2024-10-18T20:07:07,605 Created temporary directory: /tmp/pip-build-tracker-2k19lknl
2024-10-18T20:07:07,606 Initialized build tracking at /tmp/pip-build-tracker-2k19lknl
2024-10-18T20:07:07,607 Created build tracker: /tmp/pip-build-tracker-2k19lknl
2024-10-18T20:07:07,607 Entered build tracker: /tmp/pip-build-tracker-2k19lknl
2024-10-18T20:07:07,608 Created temporary directory: /tmp/pip-wheel-bgk0q681
2024-10-18T20:07:07,612 Created temporary directory: /tmp/pip-ephem-wheel-cache-8sp8fhhf
2024-10-18T20:07:07,656 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-10-18T20:07:07,658 2 location(s) to search for versions of homi-pipeline:
2024-10-18T20:07:07,658 * https://pypi.org/simple/homi-pipeline/
2024-10-18T20:07:07,658 * https://www.piwheels.org/simple/homi-pipeline/
2024-10-18T20:07:07,659 Fetching project page and analyzing links: https://pypi.org/simple/homi-pipeline/
2024-10-18T20:07:07,660 Getting page https://pypi.org/simple/homi-pipeline/
2024-10-18T20:07:07,661 Found index url https://pypi.org/simple/
2024-10-18T20:07:07,884 Fetched page https://pypi.org/simple/homi-pipeline/ as application/vnd.pypi.simple.v1+json
2024-10-18T20:07:07,887   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/2b/2f/d7f737bbbcf5acdb21caad36381ddf833f3ae20a98eb9f38a60d630f8b19/HoMi_pipeline-1.0.4-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:07,888   Found link https://files.pythonhosted.org/packages/56/81/2de14d31804045b5b7a0c582de19188c01a8de5ad3f953841f01aef86419/homi_pipeline-1.0.4.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.4
2024-10-18T20:07:07,889   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/14/73/530144aadf2b945ecb5d635e333dfc6038a5ce1a1ea03a1d54f1cf4a40a5/HoMi_pipeline-1.0.5-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:07,890   Found link https://files.pythonhosted.org/packages/81/4c/0bfa30002f2c33ff1bb90392ccdf509e1f38a472e5807bc4238fb1842d7c/homi_pipeline-1.0.5.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.5
2024-10-18T20:07:07,890   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/1e/5f/eaa4752e3474d13c00c1e7a1e6e797c898bb925f2b3bcb39fd57474bbf72/HoMi_pipeline-1.0.6-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:07,891   Found link https://files.pythonhosted.org/packages/96/1c/d8cf18b86b78600bbd4b771fd8c2c1965c2397e162575c65e4e1d081a12e/homi_pipeline-1.0.6.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.6
2024-10-18T20:07:07,892   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/e7/82/b5cf93b605bb58cf43d5086e05573f7b960410768cfd10c9212c884356fe/HoMi_pipeline-1.0.7-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:07,893   Found link https://files.pythonhosted.org/packages/8c/ce/d1098487cb2f77ab95dab26bd6fdb548572494e84034a9ce6deb2f986b0b/homi_pipeline-1.0.7.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.7
2024-10-18T20:07:07,894   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/67/28/51f5cc23bbf4b5db0b1afb91dc058649b690bf64beaea710305f5014b2c1/HoMi_pipeline-1.0.8-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:07,895   Found link https://files.pythonhosted.org/packages/58/bf/fa627d33c0c8a77ef1f2bf3ad69560a790a8b2c8cce78041b3723fa24a8d/homi_pipeline-1.0.8.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.8
2024-10-18T20:07:07,895   Skipping link: No binaries permitted for homi-pipeline: https://files.pythonhosted.org/packages/b3/f4/88f0f43ae830bcde620a8013bf0385035eb78e6ae8dd5ef66e9499e417cd/homi_pipeline-1.0.9-py3-none-any.whl (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:07,896   Found link https://files.pythonhosted.org/packages/5e/66/35b815aa9f646b0adaa5a6b98ead6067515c76903ca272eb913d78f2c379/homi_pipeline-1.0.9.tar.gz (from https://pypi.org/simple/homi-pipeline/) (requires-python:<3.12.0), version: 1.0.9
2024-10-18T20:07:07,897 Fetching project page and analyzing links: https://www.piwheels.org/simple/homi-pipeline/
2024-10-18T20:07:07,898 Getting page https://www.piwheels.org/simple/homi-pipeline/
2024-10-18T20:07:07,899 Found index url https://www.piwheels.org/simple/
2024-10-18T20:07:08,061 Fetched page https://www.piwheels.org/simple/homi-pipeline/ as text/html
2024-10-18T20:07:08,064   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.8-py3-none-any.whl#sha256=51b4b72a1a7278e9e56e84f3c6747b186a3e4745ad6ab68800b30a50bc914f86 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:08,064   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.7-py3-none-any.whl#sha256=f0dc342ef3431deb1fe0119908dfaf6639c2172a72f2e024cd0ed49f2835183a (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:08,065   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.6-py3-none-any.whl#sha256=db11d135158a25a6e0c26125df20efe6c4215670508e11b243dc26bde8fa475d (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:08,065   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.5-py3-none-any.whl#sha256=e3d12dbe9433bef87e816014c345a09af2f99a91d543497606b0105bf3c73421 (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:08,066   Skipping link: No binaries permitted for homi-pipeline: https://www.piwheels.org/simple/homi-pipeline/HoMi_pipeline-1.0.4-py3-none-any.whl#sha256=a28da3efa0ab27e400f13a9e67038b54c72121a15fcebb90b87e2520fb85756f (from https://www.piwheels.org/simple/homi-pipeline/) (requires-python:<3.12.0)
2024-10-18T20:07:08,066 Skipping link: not a file: https://www.piwheels.org/simple/homi-pipeline/
2024-10-18T20:07:08,067 Skipping link: not a file: https://pypi.org/simple/homi-pipeline/
2024-10-18T20:07:08,086 Given no hashes to check 1 links for project 'homi-pipeline': discarding no candidates
2024-10-18T20:07:08,088 Collecting homi-pipeline==1.0.9
2024-10-18T20:07:08,090   Created temporary directory: /tmp/pip-unpack-2n4x3imu
2024-10-18T20:07:08,307   Downloading homi_pipeline-1.0.9.tar.gz (49 kB)
2024-10-18T20:07:08,446   Added homi-pipeline==1.0.9 from https://files.pythonhosted.org/packages/5e/66/35b815aa9f646b0adaa5a6b98ead6067515c76903ca272eb913d78f2c379/homi_pipeline-1.0.9.tar.gz to build tracker '/tmp/pip-build-tracker-2k19lknl'
2024-10-18T20:07:08,448   Running setup.py (path:/tmp/pip-wheel-bgk0q681/homi-pipeline_1ec5b972afbe4d068f9027f216dfc4a0/setup.py) egg_info for package homi-pipeline
2024-10-18T20:07:08,449   Created temporary directory: /tmp/pip-pip-egg-info-fa_n5c7w
2024-10-18T20:07:08,450   Preparing metadata (setup.py): started
2024-10-18T20:07:08,451   Running command python setup.py egg_info
2024-10-18T20:07:09,221   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2024-10-18T20:07:09,222   !!

2024-10-18T20:07:09,223           ********************************************************************************
2024-10-18T20:07:09,223           Requirements should be satisfied by a PEP 517 installer.
2024-10-18T20:07:09,224           If you are using pip, you can try `pip install --use-pep517`.
2024-10-18T20:07:09,225           ********************************************************************************

2024-10-18T20:07:09,226   !!
2024-10-18T20:07:09,226     dist.fetch_build_eggs(dist.setup_requires)
2024-10-18T20:07:11,945   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
2024-10-18T20:07:11,945     warnings.warn(msg)
2024-10-18T20:07:12,040   running egg_info
2024-10-18T20:07:12,042   creating /tmp/pip-pip-egg-info-fa_n5c7w/homi_pipeline.egg-info
2024-10-18T20:07:12,071   writing /tmp/pip-pip-egg-info-fa_n5c7w/homi_pipeline.egg-info/PKG-INFO
2024-10-18T20:07:12,075   writing dependency_links to /tmp/pip-pip-egg-info-fa_n5c7w/homi_pipeline.egg-info/dependency_links.txt
2024-10-18T20:07:12,076   writing requirements to /tmp/pip-pip-egg-info-fa_n5c7w/homi_pipeline.egg-info/requires.txt
2024-10-18T20:07:12,077   writing top-level names to /tmp/pip-pip-egg-info-fa_n5c7w/homi_pipeline.egg-info/top_level.txt
2024-10-18T20:07:12,079   writing manifest file '/tmp/pip-pip-egg-info-fa_n5c7w/homi_pipeline.egg-info/SOURCES.txt'
2024-10-18T20:07:12,208   reading manifest file '/tmp/pip-pip-egg-info-fa_n5c7w/homi_pipeline.egg-info/SOURCES.txt'
2024-10-18T20:07:12,209   adding license file 'LICENSE'
2024-10-18T20:07:12,213   writing manifest file '/tmp/pip-pip-egg-info-fa_n5c7w/homi_pipeline.egg-info/SOURCES.txt'
2024-10-18T20:07:12,326   Preparing metadata (setup.py): finished with status 'done'
2024-10-18T20:07:12,330   Source in /tmp/pip-wheel-bgk0q681/homi-pipeline_1ec5b972afbe4d068f9027f216dfc4a0 has version 1.0.9, which satisfies requirement homi-pipeline==1.0.9 from https://files.pythonhosted.org/packages/5e/66/35b815aa9f646b0adaa5a6b98ead6067515c76903ca272eb913d78f2c379/homi_pipeline-1.0.9.tar.gz
2024-10-18T20:07:12,331   Removed homi-pipeline==1.0.9 from https://files.pythonhosted.org/packages/5e/66/35b815aa9f646b0adaa5a6b98ead6067515c76903ca272eb913d78f2c379/homi_pipeline-1.0.9.tar.gz from build tracker '/tmp/pip-build-tracker-2k19lknl'
2024-10-18T20:07:12,338 Created temporary directory: /tmp/pip-unpack-2bpa3tbs
2024-10-18T20:07:12,339 Created temporary directory: /tmp/pip-unpack-evsvw5eq
2024-10-18T20:07:12,339 Building wheels for collected packages: homi-pipeline
2024-10-18T20:07:12,343   Created temporary directory: /tmp/pip-wheel-uuow_7jp
2024-10-18T20:07:12,344   Building wheel for homi-pipeline (setup.py): started
2024-10-18T20:07:12,345   Destination directory: /tmp/pip-wheel-uuow_7jp
2024-10-18T20:07:12,346   Running command python setup.py bdist_wheel
2024-10-18T20:07:13,049   /usr/local/lib/python3.11/dist-packages/setuptools/__init__.py:94: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
2024-10-18T20:07:13,049   !!

2024-10-18T20:07:13,050           ********************************************************************************
2024-10-18T20:07:13,051           Requirements should be satisfied by a PEP 517 installer.
2024-10-18T20:07:13,051           If you are using pip, you can try `pip install --use-pep517`.
2024-10-18T20:07:13,052           ********************************************************************************

2024-10-18T20:07:13,053   !!
2024-10-18T20:07:13,053     dist.fetch_build_eggs(dist.setup_requires)
2024-10-18T20:07:13,256   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'tests_require'
2024-10-18T20:07:13,257     warnings.warn(msg)
2024-10-18T20:07:13,556   running bdist_wheel
2024-10-18T20:07:13,693   running build
2024-10-18T20:07:13,694   running build_py
2024-10-18T20:07:13,727   creating build/lib/homi_pipeline
2024-10-18T20:07:13,729   copying src/homi_pipeline/check_config.py -> build/lib/homi_pipeline
2024-10-18T20:07:13,732   copying src/homi_pipeline/HoMi.py -> build/lib/homi_pipeline
2024-10-18T20:07:13,734   copying src/homi_pipeline/__init__.py -> build/lib/homi_pipeline
2024-10-18T20:07:13,736   copying src/homi_pipeline/HoMi_cleanup.py -> build/lib/homi_pipeline
2024-10-18T20:07:13,738   copying src/homi_pipeline/profile_setup.py -> build/lib/homi_pipeline
2024-10-18T20:07:13,741   copying src/homi_pipeline/snake_utils.py -> build/lib/homi_pipeline
2024-10-18T20:07:13,742   running egg_info
2024-10-18T20:07:13,771   writing src/homi_pipeline.egg-info/PKG-INFO
2024-10-18T20:07:13,774   writing dependency_links to src/homi_pipeline.egg-info/dependency_links.txt
2024-10-18T20:07:13,776   writing requirements to src/homi_pipeline.egg-info/requires.txt
2024-10-18T20:07:13,777   writing top-level names to src/homi_pipeline.egg-info/top_level.txt
2024-10-18T20:07:13,812   reading manifest file 'src/homi_pipeline.egg-info/SOURCES.txt'
2024-10-18T20:07:13,816   adding license file 'LICENSE'
2024-10-18T20:07:13,820   writing manifest file 'src/homi_pipeline.egg-info/SOURCES.txt'
2024-10-18T20:07:13,822   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'homi_pipeline.conda_envs' is absent from the `packages` configuration.
2024-10-18T20:07:13,822   !!

2024-10-18T20:07:13,823           ********************************************************************************
2024-10-18T20:07:13,824           ############################
2024-10-18T20:07:13,824           # Package would be ignored #
2024-10-18T20:07:13,825           ############################
2024-10-18T20:07:13,825           Python recognizes 'homi_pipeline.conda_envs' as an importable package[^1],
2024-10-18T20:07:13,825           but it is absent from setuptools' `packages` configuration.

2024-10-18T20:07:13,826           This leads to an ambiguous overall configuration. If you want to distribute this
2024-10-18T20:07:13,827           package, please make sure that 'homi_pipeline.conda_envs' is explicitly added
2024-10-18T20:07:13,827           to the `packages` configuration field.

2024-10-18T20:07:13,828           Alternatively, you can also rely on setuptools' discovery methods
2024-10-18T20:07:13,828           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-10-18T20:07:13,829           instead of `find_packages(...)`/`find:`).

2024-10-18T20:07:13,831           You can read more about "package discovery" on setuptools documentation page:

2024-10-18T20:07:13,831           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-10-18T20:07:13,832           If you don't want 'homi_pipeline.conda_envs' to be distributed and are
2024-10-18T20:07:13,833           already explicitly excluding 'homi_pipeline.conda_envs' via
2024-10-18T20:07:13,833           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-10-18T20:07:13,834           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-10-18T20:07:13,834           combination with a more fine grained `package-data` configuration.

2024-10-18T20:07:13,835           You can read more about "package data files" on setuptools documentation page:

2024-10-18T20:07:13,836           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-10-18T20:07:13,838           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-10-18T20:07:13,838                 even if it does not contain any `.py` files.
2024-10-18T20:07:13,839                 On the other hand, currently there is no concept of package data
2024-10-18T20:07:13,839                 directory, all directories are treated like packages.
2024-10-18T20:07:13,840           ********************************************************************************

2024-10-18T20:07:13,841   !!
2024-10-18T20:07:13,841     check.warn(importable)
2024-10-18T20:07:13,842   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'homi_pipeline.data' is absent from the `packages` configuration.
2024-10-18T20:07:13,842   !!

2024-10-18T20:07:13,843           ********************************************************************************
2024-10-18T20:07:13,844           ############################
2024-10-18T20:07:13,844           # Package would be ignored #
2024-10-18T20:07:13,845           ############################
2024-10-18T20:07:13,845           Python recognizes 'homi_pipeline.data' as an importable package[^1],
2024-10-18T20:07:13,846           but it is absent from setuptools' `packages` configuration.

2024-10-18T20:07:13,847           This leads to an ambiguous overall configuration. If you want to distribute this
2024-10-18T20:07:13,847           package, please make sure that 'homi_pipeline.data' is explicitly added
2024-10-18T20:07:13,847           to the `packages` configuration field.

2024-10-18T20:07:13,848           Alternatively, you can also rely on setuptools' discovery methods
2024-10-18T20:07:13,849           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-10-18T20:07:13,849           instead of `find_packages(...)`/`find:`).

2024-10-18T20:07:13,850           You can read more about "package discovery" on setuptools documentation page:

2024-10-18T20:07:13,851           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-10-18T20:07:13,851           If you don't want 'homi_pipeline.data' to be distributed and are
2024-10-18T20:07:13,852           already explicitly excluding 'homi_pipeline.data' via
2024-10-18T20:07:13,852           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-10-18T20:07:13,852           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-10-18T20:07:13,853           combination with a more fine grained `package-data` configuration.

2024-10-18T20:07:13,854           You can read more about "package data files" on setuptools documentation page:

2024-10-18T20:07:13,855           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-10-18T20:07:13,856           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-10-18T20:07:13,857                 even if it does not contain any `.py` files.
2024-10-18T20:07:13,857                 On the other hand, currently there is no concept of package data
2024-10-18T20:07:13,857                 directory, all directories are treated like packages.
2024-10-18T20:07:13,858           ********************************************************************************

2024-10-18T20:07:13,859   !!
2024-10-18T20:07:13,859     check.warn(importable)
2024-10-18T20:07:13,860   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:218: _Warning: Package 'homi_pipeline.rule_utils' is absent from the `packages` configuration.
2024-10-18T20:07:13,860   !!

2024-10-18T20:07:13,861           ********************************************************************************
2024-10-18T20:07:13,862           ############################
2024-10-18T20:07:13,862           # Package would be ignored #
2024-10-18T20:07:13,863           ############################
2024-10-18T20:07:13,863           Python recognizes 'homi_pipeline.rule_utils' as an importable package[^1],
2024-10-18T20:07:13,864           but it is absent from setuptools' `packages` configuration.

2024-10-18T20:07:13,865           This leads to an ambiguous overall configuration. If you want to distribute this
2024-10-18T20:07:13,865           package, please make sure that 'homi_pipeline.rule_utils' is explicitly added
2024-10-18T20:07:13,866           to the `packages` configuration field.

2024-10-18T20:07:13,867           Alternatively, you can also rely on setuptools' discovery methods
2024-10-18T20:07:13,867           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-10-18T20:07:13,868           instead of `find_packages(...)`/`find:`).

2024-10-18T20:07:13,869           You can read more about "package discovery" on setuptools documentation page:

2024-10-18T20:07:13,870           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-10-18T20:07:13,871           If you don't want 'homi_pipeline.rule_utils' to be distributed and are
2024-10-18T20:07:13,872           already explicitly excluding 'homi_pipeline.rule_utils' via
2024-10-18T20:07:13,872           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-10-18T20:07:13,873           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-10-18T20:07:13,873           combination with a more fine grained `package-data` configuration.

2024-10-18T20:07:13,874           You can read more about "package data files" on setuptools documentation page:

2024-10-18T20:07:13,875           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-10-18T20:07:13,876           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-10-18T20:07:13,877                 even if it does not contain any `.py` files.
2024-10-18T20:07:13,877                 On the other hand, currently there is no concept of package data
2024-10-18T20:07:13,878                 directory, all directories are treated like packages.
2024-10-18T20:07:13,878           ********************************************************************************

2024-10-18T20:07:13,879   !!
2024-10-18T20:07:13,879     check.warn(importable)
2024-10-18T20:07:13,880   copying src/homi_pipeline/snakefile -> build/lib/homi_pipeline
2024-10-18T20:07:13,880   creating build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,881   copying src/homi_pipeline/conda_envs/bbmap.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,881   copying src/homi_pipeline/conda_envs/fastqc.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,882   copying src/homi_pipeline/conda_envs/featureCounts.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,882   copying src/homi_pipeline/conda_envs/hisat2.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,883   copying src/homi_pipeline/conda_envs/hostile.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,883   copying src/homi_pipeline/conda_envs/humann.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,884   copying src/homi_pipeline/conda_envs/kraken.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,884   copying src/homi_pipeline/conda_envs/nonpareil.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,885   copying src/homi_pipeline/conda_envs/r_env.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,885   copying src/homi_pipeline/conda_envs/seqtk.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,886   copying src/homi_pipeline/conda_envs/trimmomatic.yaml -> build/lib/homi_pipeline/conda_envs
2024-10-18T20:07:13,886   creating build/lib/homi_pipeline/data
2024-10-18T20:07:13,887   copying src/homi_pipeline/data/adapters.fa -> build/lib/homi_pipeline/data
2024-10-18T20:07:13,887   creating build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,888   copying src/homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,888   copying src/homi_pipeline/rule_utils/HUMAnN_microshades.Rmd -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,889   copying src/homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,890   copying src/homi_pipeline/rule_utils/Kraken_microshades.Rmd -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,890   copying src/homi_pipeline/rule_utils/Metaphlan_microshades.Rmd -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,890   copying src/homi_pipeline/rule_utils/R_packages.R -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,891   copying src/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,891   copying src/homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,892   copying src/homi_pipeline/rule_utils/combine_kreports.py -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,892   copying src/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,893   copying src/homi_pipeline/rule_utils/counts_to_tpm.py -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,894   copying src/homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,896   copying src/homi_pipeline/rule_utils/read_reports.py -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,898   copying src/homi_pipeline/rule_utils/sam2bam.sh -> build/lib/homi_pipeline/rule_utils
2024-10-18T20:07:13,901   running build_scripts
2024-10-18T20:07:13,901   creating build/scripts-3.11
2024-10-18T20:07:13,902   copying and adjusting src/homi_pipeline/HoMi.py -> build/scripts-3.11
2024-10-18T20:07:13,904   copying src/homi_pipeline/snake_utils.py -> build/scripts-3.11
2024-10-18T20:07:13,907   copying and adjusting src/homi_pipeline/HoMi_cleanup.py -> build/scripts-3.11
2024-10-18T20:07:13,908   copying and adjusting src/homi_pipeline/profile_setup.py -> build/scripts-3.11
2024-10-18T20:07:13,910   copying and adjusting src/homi_pipeline/check_config.py -> build/scripts-3.11
2024-10-18T20:07:13,912   copying and adjusting src/homi_pipeline/rule_utils/combine_kreports.py -> build/scripts-3.11
2024-10-18T20:07:13,914   copying and adjusting src/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/scripts-3.11
2024-10-18T20:07:13,915   copying and adjusting src/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/scripts-3.11
2024-10-18T20:07:13,916   copying and adjusting src/homi_pipeline/rule_utils/counts_to_tpm.py -> build/scripts-3.11
2024-10-18T20:07:13,918   copying and adjusting src/homi_pipeline/rule_utils/read_reports.py -> build/scripts-3.11
2024-10-18T20:07:13,919   changing mode of build/scripts-3.11/HoMi.py from 644 to 755
2024-10-18T20:07:13,920   changing mode of build/scripts-3.11/snake_utils.py from 644 to 755
2024-10-18T20:07:13,920   changing mode of build/scripts-3.11/HoMi_cleanup.py from 644 to 755
2024-10-18T20:07:13,921   changing mode of build/scripts-3.11/profile_setup.py from 644 to 755
2024-10-18T20:07:13,922   changing mode of build/scripts-3.11/check_config.py from 644 to 755
2024-10-18T20:07:13,922   changing mode of build/scripts-3.11/combine_kreports.py from 644 to 755
2024-10-18T20:07:13,922   changing mode of build/scripts-3.11/aggregate_metaphlan_bugslists.py from 644 to 755
2024-10-18T20:07:13,923   changing mode of build/scripts-3.11/convert_mphlan_v4_to_v3.py from 644 to 755
2024-10-18T20:07:13,923   changing mode of build/scripts-3.11/counts_to_tpm.py from 644 to 755
2024-10-18T20:07:13,924   changing mode of build/scripts-3.11/read_reports.py from 644 to 755
2024-10-18T20:07:13,953   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-10-18T20:07:13,953   !!

2024-10-18T20:07:13,955           ********************************************************************************
2024-10-18T20:07:13,955           Please avoid running ``setup.py`` directly.
2024-10-18T20:07:13,956           Instead, use pypa/build, pypa/installer or other
2024-10-18T20:07:13,956           standards-based tools.

2024-10-18T20:07:13,957           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-10-18T20:07:13,958           ********************************************************************************

2024-10-18T20:07:13,959   !!
2024-10-18T20:07:13,960     self.initialize_options()
2024-10-18T20:07:13,983   installing to build/bdist.linux-armv7l/wheel
2024-10-18T20:07:13,984   running install
2024-10-18T20:07:14,008   running install_lib
2024-10-18T20:07:14,036   creating build/bdist.linux-armv7l/wheel
2024-10-18T20:07:14,039   creating build/bdist.linux-armv7l/wheel/homi_pipeline
2024-10-18T20:07:14,040   copying build/lib/homi_pipeline/check_config.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-10-18T20:07:14,043   copying build/lib/homi_pipeline/HoMi.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-10-18T20:07:14,045   copying build/lib/homi_pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-10-18T20:07:14,046   copying build/lib/homi_pipeline/HoMi_cleanup.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-10-18T20:07:14,049   creating build/bdist.linux-armv7l/wheel/homi_pipeline/rule_utils
2024-10-18T20:07:14,050   copying build/lib/homi_pipeline/rule_utils/HUMAnN_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,052   copying build/lib/homi_pipeline/rule_utils/counts_to_tpm.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,055   copying build/lib/homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,056   copying build/lib/homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,058   copying build/lib/homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,060   copying build/lib/homi_pipeline/rule_utils/R_packages.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,062   copying build/lib/homi_pipeline/rule_utils/Metaphlan_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,064   copying build/lib/homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,066   copying build/lib/homi_pipeline/rule_utils/sam2bam.sh -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,067   copying build/lib/homi_pipeline/rule_utils/read_reports.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,069   copying build/lib/homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,071   copying build/lib/homi_pipeline/rule_utils/combine_kreports.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,074   copying build/lib/homi_pipeline/rule_utils/Kraken_microshades.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,076   copying build/lib/homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd -> build/bdist.linux-armv7l/wheel/./homi_pipeline/rule_utils
2024-10-18T20:07:14,078   copying build/lib/homi_pipeline/snakefile -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-10-18T20:07:14,081   copying build/lib/homi_pipeline/profile_setup.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-10-18T20:07:14,084   creating build/bdist.linux-armv7l/wheel/homi_pipeline/conda_envs
2024-10-18T20:07:14,085   copying build/lib/homi_pipeline/conda_envs/nonpareil.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,087   copying build/lib/homi_pipeline/conda_envs/seqtk.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,088   copying build/lib/homi_pipeline/conda_envs/trimmomatic.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,090   copying build/lib/homi_pipeline/conda_envs/kraken.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,092   copying build/lib/homi_pipeline/conda_envs/humann.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,094   copying build/lib/homi_pipeline/conda_envs/r_env.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,095   copying build/lib/homi_pipeline/conda_envs/bbmap.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,097   copying build/lib/homi_pipeline/conda_envs/featureCounts.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,099   copying build/lib/homi_pipeline/conda_envs/fastqc.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,101   copying build/lib/homi_pipeline/conda_envs/hisat2.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,103   copying build/lib/homi_pipeline/conda_envs/hostile.yaml -> build/bdist.linux-armv7l/wheel/./homi_pipeline/conda_envs
2024-10-18T20:07:14,104   copying build/lib/homi_pipeline/snake_utils.py -> build/bdist.linux-armv7l/wheel/./homi_pipeline
2024-10-18T20:07:14,107   creating build/bdist.linux-armv7l/wheel/homi_pipeline/data
2024-10-18T20:07:14,108   copying build/lib/homi_pipeline/data/adapters.fa -> build/bdist.linux-armv7l/wheel/./homi_pipeline/data
2024-10-18T20:07:14,111   running install_egg_info
2024-10-18T20:07:14,142   Copying src/homi_pipeline.egg-info to build/bdist.linux-armv7l/wheel/./homi_pipeline-1.0.9-py3.11.egg-info
2024-10-18T20:07:14,151   running install_scripts
2024-10-18T20:07:14,152   creating build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,154   copying build/scripts-3.11/check_config.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,156   copying build/scripts-3.11/HoMi.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,159   copying build/scripts-3.11/counts_to_tpm.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,161   copying build/scripts-3.11/HoMi_cleanup.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,163   copying build/scripts-3.11/aggregate_metaphlan_bugslists.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,164   copying build/scripts-3.11/convert_mphlan_v4_to_v3.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,166   copying build/scripts-3.11/read_reports.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,168   copying build/scripts-3.11/combine_kreports.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,171   copying build/scripts-3.11/profile_setup.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,173   copying build/scripts-3.11/snake_utils.py -> build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts
2024-10-18T20:07:14,174   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/check_config.py to 755
2024-10-18T20:07:14,175   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/HoMi.py to 755
2024-10-18T20:07:14,176   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/counts_to_tpm.py to 755
2024-10-18T20:07:14,176   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/HoMi_cleanup.py to 755
2024-10-18T20:07:14,177   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/aggregate_metaphlan_bugslists.py to 755
2024-10-18T20:07:14,177   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/convert_mphlan_v4_to_v3.py to 755
2024-10-18T20:07:14,178   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/read_reports.py to 755
2024-10-18T20:07:14,178   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/combine_kreports.py to 755
2024-10-18T20:07:14,179   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/profile_setup.py to 755
2024-10-18T20:07:14,179   changing mode of build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.data/scripts/snake_utils.py to 755
2024-10-18T20:07:14,193   creating build/bdist.linux-armv7l/wheel/homi_pipeline-1.0.9.dist-info/WHEEL
2024-10-18T20:07:14,195   creating '/tmp/pip-wheel-uuow_7jp/homi_pipeline-1.0.9-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-10-18T20:07:14,197   adding 'homi_pipeline/HoMi.py'
2024-10-18T20:07:14,199   adding 'homi_pipeline/HoMi_cleanup.py'
2024-10-18T20:07:14,200   adding 'homi_pipeline/__init__.py'
2024-10-18T20:07:14,201   adding 'homi_pipeline/check_config.py'
2024-10-18T20:07:14,203   adding 'homi_pipeline/profile_setup.py'
2024-10-18T20:07:14,205   adding 'homi_pipeline/snake_utils.py'
2024-10-18T20:07:14,209   adding 'homi_pipeline/snakefile'
2024-10-18T20:07:14,211   adding 'homi_pipeline/conda_envs/bbmap.yaml'
2024-10-18T20:07:14,212   adding 'homi_pipeline/conda_envs/fastqc.yaml'
2024-10-18T20:07:14,214   adding 'homi_pipeline/conda_envs/featureCounts.yaml'
2024-10-18T20:07:14,215   adding 'homi_pipeline/conda_envs/hisat2.yaml'
2024-10-18T20:07:14,216   adding 'homi_pipeline/conda_envs/hostile.yaml'
2024-10-18T20:07:14,217   adding 'homi_pipeline/conda_envs/humann.yaml'
2024-10-18T20:07:14,218   adding 'homi_pipeline/conda_envs/kraken.yaml'
2024-10-18T20:07:14,219   adding 'homi_pipeline/conda_envs/nonpareil.yaml'
2024-10-18T20:07:14,220   adding 'homi_pipeline/conda_envs/r_env.yaml'
2024-10-18T20:07:14,222   adding 'homi_pipeline/conda_envs/seqtk.yaml'
2024-10-18T20:07:14,223   adding 'homi_pipeline/conda_envs/trimmomatic.yaml'
2024-10-18T20:07:14,225   adding 'homi_pipeline/data/adapters.fa'
2024-10-18T20:07:14,227   adding 'homi_pipeline/rule_utils/Gut_metabolic_modules.Rmd'
2024-10-18T20:07:14,228   adding 'homi_pipeline/rule_utils/HUMAnN_microshades.Rmd'
2024-10-18T20:07:14,230   adding 'homi_pipeline/rule_utils/HUMAnN_to_phyloseq_helper.R'
2024-10-18T20:07:14,232   adding 'homi_pipeline/rule_utils/Kraken_microshades.Rmd'
2024-10-18T20:07:14,233   adding 'homi_pipeline/rule_utils/Metaphlan_microshades.Rmd'
2024-10-18T20:07:14,235   adding 'homi_pipeline/rule_utils/R_packages.R'
2024-10-18T20:07:14,236   adding 'homi_pipeline/rule_utils/aggregate_metaphlan_bugslists.py'
2024-10-18T20:07:14,237   adding 'homi_pipeline/rule_utils/bracken_to_phyloseq_helper.R'
2024-10-18T20:07:14,240   adding 'homi_pipeline/rule_utils/combine_kreports.py'
2024-10-18T20:07:14,241   adding 'homi_pipeline/rule_utils/convert_mphlan_v4_to_v3.py'
2024-10-18T20:07:14,242   adding 'homi_pipeline/rule_utils/counts_to_tpm.py'
2024-10-18T20:07:14,243   adding 'homi_pipeline/rule_utils/metaphlan_to_phyloseq_helper.R'
2024-10-18T20:07:14,245   adding 'homi_pipeline/rule_utils/read_reports.py'
2024-10-18T20:07:14,246   adding 'homi_pipeline/rule_utils/sam2bam.sh'
2024-10-18T20:07:14,248   adding 'homi_pipeline-1.0.9.data/scripts/HoMi.py'
2024-10-18T20:07:14,250   adding 'homi_pipeline-1.0.9.data/scripts/HoMi_cleanup.py'
2024-10-18T20:07:14,251   adding 'homi_pipeline-1.0.9.data/scripts/aggregate_metaphlan_bugslists.py'
2024-10-18T20:07:14,253   adding 'homi_pipeline-1.0.9.data/scripts/check_config.py'
2024-10-18T20:07:14,255   adding 'homi_pipeline-1.0.9.data/scripts/combine_kreports.py'
2024-10-18T20:07:14,256   adding 'homi_pipeline-1.0.9.data/scripts/convert_mphlan_v4_to_v3.py'
2024-10-18T20:07:14,257   adding 'homi_pipeline-1.0.9.data/scripts/counts_to_tpm.py'
2024-10-18T20:07:14,259   adding 'homi_pipeline-1.0.9.data/scripts/profile_setup.py'
2024-10-18T20:07:14,260   adding 'homi_pipeline-1.0.9.data/scripts/read_reports.py'
2024-10-18T20:07:14,262   adding 'homi_pipeline-1.0.9.data/scripts/snake_utils.py'
2024-10-18T20:07:14,265   adding 'homi_pipeline-1.0.9.dist-info/LICENSE'
2024-10-18T20:07:14,267   adding 'homi_pipeline-1.0.9.dist-info/METADATA'
2024-10-18T20:07:14,268   adding 'homi_pipeline-1.0.9.dist-info/WHEEL'
2024-10-18T20:07:14,269   adding 'homi_pipeline-1.0.9.dist-info/top_level.txt'
2024-10-18T20:07:14,270   adding 'homi_pipeline-1.0.9.dist-info/RECORD'
2024-10-18T20:07:14,273   removing build/bdist.linux-armv7l/wheel
2024-10-18T20:07:14,397   Building wheel for homi-pipeline (setup.py): finished with status 'done'
2024-10-18T20:07:14,401   Created wheel for homi-pipeline: filename=homi_pipeline-1.0.9-py3-none-any.whl size=71886 sha256=7e6216111167f6a7190da3e0cde77f73360b79a8177fb09035bd1ae650c1e507
2024-10-18T20:07:14,402   Stored in directory: /tmp/pip-ephem-wheel-cache-8sp8fhhf/wheels/67/fe/9b/5fc007c8569f01eaf1ecebe76b84c52957548c5b3a5245fc9d
2024-10-18T20:07:14,414 Successfully built homi-pipeline
2024-10-18T20:07:14,420 Removed build tracker: '/tmp/pip-build-tracker-2k19lknl'