2024-02-04T06:26:32,589 Created temporary directory: /tmp/pip-build-tracker-rgm1mc8y
2024-02-04T06:26:32,590 Initialized build tracking at /tmp/pip-build-tracker-rgm1mc8y
2024-02-04T06:26:32,590 Created build tracker: /tmp/pip-build-tracker-rgm1mc8y
2024-02-04T06:26:32,591 Entered build tracker: /tmp/pip-build-tracker-rgm1mc8y
2024-02-04T06:26:32,592 Created temporary directory: /tmp/pip-wheel-7zr88k6l
2024-02-04T06:26:32,595 Created temporary directory: /tmp/pip-ephem-wheel-cache-y_r5jb50
2024-02-04T06:26:32,616 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-02-04T06:26:32,620 2 location(s) to search for versions of hecatomb:
2024-02-04T06:26:32,620 * https://pypi.org/simple/hecatomb/
2024-02-04T06:26:32,620 * https://www.piwheels.org/simple/hecatomb/
2024-02-04T06:26:32,620 Fetching project page and analyzing links: https://pypi.org/simple/hecatomb/
2024-02-04T06:26:32,621 Getting page https://pypi.org/simple/hecatomb/
2024-02-04T06:26:32,623 Found index url https://pypi.org/simple/
2024-02-04T06:26:32,833 Fetched page https://pypi.org/simple/hecatomb/ as application/vnd.pypi.simple.v1+json
2024-02-04T06:26:32,835   Skipping link: No binaries permitted for hecatomb: https://files.pythonhosted.org/packages/cd/63/aaa5ce961dbf2daa1babcfd88326eb999b63b3d9b697762955b278494d51/hecatomb-1.2.0-py3-none-any.whl (from https://pypi.org/simple/hecatomb/) (requires-python:>=3.7)
2024-02-04T06:26:32,836   Found link https://files.pythonhosted.org/packages/e4/8a/60abbe18523fcf27f997b4b5e25499d58a76e6a17cb2343787c4853050f9/hecatomb-1.2.0.tar.gz (from https://pypi.org/simple/hecatomb/) (requires-python:>=3.7), version: 1.2.0
2024-02-04T06:26:32,837   Skipping link: No binaries permitted for hecatomb: https://files.pythonhosted.org/packages/6b/f0/3284cfa8ff54616784442f04b2532d7276a58b3eb2417cfd15def8e0c56f/hecatomb-1.3.0-py3-none-any.whl (from https://pypi.org/simple/hecatomb/) (requires-python:>=3.9)
2024-02-04T06:26:32,837   Found link https://files.pythonhosted.org/packages/ce/56/2dab4a7325b279174f9da6f0a213f655f4e031363974e67130ffc24261e8/hecatomb-1.3.0.tar.gz (from https://pypi.org/simple/hecatomb/) (requires-python:>=3.9), version: 1.3.0
2024-02-04T06:26:32,838   Skipping link: No binaries permitted for hecatomb: https://files.pythonhosted.org/packages/a2/7d/dc077ab4a55c89c38c2fb9d38deb3db7e7fdcff5efad9f51c11e689eaedb/hecatomb-1.3.1-py3-none-any.whl (from https://pypi.org/simple/hecatomb/) (requires-python:>=3.9)
2024-02-04T06:26:32,839   Found link https://files.pythonhosted.org/packages/9c/4a/d3baa63f70267bbfa3112d1af6dc491e105aa4dbf41f9a44c69b8c07111f/hecatomb-1.3.1.tar.gz (from https://pypi.org/simple/hecatomb/) (requires-python:>=3.9), version: 1.3.1
2024-02-04T06:26:32,840 Fetching project page and analyzing links: https://www.piwheels.org/simple/hecatomb/
2024-02-04T06:26:32,840 Getting page https://www.piwheels.org/simple/hecatomb/
2024-02-04T06:26:32,842 Found index url https://www.piwheels.org/simple/
2024-02-04T06:26:32,996 Fetched page https://www.piwheels.org/simple/hecatomb/ as text/html
2024-02-04T06:26:32,998   Skipping link: No binaries permitted for hecatomb: https://www.piwheels.org/simple/hecatomb/hecatomb-1.3.0-py3-none-any.whl#sha256=7c88ee5207d15214efcf06eab485fc2b867d86cc43648f88f8ca409228d62d42 (from https://www.piwheels.org/simple/hecatomb/) (requires-python:>=3.9)
2024-02-04T06:26:32,998   Skipping link: No binaries permitted for hecatomb: https://www.piwheels.org/simple/hecatomb/hecatomb-1.2.0-py3-none-any.whl#sha256=ad0eaa01aaa37d90124282fa20269ed0e9153ae6f03c8ab3f713b7245f58e98b (from https://www.piwheels.org/simple/hecatomb/) (requires-python:>=3.7)
2024-02-04T06:26:32,999 Skipping link: not a file: https://www.piwheels.org/simple/hecatomb/
2024-02-04T06:26:33,000 Skipping link: not a file: https://pypi.org/simple/hecatomb/
2024-02-04T06:26:33,018 Given no hashes to check 1 links for project 'hecatomb': discarding no candidates
2024-02-04T06:26:33,036 Collecting hecatomb==1.3.1
2024-02-04T06:26:33,038   Created temporary directory: /tmp/pip-unpack-2_cpfy5y
2024-02-04T06:26:33,251   Downloading hecatomb-1.3.1.tar.gz (98.5 MB)
2024-02-04T06:26:53,390   Added hecatomb==1.3.1 from https://files.pythonhosted.org/packages/9c/4a/d3baa63f70267bbfa3112d1af6dc491e105aa4dbf41f9a44c69b8c07111f/hecatomb-1.3.1.tar.gz to build tracker '/tmp/pip-build-tracker-rgm1mc8y'
2024-02-04T06:26:53,392   Running setup.py (path:/tmp/pip-wheel-7zr88k6l/hecatomb_89ceeb53e99746d3ba6779daf230986a/setup.py) egg_info for package hecatomb
2024-02-04T06:26:53,393   Created temporary directory: /tmp/pip-pip-egg-info-_7ndg491
2024-02-04T06:26:53,393   Preparing metadata (setup.py): started
2024-02-04T06:26:53,394   Running command python setup.py egg_info
2024-02-04T06:26:54,355   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing 'v1.3.1' to '1.3.1'
2024-02-04T06:26:54,356     self.metadata.version = self._normalize_version(self.metadata.version)
2024-02-04T06:26:54,394   running egg_info
2024-02-04T06:26:54,395   creating /tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info
2024-02-04T06:26:54,420   writing /tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info/PKG-INFO
2024-02-04T06:26:54,423   writing dependency_links to /tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info/dependency_links.txt
2024-02-04T06:26:54,425   writing entry points to /tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info/entry_points.txt
2024-02-04T06:26:54,427   writing requirements to /tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info/requires.txt
2024-02-04T06:26:54,459   writing top-level names to /tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info/top_level.txt
2024-02-04T06:26:54,461   writing manifest file '/tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info/SOURCES.txt'
2024-02-04T06:26:54,532   file hecatomb.py (for module hecatomb) not found
2024-02-04T06:26:54,561   reading manifest file '/tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info/SOURCES.txt'
2024-02-04T06:26:54,563   reading manifest template 'MANIFEST.in'
2024-02-04T06:26:54,616   warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/conda/'
2024-02-04T06:26:54,617   warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/databases/'
2024-02-04T06:26:54,618   adding license file 'LICENSE'
2024-02-04T06:26:54,622   writing manifest file '/tmp/pip-pip-egg-info-_7ndg491/hecatomb.egg-info/SOURCES.txt'
2024-02-04T06:26:54,729   Preparing metadata (setup.py): finished with status 'done'
2024-02-04T06:26:54,734   Source in /tmp/pip-wheel-7zr88k6l/hecatomb_89ceeb53e99746d3ba6779daf230986a has version 1.3.1, which satisfies requirement hecatomb==1.3.1 from https://files.pythonhosted.org/packages/9c/4a/d3baa63f70267bbfa3112d1af6dc491e105aa4dbf41f9a44c69b8c07111f/hecatomb-1.3.1.tar.gz
2024-02-04T06:26:54,735   Removed hecatomb==1.3.1 from https://files.pythonhosted.org/packages/9c/4a/d3baa63f70267bbfa3112d1af6dc491e105aa4dbf41f9a44c69b8c07111f/hecatomb-1.3.1.tar.gz from build tracker '/tmp/pip-build-tracker-rgm1mc8y'
2024-02-04T06:26:54,741 Created temporary directory: /tmp/pip-unpack-aqzbsmmq
2024-02-04T06:26:54,742 Created temporary directory: /tmp/pip-unpack-jin71ska
2024-02-04T06:26:54,752 Building wheels for collected packages: hecatomb
2024-02-04T06:26:54,757   Created temporary directory: /tmp/pip-wheel-y9zsrxjl
2024-02-04T06:26:54,758   Building wheel for hecatomb (setup.py): started
2024-02-04T06:26:54,759   Destination directory: /tmp/pip-wheel-y9zsrxjl
2024-02-04T06:26:54,759   Running command python setup.py bdist_wheel
2024-02-04T06:26:56,140   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing 'v1.3.1' to '1.3.1'
2024-02-04T06:26:56,140     self.metadata.version = self._normalize_version(self.metadata.version)
2024-02-04T06:26:56,191   running bdist_wheel
2024-02-04T06:26:56,371   running build
2024-02-04T06:26:56,372   running build_py
2024-02-04T06:26:56,407   file hecatomb.py (for module hecatomb) not found
2024-02-04T06:26:56,409   creating build
2024-02-04T06:26:56,409   creating build/lib
2024-02-04T06:26:56,417   creating build/lib/hecatomb
2024-02-04T06:26:56,422   copying hecatomb/__main__.py -> build/lib/hecatomb
2024-02-04T06:26:56,433   copying hecatomb/__init__.py -> build/lib/hecatomb
2024-02-04T06:26:56,435   running egg_info
2024-02-04T06:26:56,511   writing hecatomb.egg-info/PKG-INFO
2024-02-04T06:26:56,515   writing dependency_links to hecatomb.egg-info/dependency_links.txt
2024-02-04T06:26:56,517   writing entry points to hecatomb.egg-info/entry_points.txt
2024-02-04T06:26:56,519   writing requirements to hecatomb.egg-info/requires.txt
2024-02-04T06:26:56,520   writing top-level names to hecatomb.egg-info/top_level.txt
2024-02-04T06:26:56,524   file hecatomb.py (for module hecatomb) not found
2024-02-04T06:26:56,552   reading manifest file 'hecatomb.egg-info/SOURCES.txt'
2024-02-04T06:26:56,556   reading manifest template 'MANIFEST.in'
2024-02-04T06:26:58,458   warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/conda/'
2024-02-04T06:26:58,460   warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/databases/'
2024-02-04T06:26:58,462   adding license file 'LICENSE'
2024-02-04T06:26:58,475   writing manifest file 'hecatomb.egg-info/SOURCES.txt'
2024-02-04T06:26:58,481   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.config' is absent from the `packages` configuration.
2024-02-04T06:26:58,482   !!

2024-02-04T06:26:58,484           ********************************************************************************
2024-02-04T06:26:58,485           ############################
2024-02-04T06:26:58,486           # Package would be ignored #
2024-02-04T06:26:58,487           ############################
2024-02-04T06:26:58,487           Python recognizes 'hecatomb.snakemake.config' as an importable package[^1],
2024-02-04T06:26:58,488           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,490           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,490           package, please make sure that 'hecatomb.snakemake.config' is explicitly added
2024-02-04T06:26:58,491           to the `packages` configuration field.

2024-02-04T06:26:58,493           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,493           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,494           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,496           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,497           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,499           If you don't want 'hecatomb.snakemake.config' to be distributed and are
2024-02-04T06:26:58,500           already explicitly excluding 'hecatomb.snakemake.config' via
2024-02-04T06:26:58,500           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,501           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,502           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,503           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,505           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,507           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,508                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,510                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,511                 directory, all directories are treated like packages.
2024-02-04T06:26:58,512           ********************************************************************************

2024-02-04T06:26:58,513   !!
2024-02-04T06:26:58,514     check.warn(importable)
2024-02-04T06:26:58,515   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.profile.example_slurm' is absent from the `packages` configuration.
2024-02-04T06:26:58,516   !!

2024-02-04T06:26:58,518           ********************************************************************************
2024-02-04T06:26:58,518           ############################
2024-02-04T06:26:58,519           # Package would be ignored #
2024-02-04T06:26:58,520           ############################
2024-02-04T06:26:58,520           Python recognizes 'hecatomb.snakemake.profile.example_slurm' as an importable package[^1],
2024-02-04T06:26:58,521           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,522           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,523           package, please make sure that 'hecatomb.snakemake.profile.example_slurm' is explicitly added
2024-02-04T06:26:58,524           to the `packages` configuration field.

2024-02-04T06:26:58,526           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,526           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,527           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,528           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,530           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,531           If you don't want 'hecatomb.snakemake.profile.example_slurm' to be distributed and are
2024-02-04T06:26:58,532           already explicitly excluding 'hecatomb.snakemake.profile.example_slurm' via
2024-02-04T06:26:58,532           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,533           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,534           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,535           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,537           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,539           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,540                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,541                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,542                 directory, all directories are treated like packages.
2024-02-04T06:26:58,542           ********************************************************************************

2024-02-04T06:26:58,544   !!
2024-02-04T06:26:58,545     check.warn(importable)
2024-02-04T06:26:58,545   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow' is absent from the `packages` configuration.
2024-02-04T06:26:58,546   !!

2024-02-04T06:26:58,548           ********************************************************************************
2024-02-04T06:26:58,548           ############################
2024-02-04T06:26:58,549           # Package would be ignored #
2024-02-04T06:26:58,550           ############################
2024-02-04T06:26:58,551           Python recognizes 'hecatomb.snakemake.workflow' as an importable package[^1],
2024-02-04T06:26:58,552           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,553           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,554           package, please make sure that 'hecatomb.snakemake.workflow' is explicitly added
2024-02-04T06:26:58,555           to the `packages` configuration field.

2024-02-04T06:26:58,556           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,557           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,558           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,560           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,561           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,563           If you don't want 'hecatomb.snakemake.workflow' to be distributed and are
2024-02-04T06:26:58,564           already explicitly excluding 'hecatomb.snakemake.workflow' via
2024-02-04T06:26:58,564           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,565           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,566           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,568           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,570           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,572           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,573                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,573                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,574                 directory, all directories are treated like packages.
2024-02-04T06:26:58,575           ********************************************************************************

2024-02-04T06:26:58,576   !!
2024-02-04T06:26:58,577     check.warn(importable)
2024-02-04T06:26:58,578   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow.envs' is absent from the `packages` configuration.
2024-02-04T06:26:58,579   !!

2024-02-04T06:26:58,581           ********************************************************************************
2024-02-04T06:26:58,581           ############################
2024-02-04T06:26:58,582           # Package would be ignored #
2024-02-04T06:26:58,583           ############################
2024-02-04T06:26:58,583           Python recognizes 'hecatomb.snakemake.workflow.envs' as an importable package[^1],
2024-02-04T06:26:58,584           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,585           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,586           package, please make sure that 'hecatomb.snakemake.workflow.envs' is explicitly added
2024-02-04T06:26:58,587           to the `packages` configuration field.

2024-02-04T06:26:58,588           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,588           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,589           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,590           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,592           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,593           If you don't want 'hecatomb.snakemake.workflow.envs' to be distributed and are
2024-02-04T06:26:58,593           already explicitly excluding 'hecatomb.snakemake.workflow.envs' via
2024-02-04T06:26:58,594           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,594           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,595           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,596           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,597           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,600           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,600                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,601                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,602                 directory, all directories are treated like packages.
2024-02-04T06:26:58,602           ********************************************************************************

2024-02-04T06:26:58,603   !!
2024-02-04T06:26:58,604     check.warn(importable)
2024-02-04T06:26:58,604   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow.report' is absent from the `packages` configuration.
2024-02-04T06:26:58,605   !!

2024-02-04T06:26:58,606           ********************************************************************************
2024-02-04T06:26:58,606           ############################
2024-02-04T06:26:58,607           # Package would be ignored #
2024-02-04T06:26:58,608           ############################
2024-02-04T06:26:58,608           Python recognizes 'hecatomb.snakemake.workflow.report' as an importable package[^1],
2024-02-04T06:26:58,609           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,610           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,610           package, please make sure that 'hecatomb.snakemake.workflow.report' is explicitly added
2024-02-04T06:26:58,611           to the `packages` configuration field.

2024-02-04T06:26:58,612           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,613           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,613           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,614           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,616           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,617           If you don't want 'hecatomb.snakemake.workflow.report' to be distributed and are
2024-02-04T06:26:58,617           already explicitly excluding 'hecatomb.snakemake.workflow.report' via
2024-02-04T06:26:58,618           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,618           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,619           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,620           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,621           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,623           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,624                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,625                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,625                 directory, all directories are treated like packages.
2024-02-04T06:26:58,626           ********************************************************************************

2024-02-04T06:26:58,627   !!
2024-02-04T06:26:58,627     check.warn(importable)
2024-02-04T06:26:58,628   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow.rules.annotation' is absent from the `packages` configuration.
2024-02-04T06:26:58,629   !!

2024-02-04T06:26:58,630           ********************************************************************************
2024-02-04T06:26:58,631           ############################
2024-02-04T06:26:58,631           # Package would be ignored #
2024-02-04T06:26:58,632           ############################
2024-02-04T06:26:58,632           Python recognizes 'hecatomb.snakemake.workflow.rules.annotation' as an importable package[^1],
2024-02-04T06:26:58,633           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,635           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,635           package, please make sure that 'hecatomb.snakemake.workflow.rules.annotation' is explicitly added
2024-02-04T06:26:58,636           to the `packages` configuration field.

2024-02-04T06:26:58,637           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,638           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,638           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,639           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,640           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,641           If you don't want 'hecatomb.snakemake.workflow.rules.annotation' to be distributed and are
2024-02-04T06:26:58,642           already explicitly excluding 'hecatomb.snakemake.workflow.rules.annotation' via
2024-02-04T06:26:58,643           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,643           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,644           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,645           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,646           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,647           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,648                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,648                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,649                 directory, all directories are treated like packages.
2024-02-04T06:26:58,649           ********************************************************************************

2024-02-04T06:26:58,651   !!
2024-02-04T06:26:58,651     check.warn(importable)
2024-02-04T06:26:58,652   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow.rules.assembly' is absent from the `packages` configuration.
2024-02-04T06:26:58,652   !!

2024-02-04T06:26:58,657           ********************************************************************************
2024-02-04T06:26:58,658           ############################
2024-02-04T06:26:58,658           # Package would be ignored #
2024-02-04T06:26:58,659           ############################
2024-02-04T06:26:58,660           Python recognizes 'hecatomb.snakemake.workflow.rules.assembly' as an importable package[^1],
2024-02-04T06:26:58,660           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,662           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,662           package, please make sure that 'hecatomb.snakemake.workflow.rules.assembly' is explicitly added
2024-02-04T06:26:58,663           to the `packages` configuration field.

2024-02-04T06:26:58,664           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,665           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,665           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,666           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,667           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,669           If you don't want 'hecatomb.snakemake.workflow.rules.assembly' to be distributed and are
2024-02-04T06:26:58,669           already explicitly excluding 'hecatomb.snakemake.workflow.rules.assembly' via
2024-02-04T06:26:58,670           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,671           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,672           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,673           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,674           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,675           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,676                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,677                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,677                 directory, all directories are treated like packages.
2024-02-04T06:26:58,678           ********************************************************************************

2024-02-04T06:26:58,679   !!
2024-02-04T06:26:58,680     check.warn(importable)
2024-02-04T06:26:58,680   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow.rules.preflight' is absent from the `packages` configuration.
2024-02-04T06:26:58,681   !!

2024-02-04T06:26:58,682           ********************************************************************************
2024-02-04T06:26:58,683           ############################
2024-02-04T06:26:58,683           # Package would be ignored #
2024-02-04T06:26:58,684           ############################
2024-02-04T06:26:58,684           Python recognizes 'hecatomb.snakemake.workflow.rules.preflight' as an importable package[^1],
2024-02-04T06:26:58,685           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,687           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,687           package, please make sure that 'hecatomb.snakemake.workflow.rules.preflight' is explicitly added
2024-02-04T06:26:58,688           to the `packages` configuration field.

2024-02-04T06:26:58,689           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,689           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,690           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,691           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,692           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,693           If you don't want 'hecatomb.snakemake.workflow.rules.preflight' to be distributed and are
2024-02-04T06:26:58,694           already explicitly excluding 'hecatomb.snakemake.workflow.rules.preflight' via
2024-02-04T06:26:58,694           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,695           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,696           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,697           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,699           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,700           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,701                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,702                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,702                 directory, all directories are treated like packages.
2024-02-04T06:26:58,703           ********************************************************************************

2024-02-04T06:26:58,704   !!
2024-02-04T06:26:58,705     check.warn(importable)
2024-02-04T06:26:58,706   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow.rules.preprocessing' is absent from the `packages` configuration.
2024-02-04T06:26:58,706   !!

2024-02-04T06:26:58,707           ********************************************************************************
2024-02-04T06:26:58,708           ############################
2024-02-04T06:26:58,708           # Package would be ignored #
2024-02-04T06:26:58,709           ############################
2024-02-04T06:26:58,709           Python recognizes 'hecatomb.snakemake.workflow.rules.preprocessing' as an importable package[^1],
2024-02-04T06:26:58,710           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,711           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,712           package, please make sure that 'hecatomb.snakemake.workflow.rules.preprocessing' is explicitly added
2024-02-04T06:26:58,712           to the `packages` configuration field.

2024-02-04T06:26:58,714           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,714           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,715           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,716           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,720           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,721           If you don't want 'hecatomb.snakemake.workflow.rules.preprocessing' to be distributed and are
2024-02-04T06:26:58,722           already explicitly excluding 'hecatomb.snakemake.workflow.rules.preprocessing' via
2024-02-04T06:26:58,722           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,723           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,723           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,725           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,726           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,728           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,729                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,730                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,730                 directory, all directories are treated like packages.
2024-02-04T06:26:58,731           ********************************************************************************

2024-02-04T06:26:58,732   !!
2024-02-04T06:26:58,733     check.warn(importable)
2024-02-04T06:26:58,734   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow.rules.reports' is absent from the `packages` configuration.
2024-02-04T06:26:58,734   !!

2024-02-04T06:26:58,736           ********************************************************************************
2024-02-04T06:26:58,736           ############################
2024-02-04T06:26:58,737           # Package would be ignored #
2024-02-04T06:26:58,737           ############################
2024-02-04T06:26:58,738           Python recognizes 'hecatomb.snakemake.workflow.rules.reports' as an importable package[^1],
2024-02-04T06:26:58,739           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,740           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,741           package, please make sure that 'hecatomb.snakemake.workflow.rules.reports' is explicitly added
2024-02-04T06:26:58,741           to the `packages` configuration field.

2024-02-04T06:26:58,743           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,744           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,745           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,746           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,747           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,748           If you don't want 'hecatomb.snakemake.workflow.rules.reports' to be distributed and are
2024-02-04T06:26:58,749           already explicitly excluding 'hecatomb.snakemake.workflow.rules.reports' via
2024-02-04T06:26:58,749           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,749           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,750           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,751           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,752           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,754           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,755                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,755                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,756                 directory, all directories are treated like packages.
2024-02-04T06:26:58,757           ********************************************************************************

2024-02-04T06:26:58,758   !!
2024-02-04T06:26:58,758     check.warn(importable)
2024-02-04T06:26:58,759   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow.scripts' is absent from the `packages` configuration.
2024-02-04T06:26:58,760   !!

2024-02-04T06:26:58,761           ********************************************************************************
2024-02-04T06:26:58,761           ############################
2024-02-04T06:26:58,762           # Package would be ignored #
2024-02-04T06:26:58,763           ############################
2024-02-04T06:26:58,763           Python recognizes 'hecatomb.snakemake.workflow.scripts' as an importable package[^1],
2024-02-04T06:26:58,764           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,765           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,765           package, please make sure that 'hecatomb.snakemake.workflow.scripts' is explicitly added
2024-02-04T06:26:58,766           to the `packages` configuration field.

2024-02-04T06:26:58,767           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,768           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,768           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,770           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,771           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,772           If you don't want 'hecatomb.snakemake.workflow.scripts' to be distributed and are
2024-02-04T06:26:58,773           already explicitly excluding 'hecatomb.snakemake.workflow.scripts' via
2024-02-04T06:26:58,773           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,774           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,774           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,776           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,777           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,779           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,779                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,780                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,780                 directory, all directories are treated like packages.
2024-02-04T06:26:58,780           ********************************************************************************

2024-02-04T06:26:58,782   !!
2024-02-04T06:26:58,782     check.warn(importable)
2024-02-04T06:26:58,783   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.test_data' is absent from the `packages` configuration.
2024-02-04T06:26:58,783   !!

2024-02-04T06:26:58,784           ********************************************************************************
2024-02-04T06:26:58,785           ############################
2024-02-04T06:26:58,785           # Package would be ignored #
2024-02-04T06:26:58,786           ############################
2024-02-04T06:26:58,786           Python recognizes 'hecatomb.test_data' as an importable package[^1],
2024-02-04T06:26:58,787           but it is absent from setuptools' `packages` configuration.

2024-02-04T06:26:58,788           This leads to an ambiguous overall configuration. If you want to distribute this
2024-02-04T06:26:58,788           package, please make sure that 'hecatomb.test_data' is explicitly added
2024-02-04T06:26:58,788           to the `packages` configuration field.

2024-02-04T06:26:58,790           Alternatively, you can also rely on setuptools' discovery methods
2024-02-04T06:26:58,790           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-02-04T06:26:58,791           instead of `find_packages(...)`/`find:`).

2024-02-04T06:26:58,792           You can read more about "package discovery" on setuptools documentation page:

2024-02-04T06:26:58,793           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-02-04T06:26:58,794           If you don't want 'hecatomb.test_data' to be distributed and are
2024-02-04T06:26:58,795           already explicitly excluding 'hecatomb.test_data' via
2024-02-04T06:26:58,796           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-02-04T06:26:58,797           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-02-04T06:26:58,798           combination with a more fine grained `package-data` configuration.

2024-02-04T06:26:58,809           You can read more about "package data files" on setuptools documentation page:

2024-02-04T06:26:58,818           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-02-04T06:26:58,824           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-02-04T06:26:58,826                 even if it does not contain any `.py` files.
2024-02-04T06:26:58,827                 On the other hand, currently there is no concept of package data
2024-02-04T06:26:58,827                 directory, all directories are treated like packages.
2024-02-04T06:26:58,829           ********************************************************************************

2024-02-04T06:26:58,832   !!
2024-02-04T06:26:58,834     check.warn(importable)
2024-02-04T06:26:58,834   copying hecatomb/hecatomb.CITATION -> build/lib/hecatomb
2024-02-04T06:26:58,836   copying hecatomb/hecatomb.LICENSE -> build/lib/hecatomb
2024-02-04T06:26:58,838   copying hecatomb/hecatomb.VERSION -> build/lib/hecatomb
2024-02-04T06:26:58,840   creating build/lib/hecatomb/snakemake
2024-02-04T06:26:58,842   creating build/lib/hecatomb/snakemake/config
2024-02-04T06:26:58,844   copying hecatomb/snakemake/config/config.yaml -> build/lib/hecatomb/snakemake/config
2024-02-04T06:26:58,847   copying hecatomb/snakemake/config/dbFiles.yaml -> build/lib/hecatomb/snakemake/config
2024-02-04T06:26:58,849   copying hecatomb/snakemake/config/immutable.yaml -> build/lib/hecatomb/snakemake/config
2024-02-04T06:26:58,852   creating build/lib/hecatomb/snakemake/profile
2024-02-04T06:26:58,857   creating build/lib/hecatomb/snakemake/profile/example_slurm
2024-02-04T06:26:58,860   copying hecatomb/snakemake/profile/example_slurm/config.yaml -> build/lib/hecatomb/snakemake/profile/example_slurm
2024-02-04T06:26:58,863   copying hecatomb/snakemake/profile/example_slurm/slurm-status.py -> build/lib/hecatomb/snakemake/profile/example_slurm
2024-02-04T06:26:58,868   creating build/lib/hecatomb/snakemake/workflow
2024-02-04T06:26:58,870   copying hecatomb/snakemake/workflow/AddHost.smk -> build/lib/hecatomb/snakemake/workflow
2024-02-04T06:26:58,873   copying hecatomb/snakemake/workflow/DownloadDB.smk -> build/lib/hecatomb/snakemake/workflow
2024-02-04T06:26:58,877   copying hecatomb/snakemake/workflow/Hecatomb.smk -> build/lib/hecatomb/snakemake/workflow
2024-02-04T06:26:58,879   copying hecatomb/snakemake/workflow/combineOutputs.smk -> build/lib/hecatomb/snakemake/workflow
2024-02-04T06:26:58,882   creating build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,884   copying hecatomb/snakemake/workflow/envs/bbmap.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,886   copying hecatomb/snakemake/workflow/envs/bedtools.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,889   copying hecatomb/snakemake/workflow/envs/canu.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,891   copying hecatomb/snakemake/workflow/envs/curl.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,893   copying hecatomb/snakemake/workflow/envs/koverage.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,896   copying hecatomb/snakemake/workflow/envs/krona.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,898   copying hecatomb/snakemake/workflow/envs/megahit.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,899   copying hecatomb/snakemake/workflow/envs/metaflye.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,900   copying hecatomb/snakemake/workflow/envs/minimap2.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,901   copying hecatomb/snakemake/workflow/envs/mmseqs2.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,902   copying hecatomb/snakemake/workflow/envs/pigz.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,914   copying hecatomb/snakemake/workflow/envs/pysam.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,922   copying hecatomb/snakemake/workflow/envs/samtools.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,959   copying hecatomb/snakemake/workflow/envs/seqkit.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,959   copying hecatomb/snakemake/workflow/envs/trimnami.yaml -> build/lib/hecatomb/snakemake/workflow/envs
2024-02-04T06:26:58,960   creating build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,961   copying hecatomb/snakemake/workflow/report/host_removed_counts.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,961   copying hecatomb/snakemake/workflow/report/mapped_counts.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,962   copying hecatomb/snakemake/workflow/report/nucleotide_annotations.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,962   copying hecatomb/snakemake/workflow/report/protein_annotations.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,963   copying hecatomb/snakemake/workflow/report/raw_read_counts.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,971   copying hecatomb/snakemake/workflow/report/sankey.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,972   copying hecatomb/snakemake/workflow/report/step07.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,972   copying hecatomb/snakemake/workflow/report/step08.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,973   copying hecatomb/snakemake/workflow/report/step09.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,974   copying hecatomb/snakemake/workflow/report/step10.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,974   copying hecatomb/snakemake/workflow/report/step11.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,975   copying hecatomb/snakemake/workflow/report/step12.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,975   copying hecatomb/snakemake/workflow/report/step13.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,976   copying hecatomb/snakemake/workflow/report/summary_table.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,976   copying hecatomb/snakemake/workflow/report/tax_level_counts.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,977   copying hecatomb/snakemake/workflow/report/unclassified_seqtable.rst -> build/lib/hecatomb/snakemake/workflow/report
2024-02-04T06:26:58,977   creating build/lib/hecatomb/snakemake/workflow/rules
2024-02-04T06:26:58,978   creating build/lib/hecatomb/snakemake/workflow/rules/annotation
2024-02-04T06:26:58,978   copying hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation
2024-02-04T06:26:58,979   copying hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation
2024-02-04T06:26:58,979   copying hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation
2024-02-04T06:26:58,980   creating build/lib/hecatomb/snakemake/workflow/rules/assembly
2024-02-04T06:26:58,980   copying hecatomb/snakemake/workflow/rules/assembly/coverage.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly
2024-02-04T06:26:58,981   copying hecatomb/snakemake/workflow/rules/assembly/longreads.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly
2024-02-04T06:26:58,981   copying hecatomb/snakemake/workflow/rules/assembly/shortreads.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly
2024-02-04T06:26:58,982   creating build/lib/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:26:58,983   copying hecatomb/snakemake/workflow/rules/preflight/directories.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:26:58,983   copying hecatomb/snakemake/workflow/rules/preflight/functions.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:26:58,984   copying hecatomb/snakemake/workflow/rules/preflight/targets.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:26:58,985   copying hecatomb/snakemake/workflow/rules/preflight/validate.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:26:58,985   creating build/lib/hecatomb/snakemake/workflow/rules/preprocessing
2024-02-04T06:26:58,986   copying hecatomb/snakemake/workflow/rules/preprocessing/preprocessing.smk -> build/lib/hecatomb/snakemake/workflow/rules/preprocessing
2024-02-04T06:26:58,987   creating build/lib/hecatomb/snakemake/workflow/rules/reports
2024-02-04T06:26:58,987   copying hecatomb/snakemake/workflow/rules/reports/summaries.smk -> build/lib/hecatomb/snakemake/workflow/rules/reports
2024-02-04T06:26:58,988   copying hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk -> build/lib/hecatomb/snakemake/workflow/rules/reports
2024-02-04T06:26:58,988   creating build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:58,989   copying hecatomb/snakemake/workflow/scripts/__init__.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:58,990   copying hecatomb/snakemake/workflow/scripts/aaBigtable.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:58,990   copying hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:58,991   copying hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:58,993   copying hecatomb/snakemake/workflow/scripts/contigCountTable.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:58,994   copying hecatomb/snakemake/workflow/scripts/contigKronaText.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:58,997   copying hecatomb/snakemake/workflow/scripts/contigReadTaxon.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,000   copying hecatomb/snakemake/workflow/scripts/kronaText.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,003   copying hecatomb/snakemake/workflow/scripts/mergeSeqTable.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,015   copying hecatomb/snakemake/workflow/scripts/ntBigtable.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,035   copying hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,052   copying hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,052   copying hecatomb/snakemake/workflow/scripts/orfmFilt.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,055   copying hecatomb/snakemake/workflow/scripts/sankey.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,055   copying hecatomb/snakemake/workflow/scripts/seqPropertyTable.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,056   copying hecatomb/snakemake/workflow/scripts/taxLevelCounts.py -> build/lib/hecatomb/snakemake/workflow/scripts
2024-02-04T06:26:59,056   creating build/lib/hecatomb/test_data
2024-02-04T06:26:59,057   copying hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:26:59,061   copying hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:26:59,061   copying hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:00,092   copying hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:00,266   copying hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:00,449   copying hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:00,605   copying hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:03,365   copying hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:03,535   copying hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:03,628   copying hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:03,756   copying hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:03,829   copying hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:03,900   copying hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:03,969   copying hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:04,042   copying hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:04,128   copying hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:04,204   copying hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:04,281   copying hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:04,367   copying hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:04,447   copying hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz -> build/lib/hecatomb/test_data
2024-02-04T06:27:04,525   copying hecatomb/test_data/test_config.yaml -> build/lib/hecatomb/test_data
2024-02-04T06:27:04,527   file hecatomb.py (for module hecatomb) not found
2024-02-04T06:27:04,552   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-02-04T06:27:04,553   !!

2024-02-04T06:27:04,554           ********************************************************************************
2024-02-04T06:27:04,555           Please avoid running ``setup.py`` directly.
2024-02-04T06:27:04,555           Instead, use pypa/build, pypa/installer or other
2024-02-04T06:27:04,556           standards-based tools.

2024-02-04T06:27:04,557           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-02-04T06:27:04,557           ********************************************************************************

2024-02-04T06:27:04,558   !!
2024-02-04T06:27:04,559     self.initialize_options()
2024-02-04T06:27:04,577   installing to build/bdist.linux-armv7l/wheel
2024-02-04T06:27:04,578   running install
2024-02-04T06:27:04,602   running install_lib
2024-02-04T06:27:04,626   creating build/bdist.linux-armv7l
2024-02-04T06:27:04,627   creating build/bdist.linux-armv7l/wheel
2024-02-04T06:27:04,628   creating build/bdist.linux-armv7l/wheel/hecatomb
2024-02-04T06:27:04,629   copying build/lib/hecatomb/__main__.py -> build/bdist.linux-armv7l/wheel/hecatomb
2024-02-04T06:27:04,632   copying build/lib/hecatomb/hecatomb.CITATION -> build/bdist.linux-armv7l/wheel/hecatomb
2024-02-04T06:27:04,633   copying build/lib/hecatomb/hecatomb.VERSION -> build/bdist.linux-armv7l/wheel/hecatomb
2024-02-04T06:27:04,636   creating build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:04,637   copying build/lib/hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:04,719   copying build/lib/hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:04,799   copying build/lib/hecatomb/test_data/test_config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:04,801   copying build/lib/hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:04,920   copying build/lib/hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:04,993   copying build/lib/hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,067   copying build/lib/hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,139   copying build/lib/hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,217   copying build/lib/hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,300   copying build/lib/hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,385   copying build/lib/hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,464   copying build/lib/hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,528   copying build/lib/hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,602   copying build/lib/hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,670   copying build/lib/hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,749   copying build/lib/hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,824   copying build/lib/hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,890   copying build/lib/hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:05,964   copying build/lib/hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:06,043   copying build/lib/hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:06,121   copying build/lib/hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data
2024-02-04T06:27:06,186   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake
2024-02-04T06:27:06,187   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile
2024-02-04T06:27:06,188   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm
2024-02-04T06:27:06,189   copying build/lib/hecatomb/snakemake/profile/example_slurm/slurm-status.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm
2024-02-04T06:27:06,191   copying build/lib/hecatomb/snakemake/profile/example_slurm/config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm
2024-02-04T06:27:06,193   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config
2024-02-04T06:27:06,194   copying build/lib/hecatomb/snakemake/config/config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config
2024-02-04T06:27:06,196   copying build/lib/hecatomb/snakemake/config/dbFiles.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config
2024-02-04T06:27:06,198   copying build/lib/hecatomb/snakemake/config/immutable.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config
2024-02-04T06:27:06,201   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow
2024-02-04T06:27:06,202   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,203   copying build/lib/hecatomb/snakemake/workflow/envs/mmseqs2.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,205   copying build/lib/hecatomb/snakemake/workflow/envs/samtools.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,207   copying build/lib/hecatomb/snakemake/workflow/envs/seqkit.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,208   copying build/lib/hecatomb/snakemake/workflow/envs/pysam.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,210   copying build/lib/hecatomb/snakemake/workflow/envs/megahit.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,212   copying build/lib/hecatomb/snakemake/workflow/envs/pigz.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,214   copying build/lib/hecatomb/snakemake/workflow/envs/trimnami.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,215   copying build/lib/hecatomb/snakemake/workflow/envs/curl.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,217   copying build/lib/hecatomb/snakemake/workflow/envs/bedtools.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,219   copying build/lib/hecatomb/snakemake/workflow/envs/minimap2.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,220   copying build/lib/hecatomb/snakemake/workflow/envs/bbmap.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,223   copying build/lib/hecatomb/snakemake/workflow/envs/koverage.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,225   copying build/lib/hecatomb/snakemake/workflow/envs/canu.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,227   copying build/lib/hecatomb/snakemake/workflow/envs/metaflye.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,229   copying build/lib/hecatomb/snakemake/workflow/envs/krona.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs
2024-02-04T06:27:06,231   copying build/lib/hecatomb/snakemake/workflow/Hecatomb.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow
2024-02-04T06:27:06,232   copying build/lib/hecatomb/snakemake/workflow/combineOutputs.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow
2024-02-04T06:27:06,235   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,236   copying build/lib/hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,237   copying build/lib/hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,239   copying build/lib/hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,241   copying build/lib/hecatomb/snakemake/workflow/scripts/mergeSeqTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,243   copying build/lib/hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,244   copying build/lib/hecatomb/snakemake/workflow/scripts/taxLevelCounts.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,246   copying build/lib/hecatomb/snakemake/workflow/scripts/contigKronaText.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,248   copying build/lib/hecatomb/snakemake/workflow/scripts/contigCountTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,250   copying build/lib/hecatomb/snakemake/workflow/scripts/aaBigtable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,252   copying build/lib/hecatomb/snakemake/workflow/scripts/ntBigtable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,253   copying build/lib/hecatomb/snakemake/workflow/scripts/seqPropertyTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,255   copying build/lib/hecatomb/snakemake/workflow/scripts/sankey.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,257   copying build/lib/hecatomb/snakemake/workflow/scripts/orfmFilt.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,259   copying build/lib/hecatomb/snakemake/workflow/scripts/kronaText.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,260   copying build/lib/hecatomb/snakemake/workflow/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,262   copying build/lib/hecatomb/snakemake/workflow/scripts/contigReadTaxon.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts
2024-02-04T06:27:06,264   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,265   copying build/lib/hecatomb/snakemake/workflow/report/tax_level_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,267   copying build/lib/hecatomb/snakemake/workflow/report/step07.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,269   copying build/lib/hecatomb/snakemake/workflow/report/raw_read_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,271   copying build/lib/hecatomb/snakemake/workflow/report/step10.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,273   copying build/lib/hecatomb/snakemake/workflow/report/unclassified_seqtable.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,275   copying build/lib/hecatomb/snakemake/workflow/report/step11.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,277   copying build/lib/hecatomb/snakemake/workflow/report/step12.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,279   copying build/lib/hecatomb/snakemake/workflow/report/host_removed_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,281   copying build/lib/hecatomb/snakemake/workflow/report/step08.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,282   copying build/lib/hecatomb/snakemake/workflow/report/step13.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,284   copying build/lib/hecatomb/snakemake/workflow/report/protein_annotations.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,286   copying build/lib/hecatomb/snakemake/workflow/report/step09.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,288   copying build/lib/hecatomb/snakemake/workflow/report/nucleotide_annotations.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,290   copying build/lib/hecatomb/snakemake/workflow/report/sankey.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,292   copying build/lib/hecatomb/snakemake/workflow/report/mapped_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,294   copying build/lib/hecatomb/snakemake/workflow/report/summary_table.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report
2024-02-04T06:27:06,296   copying build/lib/hecatomb/snakemake/workflow/DownloadDB.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow
2024-02-04T06:27:06,298   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules
2024-02-04T06:27:06,300   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation
2024-02-04T06:27:06,301   copying build/lib/hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation
2024-02-04T06:27:06,304   copying build/lib/hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation
2024-02-04T06:27:06,307   copying build/lib/hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation
2024-02-04T06:27:06,310   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:27:06,311   copying build/lib/hecatomb/snakemake/workflow/rules/preflight/validate.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:27:06,314   copying build/lib/hecatomb/snakemake/workflow/rules/preflight/targets.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:27:06,316   copying build/lib/hecatomb/snakemake/workflow/rules/preflight/directories.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:27:06,318   copying build/lib/hecatomb/snakemake/workflow/rules/preflight/functions.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight
2024-02-04T06:27:06,321   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly
2024-02-04T06:27:06,323   copying build/lib/hecatomb/snakemake/workflow/rules/assembly/shortreads.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly
2024-02-04T06:27:06,326   copying build/lib/hecatomb/snakemake/workflow/rules/assembly/longreads.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly
2024-02-04T06:27:06,328   copying build/lib/hecatomb/snakemake/workflow/rules/assembly/coverage.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly
2024-02-04T06:27:06,330   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports
2024-02-04T06:27:06,331   copying build/lib/hecatomb/snakemake/workflow/rules/reports/summaries.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports
2024-02-04T06:27:06,333   copying build/lib/hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports
2024-02-04T06:27:06,336   creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing
2024-02-04T06:27:06,337   copying build/lib/hecatomb/snakemake/workflow/rules/preprocessing/preprocessing.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing
2024-02-04T06:27:06,340   copying build/lib/hecatomb/snakemake/workflow/AddHost.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow
2024-02-04T06:27:06,342   copying build/lib/hecatomb/hecatomb.LICENSE -> build/bdist.linux-armv7l/wheel/hecatomb
2024-02-04T06:27:06,344   copying build/lib/hecatomb/__init__.py -> build/bdist.linux-armv7l/wheel/hecatomb
2024-02-04T06:27:06,345   running install_data
2024-02-04T06:27:06,369   creating build/bdist.linux-armv7l/wheel/hecatomb-1.3.1.data
2024-02-04T06:27:06,370   creating build/bdist.linux-armv7l/wheel/hecatomb-1.3.1.data/data
2024-02-04T06:27:06,371   copying README.md -> build/bdist.linux-armv7l/wheel/hecatomb-1.3.1.data/data/.
2024-02-04T06:27:06,374   running install_egg_info
2024-02-04T06:27:06,404   Copying hecatomb.egg-info to build/bdist.linux-armv7l/wheel/hecatomb-1.3.1-py3.11.egg-info
2024-02-04T06:27:06,417   running install_scripts
2024-02-04T06:27:06,434   creating build/bdist.linux-armv7l/wheel/hecatomb-1.3.1.dist-info/WHEEL
2024-02-04T06:27:06,437   creating '/tmp/pip-wheel-y9zsrxjl/hecatomb-1.3.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-02-04T06:27:06,439   adding 'hecatomb/__init__.py'
2024-02-04T06:27:06,442   adding 'hecatomb/__main__.py'
2024-02-04T06:27:06,444   adding 'hecatomb/hecatomb.CITATION'
2024-02-04T06:27:06,446   adding 'hecatomb/hecatomb.LICENSE'
2024-02-04T06:27:06,447   adding 'hecatomb/hecatomb.VERSION'
2024-02-04T06:27:06,450   adding 'hecatomb/snakemake/config/config.yaml'
2024-02-04T06:27:06,452   adding 'hecatomb/snakemake/config/dbFiles.yaml'
2024-02-04T06:27:06,454   adding 'hecatomb/snakemake/config/immutable.yaml'
2024-02-04T06:27:06,456   adding 'hecatomb/snakemake/profile/example_slurm/config.yaml'
2024-02-04T06:27:06,458   adding 'hecatomb/snakemake/profile/example_slurm/slurm-status.py'
2024-02-04T06:27:06,460   adding 'hecatomb/snakemake/workflow/AddHost.smk'
2024-02-04T06:27:06,462   adding 'hecatomb/snakemake/workflow/DownloadDB.smk'
2024-02-04T06:27:06,464   adding 'hecatomb/snakemake/workflow/Hecatomb.smk'
2024-02-04T06:27:06,466   adding 'hecatomb/snakemake/workflow/combineOutputs.smk'
2024-02-04T06:27:06,468   adding 'hecatomb/snakemake/workflow/envs/bbmap.yaml'
2024-02-04T06:27:06,469   adding 'hecatomb/snakemake/workflow/envs/bedtools.yaml'
2024-02-04T06:27:06,471   adding 'hecatomb/snakemake/workflow/envs/canu.yaml'
2024-02-04T06:27:06,472   adding 'hecatomb/snakemake/workflow/envs/curl.yaml'
2024-02-04T06:27:06,474   adding 'hecatomb/snakemake/workflow/envs/koverage.yaml'
2024-02-04T06:27:06,475   adding 'hecatomb/snakemake/workflow/envs/krona.yaml'
2024-02-04T06:27:06,477   adding 'hecatomb/snakemake/workflow/envs/megahit.yaml'
2024-02-04T06:27:06,478   adding 'hecatomb/snakemake/workflow/envs/metaflye.yaml'
2024-02-04T06:27:06,480   adding 'hecatomb/snakemake/workflow/envs/minimap2.yaml'
2024-02-04T06:27:06,482   adding 'hecatomb/snakemake/workflow/envs/mmseqs2.yaml'
2024-02-04T06:27:06,483   adding 'hecatomb/snakemake/workflow/envs/pigz.yaml'
2024-02-04T06:27:06,484   adding 'hecatomb/snakemake/workflow/envs/pysam.yaml'
2024-02-04T06:27:06,486   adding 'hecatomb/snakemake/workflow/envs/samtools.yaml'
2024-02-04T06:27:06,487   adding 'hecatomb/snakemake/workflow/envs/seqkit.yaml'
2024-02-04T06:27:06,489   adding 'hecatomb/snakemake/workflow/envs/trimnami.yaml'
2024-02-04T06:27:06,491   adding 'hecatomb/snakemake/workflow/report/host_removed_counts.rst'
2024-02-04T06:27:06,492   adding 'hecatomb/snakemake/workflow/report/mapped_counts.rst'
2024-02-04T06:27:06,494   adding 'hecatomb/snakemake/workflow/report/nucleotide_annotations.rst'
2024-02-04T06:27:06,495   adding 'hecatomb/snakemake/workflow/report/protein_annotations.rst'
2024-02-04T06:27:06,497   adding 'hecatomb/snakemake/workflow/report/raw_read_counts.rst'
2024-02-04T06:27:06,498   adding 'hecatomb/snakemake/workflow/report/sankey.rst'
2024-02-04T06:27:06,499   adding 'hecatomb/snakemake/workflow/report/step07.rst'
2024-02-04T06:27:06,501   adding 'hecatomb/snakemake/workflow/report/step08.rst'
2024-02-04T06:27:06,502   adding 'hecatomb/snakemake/workflow/report/step09.rst'
2024-02-04T06:27:06,504   adding 'hecatomb/snakemake/workflow/report/step10.rst'
2024-02-04T06:27:06,505   adding 'hecatomb/snakemake/workflow/report/step11.rst'
2024-02-04T06:27:06,507   adding 'hecatomb/snakemake/workflow/report/step12.rst'
2024-02-04T06:27:06,508   adding 'hecatomb/snakemake/workflow/report/step13.rst'
2024-02-04T06:27:06,510   adding 'hecatomb/snakemake/workflow/report/summary_table.rst'
2024-02-04T06:27:06,511   adding 'hecatomb/snakemake/workflow/report/tax_level_counts.rst'
2024-02-04T06:27:06,513   adding 'hecatomb/snakemake/workflow/report/unclassified_seqtable.rst'
2024-02-04T06:27:06,515   adding 'hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk'
2024-02-04T06:27:06,517   adding 'hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk'
2024-02-04T06:27:06,519   adding 'hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk'
2024-02-04T06:27:06,521   adding 'hecatomb/snakemake/workflow/rules/assembly/coverage.smk'
2024-02-04T06:27:06,523   adding 'hecatomb/snakemake/workflow/rules/assembly/longreads.smk'
2024-02-04T06:27:06,525   adding 'hecatomb/snakemake/workflow/rules/assembly/shortreads.smk'
2024-02-04T06:27:06,527   adding 'hecatomb/snakemake/workflow/rules/preflight/directories.smk'
2024-02-04T06:27:06,529   adding 'hecatomb/snakemake/workflow/rules/preflight/functions.smk'
2024-02-04T06:27:06,531   adding 'hecatomb/snakemake/workflow/rules/preflight/targets.smk'
2024-02-04T06:27:06,532   adding 'hecatomb/snakemake/workflow/rules/preflight/validate.smk'
2024-02-04T06:27:06,535   adding 'hecatomb/snakemake/workflow/rules/preprocessing/preprocessing.smk'
2024-02-04T06:27:06,537   adding 'hecatomb/snakemake/workflow/rules/reports/summaries.smk'
2024-02-04T06:27:06,538   adding 'hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk'
2024-02-04T06:27:06,540   adding 'hecatomb/snakemake/workflow/scripts/__init__.py'
2024-02-04T06:27:06,542   adding 'hecatomb/snakemake/workflow/scripts/aaBigtable.py'
2024-02-04T06:27:06,544   adding 'hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py'
2024-02-04T06:27:06,545   adding 'hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py'
2024-02-04T06:27:06,547   adding 'hecatomb/snakemake/workflow/scripts/contigCountTable.py'
2024-02-04T06:27:06,548   adding 'hecatomb/snakemake/workflow/scripts/contigKronaText.py'
2024-02-04T06:27:06,550   adding 'hecatomb/snakemake/workflow/scripts/contigReadTaxon.py'
2024-02-04T06:27:06,551   adding 'hecatomb/snakemake/workflow/scripts/kronaText.py'
2024-02-04T06:27:06,553   adding 'hecatomb/snakemake/workflow/scripts/mergeSeqTable.py'
2024-02-04T06:27:06,555   adding 'hecatomb/snakemake/workflow/scripts/ntBigtable.py'
2024-02-04T06:27:06,556   adding 'hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py'
2024-02-04T06:27:06,558   adding 'hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py'
2024-02-04T06:27:06,560   adding 'hecatomb/snakemake/workflow/scripts/orfmFilt.py'
2024-02-04T06:27:06,561   adding 'hecatomb/snakemake/workflow/scripts/sankey.py'
2024-02-04T06:27:06,563   adding 'hecatomb/snakemake/workflow/scripts/seqPropertyTable.py'
2024-02-04T06:27:06,565   adding 'hecatomb/snakemake/workflow/scripts/taxLevelCounts.py'
2024-02-04T06:27:07,074   adding 'hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz'
2024-02-04T06:27:07,652   adding 'hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz'
2024-02-04T06:27:08,226   adding 'hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz'
2024-02-04T06:27:08,808   adding 'hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz'
2024-02-04T06:27:09,335   adding 'hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz'
2024-02-04T06:27:09,907   adding 'hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz'
2024-02-04T06:27:10,445   adding 'hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz'
2024-02-04T06:27:11,035   adding 'hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz'
2024-02-04T06:27:11,587   adding 'hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz'
2024-02-04T06:27:12,201   adding 'hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz'
2024-02-04T06:27:12,717   adding 'hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz'
2024-02-04T06:27:13,355   adding 'hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz'
2024-02-04T06:27:13,901   adding 'hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz'
2024-02-04T06:27:14,436   adding 'hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz'
2024-02-04T06:27:15,019   adding 'hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz'
2024-02-04T06:27:15,621   adding 'hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz'
2024-02-04T06:27:16,284   adding 'hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz'
2024-02-04T06:27:16,856   adding 'hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz'
2024-02-04T06:27:17,370   adding 'hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz'
2024-02-04T06:27:17,966   adding 'hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz'
2024-02-04T06:27:18,000   adding 'hecatomb/test_data/test_config.yaml'
2024-02-04T06:27:18,003   adding 'hecatomb-1.3.1.data/data/README.md'
2024-02-04T06:27:18,005   adding 'hecatomb-1.3.1.dist-info/LICENSE'
2024-02-04T06:27:18,007   adding 'hecatomb-1.3.1.dist-info/METADATA'
2024-02-04T06:27:18,008   adding 'hecatomb-1.3.1.dist-info/WHEEL'
2024-02-04T06:27:18,009   adding 'hecatomb-1.3.1.dist-info/entry_points.txt'
2024-02-04T06:27:18,011   adding 'hecatomb-1.3.1.dist-info/top_level.txt'
2024-02-04T06:27:18,013   adding 'hecatomb-1.3.1.dist-info/RECORD'
2024-02-04T06:27:18,931   removing build/bdist.linux-armv7l/wheel
2024-02-04T06:27:19,211   Building wheel for hecatomb (setup.py): finished with status 'done'
2024-02-04T06:27:21,580   Created wheel for hecatomb: filename=hecatomb-1.3.1-py3-none-any.whl size=98564592 sha256=8f0817abc80281adfc7773bdc4a03ddc88bf1432032a5e8440dba75f23489930
2024-02-04T06:27:21,581   Stored in directory: /tmp/pip-ephem-wheel-cache-y_r5jb50/wheels/2a/f7/66/36a731d5070409a4a7cf98d49b0ca0dcb0ec16244aeb8301fa
2024-02-04T06:27:21,625 Successfully built hecatomb
2024-02-04T06:27:23,934 Removed build tracker: '/tmp/pip-build-tracker-rgm1mc8y'