43,814   !!
2026-07-09T10:07:43,814     check.warn(importable)
2026-07-09T10:07:43,815   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.bin.anno.fasta' is absent from the `packages` configuration.
2026-07-09T10:07:43,816   !!

2026-07-09T10:07:43,817           ********************************************************************************
2026-07-09T10:07:43,817           ############################
2026-07-09T10:07:43,818           # Package would be ignored #
2026-07-09T10:07:43,818           ############################
2026-07-09T10:07:43,819           Python recognizes 'mgatk.bin.anno.fasta' as an importable package[^1],
2026-07-09T10:07:43,819           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,821           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,821           package, please make sure that 'mgatk.bin.anno.fasta' is explicitly added
2026-07-09T10:07:43,822           to the `packages` configuration field.

2026-07-09T10:07:43,823           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,823           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,824           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,825           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,826           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,827           If you don't want 'mgatk.bin.anno.fasta' to be distributed and are
2026-07-09T10:07:43,828           already explicitly excluding 'mgatk.bin.anno.fasta' via
2026-07-09T10:07:43,828           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,829           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,829           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,831           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,832           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,833           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,833                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,834                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,834                 directory, all directories are treated like packages.
2026-07-09T10:07:43,835           ********************************************************************************

2026-07-09T10:07:43,836   !!
2026-07-09T10:07:43,837     check.warn(importable)
2026-07-09T10:07:43,837   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.bin.snake' is absent from the `packages` configuration.
2026-07-09T10:07:43,837   !!

2026-07-09T10:07:43,839           ********************************************************************************
2026-07-09T10:07:43,839           ############################
2026-07-09T10:07:43,840           # Package would be ignored #
2026-07-09T10:07:43,840           ############################
2026-07-09T10:07:43,841           Python recognizes 'mgatk.bin.snake' as an importable package[^1],
2026-07-09T10:07:43,841           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,842           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,843           package, please make sure that 'mgatk.bin.snake' is explicitly added
2026-07-09T10:07:43,843           to the `packages` configuration field.

2026-07-09T10:07:43,844           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,845           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,845           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,846           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,847           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,848           If you don't want 'mgatk.bin.snake' to be distributed and are
2026-07-09T10:07:43,849           already explicitly excluding 'mgatk.bin.snake' via
2026-07-09T10:07:43,850           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,850           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,851           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,852           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,853           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,855           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,855                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,856                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,856                 directory, all directories are treated like packages.
2026-07-09T10:07:43,857           ********************************************************************************

2026-07-09T10:07:43,858   !!
2026-07-09T10:07:43,859     check.warn(importable)
2026-07-09T10:07:43,859   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.deletioncalling' is absent from the `packages` configuration.
2026-07-09T10:07:43,860   !!

2026-07-09T10:07:43,861           ********************************************************************************
2026-07-09T10:07:43,861           ############################
2026-07-09T10:07:43,862           # Package would be ignored #
2026-07-09T10:07:43,863           ############################
2026-07-09T10:07:43,863           Python recognizes 'mgatk.deletioncalling' as an importable package[^1],
2026-07-09T10:07:43,864           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,865           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,865           package, please make sure that 'mgatk.deletioncalling' is explicitly added
2026-07-09T10:07:43,866           to the `packages` configuration field.

2026-07-09T10:07:43,867           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,867           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,868           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,869           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,870           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,871           If you don't want 'mgatk.deletioncalling' to be distributed and are
2026-07-09T10:07:43,871           already explicitly excluding 'mgatk.deletioncalling' via
2026-07-09T10:07:43,871           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,872           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,873           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,874           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,875           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,876           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,877                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,877                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,878                 directory, all directories are treated like packages.
2026-07-09T10:07:43,878           ********************************************************************************

2026-07-09T10:07:43,879   !!
2026-07-09T10:07:43,880     check.warn(importable)
2026-07-09T10:07:43,881   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.deletioncalling.__pycache__' is absent from the `packages` configuration.
2026-07-09T10:07:43,881   !!

2026-07-09T10:07:43,882           ********************************************************************************
2026-07-09T10:07:43,883           ############################
2026-07-09T10:07:43,883           # Package would be ignored #
2026-07-09T10:07:43,884           ############################
2026-07-09T10:07:43,885           Python recognizes 'mgatk.deletioncalling.__pycache__' as an importable package[^1],
2026-07-09T10:07:43,885           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,886           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,887           package, please make sure that 'mgatk.deletioncalling.__pycache__' is explicitly added
2026-07-09T10:07:43,887           to the `packages` configuration field.

2026-07-09T10:07:43,889           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,889           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,890           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,891           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,892           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,893           If you don't want 'mgatk.deletioncalling.__pycache__' to be distributed and are
2026-07-09T10:07:43,894           already explicitly excluding 'mgatk.deletioncalling.__pycache__' via
2026-07-09T10:07:43,895           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,896           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,896           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,897           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,898           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,900           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,900                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,900                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,901                 directory, all directories are treated like packages.
2026-07-09T10:07:43,901           ********************************************************************************

2026-07-09T10:07:43,902   !!
2026-07-09T10:07:43,903     check.warn(importable)
2026-07-09T10:07:43,903   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.deletioncalling.bulk_del' is absent from the `packages` configuration.
2026-07-09T10:07:43,904   !!

2026-07-09T10:07:43,905           ********************************************************************************
2026-07-09T10:07:43,905           ############################
2026-07-09T10:07:43,906           # Package would be ignored #
2026-07-09T10:07:43,906           ############################
2026-07-09T10:07:43,907           Python recognizes 'mgatk.deletioncalling.bulk_del' as an importable package[^1],
2026-07-09T10:07:43,908           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,909           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,909           package, please make sure that 'mgatk.deletioncalling.bulk_del' is explicitly added
2026-07-09T10:07:43,910           to the `packages` configuration field.

2026-07-09T10:07:43,911           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,911           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,912           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,913           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,914           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,915           If you don't want 'mgatk.deletioncalling.bulk_del' to be distributed and are
2026-07-09T10:07:43,916           already explicitly excluding 'mgatk.deletioncalling.bulk_del' via
2026-07-09T10:07:43,917           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,917           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,918           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,919           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,920           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,922           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,922                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,923                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,924                 directory, all directories are treated like packages.
2026-07-09T10:07:43,924           ********************************************************************************

2026-07-09T10:07:43,926   !!
2026-07-09T10:07:43,926     check.warn(importable)
2026-07-09T10:07:43,927   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.deletioncalling.singles_del' is absent from the `packages` configuration.
2026-07-09T10:07:43,927   !!

2026-07-09T10:07:43,929           ********************************************************************************
2026-07-09T10:07:43,929           ############################
2026-07-09T10:07:43,930           # Package would be ignored #
2026-07-09T10:07:43,930           ############################
2026-07-09T10:07:43,931           Python recognizes 'mgatk.deletioncalling.singles_del' as an importable package[^1],
2026-07-09T10:07:43,932           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,932           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,933           package, please make sure that 'mgatk.deletioncalling.singles_del' is explicitly added
2026-07-09T10:07:43,933           to the `packages` configuration field.

2026-07-09T10:07:43,935           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,935           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,935           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,936           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,937           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,938           If you don't want 'mgatk.deletioncalling.singles_del' to be distributed and are
2026-07-09T10:07:43,939           already explicitly excluding 'mgatk.deletioncalling.singles_del' via
2026-07-09T10:07:43,939           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,940           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,941           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,942           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,943           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,945           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,945                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,946                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,946                 directory, all directories are treated like packages.
2026-07-09T10:07:43,947           ********************************************************************************

2026-07-09T10:07:43,948   !!
2026-07-09T10:07:43,949     check.warn(importable)
2026-07-09T10:07:43,950   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'mgatk.processing.__pycache__' is absent from the `packages` configuration.
2026-07-09T10:07:43,950   !!

2026-07-09T10:07:43,951           ********************************************************************************
2026-07-09T10:07:43,952           ############################
2026-07-09T10:07:43,953           # Package would be ignored #
2026-07-09T10:07:43,953           ############################
2026-07-09T10:07:43,954           Python recognizes 'mgatk.processing.__pycache__' as an importable package[^1],
2026-07-09T10:07:43,954           but it is absent from setuptools' `packages` configuration.

2026-07-09T10:07:43,956           This leads to an ambiguous overall configuration. If you want to distribute this
2026-07-09T10:07:43,957           package, please make sure that 'mgatk.processing.__pycache__' is explicitly added
2026-07-09T10:07:43,957           to the `packages` configuration field.

2026-07-09T10:07:43,959           Alternatively, you can also rely on setuptools' discovery methods
2026-07-09T10:07:43,959           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2026-07-09T10:07:43,960           instead of `find_packages(...)`/`find:`).

2026-07-09T10:07:43,961           You can read more about "package discovery" on setuptools documentation page:

2026-07-09T10:07:43,962           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2026-07-09T10:07:43,963           If you don't want 'mgatk.processing.__pycache__' to be distributed and are
2026-07-09T10:07:43,963           already explicitly excluding 'mgatk.processing.__pycache__' via
2026-07-09T10:07:43,964           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2026-07-09T10:07:43,964           you can try to use `exclude_package_data`, or `include-package-data=False` in
2026-07-09T10:07:43,965           combination with a more fine grained `package-data` configuration.

2026-07-09T10:07:43,966           You can read more about "package data files" on setuptools documentation page:

2026-07-09T10:07:43,967           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2026-07-09T10:07:43,968           [^1]: For Python, any directory (with suitable naming) can be imported,
2026-07-09T10:07:43,969                 even if it does not contain any `.py` files.
2026-07-09T10:07:43,969                 On the other hand, currently there is no concept of package data
2026-07-09T10:07:43,970                 directory, all directories are treated like packages.
2026-07-09T10:07:43,970           ********************************************************************************

2026-07-09T10:07:43,971   !!
2026-07-09T10:07:43,972     check.warn(importable)
2026-07-09T10:07:43,972   copying mgatk/devnotes.md -> build/lib/mgatk
2026-07-09T10:07:43,973   creating build/lib/mgatk/__pycache__
2026-07-09T10:07:43,973   copying mgatk/__pycache__/__init__.cpython-312.pyc -> build/lib/mgatk/__pycache__
2026-07-09T10:07:43,974   copying mgatk/__pycache__/__init__.cpython-314.pyc -> build/lib/mgatk/__pycache__
2026-07-09T10:07:43,974   copying mgatk/__pycache__/cli.cpython-312.pyc -> build/lib/mgatk/__pycache__
2026-07-09T10:07:43,975   copying mgatk/__pycache__/mgatkHelp.cpython-312.pyc -> build/lib/mgatk/__pycache__
2026-07-09T10:07:43,975   creating build/lib/mgatk/bin/R
2026-07-09T10:07:43,976   copying mgatk/bin/R/toRDS.R -> build/lib/mgatk/bin/R
2026-07-09T10:07:43,977   creating build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,977   copying mgatk/bin/anno/fasta/GRCh37.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,978   copying mgatk/bin/anno/fasta/GRCh38.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,979   copying mgatk/bin/anno/fasta/GRCm38.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,979   copying mgatk/bin/anno/fasta/GRCz10.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,980   copying mgatk/bin/anno/fasta/NC_012920.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,981   copying mgatk/bin/anno/fasta/hg19.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,981   copying mgatk/bin/anno/fasta/hg19_chrM.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,982   copying mgatk/bin/anno/fasta/hg38.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,982   copying mgatk/bin/anno/fasta/mm10.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,983   copying mgatk/bin/anno/fasta/mm9.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,984   copying mgatk/bin/anno/fasta/rCRS.fasta -> build/lib/mgatk/bin/anno/fasta
2026-07-09T10:07:43,984   creating build/lib/mgatk/bin/snake
2026-07-09T10:07:43,985   copying mgatk/bin/snake/Snakefile.Gather -> build/lib/mgatk/bin/snake
2026-07-09T10:07:43,985   copying mgatk/bin/snake/Snakefile.Scatter -> build/lib/mgatk/bin/snake
2026-07-09T10:07:43,986   copying mgatk/bin/snake/Snakefile.tenx -> build/lib/mgatk/bin/snake
2026-07-09T10:07:43,986   creating build/lib/mgatk/deletioncalling
2026-07-09T10:07:43,987   copying mgatk/deletioncalling/clidel.py -> build/lib/mgatk/deletioncalling
2026-07-09T10:07:43,988   copying mgatk/deletioncalling/clifind.py -> build/lib/mgatk/deletioncalling
2026-07-09T10:07:43,988   copying mgatk/deletioncalling/processing.py -> build/lib/mgatk/deletioncalling
2026-07-09T10:07:43,989   creating build/lib/mgatk/deletioncalling/__pycache__
2026-07-09T10:07:43,990   copying mgatk/deletioncalling/__pycache__/clidel.cpython-312.pyc -> build/lib/mgatk/deletioncalling/__pycache__
2026-07-09T10:07:43,990   copying mgatk/deletioncalling/__pycache__/clifind.cpython-312.pyc -> build/lib/mgatk/deletioncalling/__pycache__
2026-07-09T10:07:43,990   copying mgatk/deletioncalling/__pycache__/processing.cpython-312.pyc -> build/lib/mgatk/deletioncalling/__pycache__
2026-07-09T10:07:43,991   creating build/lib/mgatk/deletioncalling/bulk_del
2026-07-09T10:07:43,991   copying mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R -> build/lib/mgatk/deletioncalling/bulk_del
2026-07-09T10:07:43,992   creating build/lib/mgatk/deletioncalling/singles_del
2026-07-09T10:07:43,992   copying mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R -> build/lib/mgatk/deletioncalling/singles_del
2026-07-09T10:07:43,993   copying mgatk/deletioncalling/singles_del/Snakefile.delSingles -> build/lib/mgatk/deletioncalling/singles_del
2026-07-09T10:07:43,993   creating build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,993   copying mgatk/processing/__pycache__/__init__.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,994   copying mgatk/processing/__pycache__/allele_counts.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,994   copying mgatk/processing/__pycache__/allele_counts_tenx.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,995   copying mgatk/processing/__pycache__/barcodes.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,995   copying mgatk/processing/__pycache__/dedup.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,996   copying mgatk/processing/__pycache__/filtering.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,996   copying mgatk/processing/__pycache__/one_sample.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,997   copying mgatk/processing/__pycache__/one_slice_tenx.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,997   copying mgatk/processing/__pycache__/variant_calling.cpython-312.pyc -> build/lib/mgatk/processing/__pycache__
2026-07-09T10:07:43,998   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2026-07-09T10:07:43,998   !!

2026-07-09T10:07:44,000           ********************************************************************************
2026-07-09T10:07:44,000           Please avoid running ``setup.py`` directly.
2026-07-09T10:07:44,001           Instead, use pypa/build, pypa/installer or other
2026-07-09T10:07:44,001           standards-based tools.

2026-07-09T10:07:44,002           This deprecation is overdue, please update your project and remove deprecated
2026-07-09T10:07:44,003           calls to avoid build errors in the future.

2026-07-09T10:07:44,004           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2026-07-09T10:07:44,005           ********************************************************************************

2026-07-09T10:07:44,006   !!
2026-07-09T10:07:44,007     self.initialize_options()
2026-07-09T10:07:44,007   installing to build/bdist.linux-armv7l/wheel
2026-07-09T10:07:44,008   running install
2026-07-09T10:07:44,009   running install_lib
2026-07-09T10:07:44,033   creating build/bdist.linux-armv7l/wheel
2026-07-09T10:07:44,036   creating build/bdist.linux-armv7l/wheel/mgatk
2026-07-09T10:07:44,037   copying build/lib/mgatk/cli.py -> build/bdist.linux-armv7l/wheel/./mgatk
2026-07-09T10:07:44,040   copying build/lib/mgatk/mgatkHelp.py -> build/bdist.linux-armv7l/wheel/./mgatk
2026-07-09T10:07:44,043   creating build/bdist.linux-armv7l/wheel/mgatk/bin
2026-07-09T10:07:44,045   creating build/bdist.linux-armv7l/wheel/mgatk/bin/snake
2026-07-09T10:07:44,046   copying build/lib/mgatk/bin/snake/Snakefile.Gather -> build/bdist.linux-armv7l/wheel/./mgatk/bin/snake
2026-07-09T10:07:44,048   copying build/lib/mgatk/bin/snake/Snakefile.Scatter -> build/bdist.linux-armv7l/wheel/./mgatk/bin/snake
2026-07-09T10:07:44,050   copying build/lib/mgatk/bin/snake/Snakefile.tenx -> build/bdist.linux-armv7l/wheel/./mgatk/bin/snake
2026-07-09T10:07:44,052   creating build/bdist.linux-armv7l/wheel/mgatk/bin/R
2026-07-09T10:07:44,053   copying build/lib/mgatk/bin/R/toRDS.R -> build/bdist.linux-armv7l/wheel/./mgatk/bin/R
2026-07-09T10:07:44,056   creating build/bdist.linux-armv7l/wheel/mgatk/bin/anno
2026-07-09T10:07:44,058   creating build/bdist.linux-armv7l/wheel/mgatk/bin/anno/fasta
2026-07-09T10:07:44,059   copying build/lib/mgatk/bin/anno/fasta/hg38.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,062   copying build/lib/mgatk/bin/anno/fasta/mm10.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,065   copying build/lib/mgatk/bin/anno/fasta/hg19_chrM.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,068   copying build/lib/mgatk/bin/anno/fasta/hg19.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,070   copying build/lib/mgatk/bin/anno/fasta/rCRS.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,073   copying build/lib/mgatk/bin/anno/fasta/mm9.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,076   copying build/lib/mgatk/bin/anno/fasta/NC_012920.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,078   copying build/lib/mgatk/bin/anno/fasta/GRCm38.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,081   copying build/lib/mgatk/bin/anno/fasta/GRCz10.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,084   copying build/lib/mgatk/bin/anno/fasta/GRCh38.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,086   copying build/lib/mgatk/bin/anno/fasta/GRCh37.fasta -> build/bdist.linux-armv7l/wheel/./mgatk/bin/anno/fasta
2026-07-09T10:07:44,089   copying build/lib/mgatk/__init__.py -> build/bdist.linux-armv7l/wheel/./mgatk
2026-07-09T10:07:44,091   creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling
2026-07-09T10:07:44,092   copying build/lib/mgatk/deletioncalling/clifind.py -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling
2026-07-09T10:07:44,095   creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/singles_del
2026-07-09T10:07:44,096   copying build/lib/mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling/singles_del
2026-07-09T10:07:44,098   copying build/lib/mgatk/deletioncalling/singles_del/Snakefile.delSingles -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling/singles_del
2026-07-09T10:07:44,100   copying build/lib/mgatk/deletioncalling/processing.py -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling
2026-07-09T10:07:44,103   creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/bulk_del
2026-07-09T10:07:44,104   copying build/lib/mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling/bulk_del
2026-07-09T10:07:44,106   copying build/lib/mgatk/deletioncalling/clidel.py -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling
2026-07-09T10:07:44,109   creating build/bdist.linux-armv7l/wheel/mgatk/deletioncalling/__pycache__
2026-07-09T10:07:44,110   copying build/lib/mgatk/deletioncalling/__pycache__/processing.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling/__pycache__
2026-07-09T10:07:44,113   copying build/lib/mgatk/deletioncalling/__pycache__/clidel.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling/__pycache__
2026-07-09T10:07:44,115   copying build/lib/mgatk/deletioncalling/__pycache__/clifind.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/deletioncalling/__pycache__
2026-07-09T10:07:44,118   copying build/lib/mgatk/devnotes.md -> build/bdist.linux-armv7l/wheel/./mgatk
2026-07-09T10:07:44,120   creating build/bdist.linux-armv7l/wheel/mgatk/__pycache__
2026-07-09T10:07:44,121   copying build/lib/mgatk/__pycache__/__init__.cpython-314.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/__pycache__
2026-07-09T10:07:44,123   copying build/lib/mgatk/__pycache__/mgatkHelp.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/__pycache__
2026-07-09T10:07:44,126   copying build/lib/mgatk/__pycache__/__init__.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/__pycache__
2026-07-09T10:07:44,128   copying build/lib/mgatk/__pycache__/cli.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/__pycache__
2026-07-09T10:07:44,131   creating build/bdist.linux-armv7l/wheel/mgatk/processing
2026-07-09T10:07:44,132   copying build/lib/mgatk/processing/allele_counts.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,135   copying build/lib/mgatk/processing/variant_calling.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,137   copying build/lib/mgatk/processing/filtering.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,139   copying build/lib/mgatk/processing/__init__.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,140   copying build/lib/mgatk/processing/barcodes.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,142   copying build/lib/mgatk/processing/allele_counts_tenx.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,145   copying build/lib/mgatk/processing/dedup.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,147   creating build/bdist.linux-armv7l/wheel/mgatk/processing/__pycache__
2026-07-09T10:07:44,148   copying build/lib/mgatk/processing/__pycache__/one_sample.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,151   copying build/lib/mgatk/processing/__pycache__/one_slice_tenx.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,153   copying build/lib/mgatk/processing/__pycache__/filtering.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,155   copying build/lib/mgatk/processing/__pycache__/dedup.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,157   copying build/lib/mgatk/processing/__pycache__/allele_counts.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,160   copying build/lib/mgatk/processing/__pycache__/allele_counts_tenx.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,162   copying build/lib/mgatk/processing/__pycache__/variant_calling.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,165   copying build/lib/mgatk/processing/__pycache__/__init__.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,167   copying build/lib/mgatk/processing/__pycache__/barcodes.cpython-312.pyc -> build/bdist.linux-armv7l/wheel/./mgatk/processing/__pycache__
2026-07-09T10:07:44,169   copying build/lib/mgatk/processing/one_slice_tenx.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,171   copying build/lib/mgatk/processing/one_sample.py -> build/bdist.linux-armv7l/wheel/./mgatk/processing
2026-07-09T10:07:44,173   running install_egg_info
2026-07-09T10:07:44,208   Copying mgatk.egg-info to build/bdist.linux-armv7l/wheel/./mgatk-0.9.0-py3.11.egg-info
2026-07-09T10:07:44,222   running install_scripts
2026-07-09T10:07:44,236   creating build/bdist.linux-armv7l/wheel/mgatk-0.9.0.dist-info/WHEEL
2026-07-09T10:07:44,238   creating '/tmp/pip-wheel-9va8wf00/mgatk-0.9.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2026-07-09T10:07:44,241   adding 'mgatk/__init__.py'
2026-07-09T10:07:44,244   adding 'mgatk/cli.py'
2026-07-09T10:07:44,245   adding 'mgatk/devnotes.md'
2026-07-09T10:07:44,247   adding 'mgatk/mgatkHelp.py'
2026-07-09T10:07:44,249   adding 'mgatk/__pycache__/__init__.cpython-312.pyc'
2026-07-09T10:07:44,250   adding 'mgatk/__pycache__/__init__.cpython-314.pyc'
2026-07-09T10:07:44,254   adding 'mgatk/__pycache__/cli.cpython-312.pyc'
2026-07-09T10:07:44,256   adding 'mgatk/__pycache__/mgatkHelp.cpython-312.pyc'
2026-07-09T10:07:44,259   adding 'mgatk/bin/R/toRDS.R'
2026-07-09T10:07:44,268   adding 'mgatk/bin/anno/fasta/GRCh37.fasta'
2026-07-09T10:07:44,276   adding 'mgatk/bin/anno/fasta/GRCh38.fasta'
2026-07-09T10:07:44,283   adding 'mgatk/bin/anno/fasta/GRCm38.fasta'
2026-07-09T10:07:44,291   adding 'mgatk/bin/anno/fasta/GRCz10.fasta'
2026-07-09T10:07:44,299   adding 'mgatk/bin/anno/fasta/NC_012920.fasta'
2026-07-09T10:07:44,307   adding 'mgatk/bin/anno/fasta/hg19.fasta'
2026-07-09T10:07:44,314   adding 'mgatk/bin/anno/fasta/hg19_chrM.fasta'
2026-07-09T10:07:44,322   adding 'mgatk/bin/anno/fasta/hg38.fasta'
2026-07-09T10:07:44,329   adding 'mgatk/bin/anno/fasta/mm10.fasta'
2026-07-09T10:07:44,337   adding 'mgatk/bin/anno/fasta/mm9.fasta'
2026-07-09T10:07:44,345   adding 'mgatk/bin/anno/fasta/rCRS.fasta'
2026-07-09T10:07:44,347   adding 'mgatk/bin/snake/Snakefile.Gather'
2026-07-09T10:07:44,348   adding 'mgatk/bin/snake/Snakefile.Scatter'
2026-07-09T10:07:44,349   adding 'mgatk/bin/snake/Snakefile.tenx'
2026-07-09T10:07:44,351   adding 'mgatk/deletioncalling/clidel.py'
2026-07-09T10:07:44,353   adding 'mgatk/deletioncalling/clifind.py'
2026-07-09T10:07:44,354   adding 'mgatk/deletioncalling/processing.py'
2026-07-09T10:07:44,357   adding 'mgatk/deletioncalling/__pycache__/clidel.cpython-312.pyc'
2026-07-09T10:07:44,359   adding 'mgatk/deletioncalling/__pycache__/clifind.cpython-312.pyc'
2026-07-09T10:07:44,361   adding 'mgatk/deletioncalling/__pycache__/processing.cpython-312.pyc'
2026-07-09T10:07:44,363   adding 'mgatk/deletioncalling/bulk_del/plot_deletion_breaks_bulk.R'
2026-07-09T10:07:44,365   adding 'mgatk/deletioncalling/singles_del/02_heteroplasmy_del_singles.R'
2026-07-09T10:07:44,366   adding 'mgatk/deletioncalling/singles_del/Snakefile.delSingles'
2026-07-09T10:07:44,368   adding 'mgatk/processing/__init__.py'
2026-07-09T10:07:44,370   adding 'mgatk/processing/allele_counts.py'
2026-07-09T10:07:44,371   adding 'mgatk/processing/allele_counts_tenx.py'
2026-07-09T10:07:44,373   adding 'mgatk/processing/barcodes.py'
2026-07-09T10:07:44,374   adding 'mgatk/processing/dedup.py'
2026-07-09T10:07:44,376   adding 'mgatk/processing/filtering.py'
2026-07-09T10:07:44,377   adding 'mgatk/processing/one_sample.py'
2026-07-09T10:07:44,378   adding 'mgatk/processing/one_slice_tenx.py'
2026-07-09T10:07:44,380   adding 'mgatk/processing/variant_calling.py'
2026-07-09T10:07:44,382   adding 'mgatk/processing/__pycache__/__init__.cpython-312.pyc'
2026-07-09T10:07:44,384   adding 'mgatk/processing/__pycache__/allele_counts.cpython-312.pyc'
2026-07-09T10:07:44,387   adding 'mgatk/processing/__pycache__/allele_counts_tenx.cpython-312.pyc'
2026-07-09T10:07:44,388   adding 'mgatk/processing/__pycache__/barcodes.cpython-312.pyc'
2026-07-09T10:07:44,390   adding 'mgatk/processing/__pycache__/dedup.cpython-312.pyc'
2026-07-09T10:07:44,391   adding 'mgatk/processing/__pycache__/filtering.cpython-312.pyc'
2026-07-09T10:07:44,393   adding 'mgatk/processing/__pycache__/one_sample.cpython-312.pyc'
2026-07-09T10:07:44,394   adding 'mgatk/processing/__pycache__/one_slice_tenx.cpython-312.pyc'
2026-07-09T10:07:44,397   adding 'mgatk/processing/__pycache__/variant_calling.cpython-312.pyc'
2026-07-09T10:07:44,399   adding 'mgatk-0.9.0.dist-info/licenses/LICENSE.txt'
2026-07-09T10:07:44,400   adding 'mgatk-0.9.0.dist-info/METADATA'
2026-07-09T10:07:44,401   adding 'mgatk-0.9.0.dist-info/WHEEL'
2026-07-09T10:07:44,402   adding 'mgatk-0.9.0.dist-info/entry_points.txt'
2026-07-09T10:07:44,403   adding 'mgatk-0.9.0.dist-info/top_level.txt'
2026-07-09T10:07:44,405   adding 'mgatk-0.9.0.dist-info/RECORD'
2026-07-09T10:07:44,408   removing build/bdist.linux-armv7l/wheel
2026-07-09T10:07:44,538   Building wheel for mgatk (setup.py): finished with status 'done'
2026-07-09T10:07:44,543   Created wheel for mgatk: filename=mgatk-0.9.0-py3-none-any.whl size=164634 sha256=71ada551b3845241f3badb8ddd2028faf652216afa7fddc86d46973bd6afb79c
2026-07-09T10:07:44,544   Stored in directory: /tmp/pip-ephem-wheel-cache-8l5rsvqy/wheels/63/e2/10/415455839aca9cebc00b2fd2ce1eb6e523355634a45d559936
2026-07-09T10:07:44,556 Successfully built mgatk
2026-07-09T10:07:44,563 Removed build tracker: '/tmp/pip-build-tracker-6chduk98'