2024-02-01T05:17:55,379 Created temporary directory: /tmp/pip-build-tracker-n3403wvk 2024-02-01T05:17:55,381 Initialized build tracking at /tmp/pip-build-tracker-n3403wvk 2024-02-01T05:17:55,382 Created build tracker: /tmp/pip-build-tracker-n3403wvk 2024-02-01T05:17:55,382 Entered build tracker: /tmp/pip-build-tracker-n3403wvk 2024-02-01T05:17:55,385 Created temporary directory: /tmp/pip-wheel-r3r9kvmx 2024-02-01T05:17:55,388 Created temporary directory: /tmp/pip-ephem-wheel-cache-0tdhw68u 2024-02-01T05:17:55,421 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-02-01T05:17:55,424 2 location(s) to search for versions of hecatomb: 2024-02-01T05:17:55,424 * https://pypi.org/simple/hecatomb/ 2024-02-01T05:17:55,424 * https://www.piwheels.org/simple/hecatomb/ 2024-02-01T05:17:55,425 Fetching project page and analyzing links: https://pypi.org/simple/hecatomb/ 2024-02-01T05:17:55,426 Getting page https://pypi.org/simple/hecatomb/ 2024-02-01T05:17:55,428 Found index url https://pypi.org/simple/ 2024-02-01T05:17:55,650 Fetched page https://pypi.org/simple/hecatomb/ as application/vnd.pypi.simple.v1+json 2024-02-01T05:17:55,683 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) 2024-02-01T05:17:55,691 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 2024-02-01T05:17:55,699 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) 2024-02-01T05:17:55,700 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 2024-02-01T05:17:55,711 Fetching project page and analyzing links: https://www.piwheels.org/simple/hecatomb/ 2024-02-01T05:17:55,712 Getting page https://www.piwheels.org/simple/hecatomb/ 2024-02-01T05:17:55,713 Found index url https://www.piwheels.org/simple/ 2024-02-01T05:18:01,179 Fetched page https://www.piwheels.org/simple/hecatomb/ as text/html 2024-02-01T05:18:01,187 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) 2024-02-01T05:18:01,189 Skipping link: not a file: https://www.piwheels.org/simple/hecatomb/ 2024-02-01T05:18:01,191 Skipping link: not a file: https://pypi.org/simple/hecatomb/ 2024-02-01T05:18:01,243 Given no hashes to check 1 links for project 'hecatomb': discarding no candidates 2024-02-01T05:18:01,280 Collecting hecatomb==1.3.0 2024-02-01T05:18:01,285 Created temporary directory: /tmp/pip-unpack-lcwctpdv 2024-02-01T05:18:01,525 Downloading hecatomb-1.3.0.tar.gz (98.5 MB) 2024-02-01T05:18:37,165 Added hecatomb==1.3.0 from https://files.pythonhosted.org/packages/ce/56/2dab4a7325b279174f9da6f0a213f655f4e031363974e67130ffc24261e8/hecatomb-1.3.0.tar.gz to build tracker '/tmp/pip-build-tracker-n3403wvk' 2024-02-01T05:18:37,167 Running setup.py (path:/tmp/pip-wheel-r3r9kvmx/hecatomb_d94f6981485e48bfa537702e5eb3889e/setup.py) egg_info for package hecatomb 2024-02-01T05:18:37,169 Created temporary directory: /tmp/pip-pip-egg-info-ha3268l4 2024-02-01T05:18:37,169 Preparing metadata (setup.py): started 2024-02-01T05:18:37,171 Running command python setup.py egg_info 2024-02-01T05:18:46,188 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing 'v1.3.0' to '1.3.0' 2024-02-01T05:18:46,188 self.metadata.version = self._normalize_version(self.metadata.version) 2024-02-01T05:18:46,256 running egg_info 2024-02-01T05:18:46,257 creating /tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info 2024-02-01T05:18:46,296 writing /tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info/PKG-INFO 2024-02-01T05:18:46,303 writing dependency_links to /tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info/dependency_links.txt 2024-02-01T05:18:46,305 writing entry points to /tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info/entry_points.txt 2024-02-01T05:18:46,307 writing requirements to /tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info/requires.txt 2024-02-01T05:18:46,308 writing top-level names to /tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info/top_level.txt 2024-02-01T05:18:46,310 writing manifest file '/tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info/SOURCES.txt' 2024-02-01T05:18:46,395 file hecatomb.py (for module hecatomb) not found 2024-02-01T05:18:46,437 reading manifest file '/tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info/SOURCES.txt' 2024-02-01T05:18:46,439 reading manifest template 'MANIFEST.in' 2024-02-01T05:18:46,512 warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/conda/' 2024-02-01T05:18:46,513 warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/databases/' 2024-02-01T05:18:46,514 adding license file 'LICENSE' 2024-02-01T05:18:46,518 writing manifest file '/tmp/pip-pip-egg-info-ha3268l4/hecatomb.egg-info/SOURCES.txt' 2024-02-01T05:18:46,626 Preparing metadata (setup.py): finished with status 'done' 2024-02-01T05:18:46,631 Source in /tmp/pip-wheel-r3r9kvmx/hecatomb_d94f6981485e48bfa537702e5eb3889e has version 1.3.0, which satisfies requirement hecatomb==1.3.0 from https://files.pythonhosted.org/packages/ce/56/2dab4a7325b279174f9da6f0a213f655f4e031363974e67130ffc24261e8/hecatomb-1.3.0.tar.gz 2024-02-01T05:18:46,632 Removed hecatomb==1.3.0 from https://files.pythonhosted.org/packages/ce/56/2dab4a7325b279174f9da6f0a213f655f4e031363974e67130ffc24261e8/hecatomb-1.3.0.tar.gz from build tracker '/tmp/pip-build-tracker-n3403wvk' 2024-02-01T05:18:46,639 Created temporary directory: /tmp/pip-unpack-e85ljdu2 2024-02-01T05:18:46,640 Created temporary directory: /tmp/pip-unpack-07fijzs0 2024-02-01T05:18:46,654 Building wheels for collected packages: hecatomb 2024-02-01T05:18:46,661 Created temporary directory: /tmp/pip-wheel-pjzfwp00 2024-02-01T05:18:46,661 Building wheel for hecatomb (setup.py): started 2024-02-01T05:18:46,663 Destination directory: /tmp/pip-wheel-pjzfwp00 2024-02-01T05:18:46,664 Running command python setup.py bdist_wheel 2024-02-01T05:18:48,052 /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:314: InformationOnly: Normalizing 'v1.3.0' to '1.3.0' 2024-02-01T05:18:48,052 self.metadata.version = self._normalize_version(self.metadata.version) 2024-02-01T05:18:48,100 running bdist_wheel 2024-02-01T05:18:48,248 running build 2024-02-01T05:18:48,249 running build_py 2024-02-01T05:18:48,287 file hecatomb.py (for module hecatomb) not found 2024-02-01T05:18:48,288 creating build 2024-02-01T05:18:48,289 creating build/lib 2024-02-01T05:18:48,290 creating build/lib/hecatomb 2024-02-01T05:18:48,291 copying hecatomb/__main__.py -> build/lib/hecatomb 2024-02-01T05:18:48,295 copying hecatomb/__init__.py -> build/lib/hecatomb 2024-02-01T05:18:48,296 running egg_info 2024-02-01T05:18:48,380 writing hecatomb.egg-info/PKG-INFO 2024-02-01T05:18:48,384 writing dependency_links to hecatomb.egg-info/dependency_links.txt 2024-02-01T05:18:48,386 writing entry points to hecatomb.egg-info/entry_points.txt 2024-02-01T05:18:48,388 writing requirements to hecatomb.egg-info/requires.txt 2024-02-01T05:18:48,389 writing top-level names to hecatomb.egg-info/top_level.txt 2024-02-01T05:18:48,392 file hecatomb.py (for module hecatomb) not found 2024-02-01T05:18:48,428 reading manifest file 'hecatomb.egg-info/SOURCES.txt' 2024-02-01T05:18:48,432 reading manifest template 'MANIFEST.in' 2024-02-01T05:18:48,481 warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/conda/' 2024-02-01T05:18:48,482 warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/databases/' 2024-02-01T05:18:48,483 adding license file 'LICENSE' 2024-02-01T05:18:48,488 writing manifest file 'hecatomb.egg-info/SOURCES.txt' 2024-02-01T05:18:48,491 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.config' is absent from the `packages` configuration. 2024-02-01T05:18:48,492 !! 2024-02-01T05:18:48,493 ******************************************************************************** 2024-02-01T05:18:48,493 ############################ 2024-02-01T05:18:48,493 # Package would be ignored # 2024-02-01T05:18:48,494 ############################ 2024-02-01T05:18:48,494 Python recognizes 'hecatomb.snakemake.config' as an importable package[^1], 2024-02-01T05:18:48,495 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:48,496 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:48,496 package, please make sure that 'hecatomb.snakemake.config' is explicitly added 2024-02-01T05:18:48,497 to the `packages` configuration field. 2024-02-01T05:18:48,498 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:48,498 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:48,499 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:48,500 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:48,501 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:48,502 If you don't want 'hecatomb.snakemake.config' to be distributed and are 2024-02-01T05:18:48,503 already explicitly excluding 'hecatomb.snakemake.config' via 2024-02-01T05:18:48,503 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:48,504 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:48,505 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:48,506 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:48,507 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:48,509 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:48,509 even if it does not contain any `.py` files. 2024-02-01T05:18:48,510 On the other hand, currently there is no concept of package data 2024-02-01T05:18:48,511 directory, all directories are treated like packages. 2024-02-01T05:18:48,511 ******************************************************************************** 2024-02-01T05:18:48,512 !! 2024-02-01T05:18:48,513 check.warn(importable) 2024-02-01T05:18:48,514 /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. 2024-02-01T05:18:48,514 !! 2024-02-01T05:18:48,516 ******************************************************************************** 2024-02-01T05:18:48,516 ############################ 2024-02-01T05:18:48,517 # Package would be ignored # 2024-02-01T05:18:48,517 ############################ 2024-02-01T05:18:48,518 Python recognizes 'hecatomb.snakemake.profile.example_slurm' as an importable package[^1], 2024-02-01T05:18:48,518 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:48,519 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:48,520 package, please make sure that 'hecatomb.snakemake.profile.example_slurm' is explicitly added 2024-02-01T05:18:48,521 to the `packages` configuration field. 2024-02-01T05:18:48,522 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:48,522 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:48,523 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:48,524 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:48,525 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:48,526 If you don't want 'hecatomb.snakemake.profile.example_slurm' to be distributed and are 2024-02-01T05:18:48,527 already explicitly excluding 'hecatomb.snakemake.profile.example_slurm' via 2024-02-01T05:18:48,534 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:48,538 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:48,539 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:48,541 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:48,542 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:48,544 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:48,544 even if it does not contain any `.py` files. 2024-02-01T05:18:48,545 On the other hand, currently there is no concept of package data 2024-02-01T05:18:48,545 directory, all directories are treated like packages. 2024-02-01T05:18:48,546 ******************************************************************************** 2024-02-01T05:18:48,547 !! 2024-02-01T05:18:48,547 check.warn(importable) 2024-02-01T05:18:48,548 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.snakemake.workflow' is absent from the `packages` configuration. 2024-02-01T05:18:48,548 !! 2024-02-01T05:18:48,549 ******************************************************************************** 2024-02-01T05:18:48,550 ############################ 2024-02-01T05:18:48,550 # Package would be ignored # 2024-02-01T05:18:48,551 ############################ 2024-02-01T05:18:48,552 Python recognizes 'hecatomb.snakemake.workflow' as an importable package[^1], 2024-02-01T05:18:48,552 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:48,553 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:48,554 package, please make sure that 'hecatomb.snakemake.workflow' is explicitly added 2024-02-01T05:18:48,554 to the `packages` configuration field. 2024-02-01T05:18:48,587 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:48,758 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:48,943 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:49,292 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:49,826 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:49,999 If you don't want 'hecatomb.snakemake.workflow' to be distributed and are 2024-02-01T05:18:50,065 already explicitly excluding 'hecatomb.snakemake.workflow' via 2024-02-01T05:18:50,144 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:50,303 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:50,304 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:50,308 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:50,311 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:50,316 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:50,317 even if it does not contain any `.py` files. 2024-02-01T05:18:50,318 On the other hand, currently there is no concept of package data 2024-02-01T05:18:50,319 directory, all directories are treated like packages. 2024-02-01T05:18:50,319 ******************************************************************************** 2024-02-01T05:18:50,321 !! 2024-02-01T05:18:50,322 check.warn(importable) 2024-02-01T05:18:50,323 /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. 2024-02-01T05:18:50,324 !! 2024-02-01T05:18:50,326 ******************************************************************************** 2024-02-01T05:18:50,327 ############################ 2024-02-01T05:18:50,328 # Package would be ignored # 2024-02-01T05:18:50,329 ############################ 2024-02-01T05:18:50,329 Python recognizes 'hecatomb.snakemake.workflow.envs' as an importable package[^1], 2024-02-01T05:18:50,330 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:50,352 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:50,353 package, please make sure that 'hecatomb.snakemake.workflow.envs' is explicitly added 2024-02-01T05:18:50,354 to the `packages` configuration field. 2024-02-01T05:18:50,356 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:50,357 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:50,358 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:50,375 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:50,377 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:50,383 If you don't want 'hecatomb.snakemake.workflow.envs' to be distributed and are 2024-02-01T05:18:50,384 already explicitly excluding 'hecatomb.snakemake.workflow.envs' via 2024-02-01T05:18:50,385 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:50,386 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:50,387 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:50,435 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:50,442 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:50,445 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:50,463 even if it does not contain any `.py` files. 2024-02-01T05:18:50,464 On the other hand, currently there is no concept of package data 2024-02-01T05:18:50,475 directory, all directories are treated like packages. 2024-02-01T05:18:50,476 ******************************************************************************** 2024-02-01T05:18:50,479 !! 2024-02-01T05:18:50,480 check.warn(importable) 2024-02-01T05:18:50,481 /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. 2024-02-01T05:18:50,482 !! 2024-02-01T05:18:50,572 ******************************************************************************** 2024-02-01T05:18:50,573 ############################ 2024-02-01T05:18:50,579 # Package would be ignored # 2024-02-01T05:18:50,581 ############################ 2024-02-01T05:18:50,587 Python recognizes 'hecatomb.snakemake.workflow.report' as an importable package[^1], 2024-02-01T05:18:50,588 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:50,590 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:50,591 package, please make sure that 'hecatomb.snakemake.workflow.report' is explicitly added 2024-02-01T05:18:50,607 to the `packages` configuration field. 2024-02-01T05:18:50,609 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:50,610 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:50,611 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:50,644 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:50,651 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:50,653 If you don't want 'hecatomb.snakemake.workflow.report' to be distributed and are 2024-02-01T05:18:50,653 already explicitly excluding 'hecatomb.snakemake.workflow.report' via 2024-02-01T05:18:50,671 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:50,679 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:50,680 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:50,682 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:50,684 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:50,689 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:50,792 even if it does not contain any `.py` files. 2024-02-01T05:18:50,793 On the other hand, currently there is no concept of package data 2024-02-01T05:18:50,799 directory, all directories are treated like packages. 2024-02-01T05:18:50,801 ******************************************************************************** 2024-02-01T05:18:50,804 !! 2024-02-01T05:18:50,810 check.warn(importable) 2024-02-01T05:18:50,828 /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. 2024-02-01T05:18:50,839 !! 2024-02-01T05:18:51,226 ******************************************************************************** 2024-02-01T05:18:51,228 ############################ 2024-02-01T05:18:51,461 # Package would be ignored # 2024-02-01T05:18:51,556 ############################ 2024-02-01T05:18:51,560 Python recognizes 'hecatomb.snakemake.workflow.rules.annotation' as an importable package[^1], 2024-02-01T05:18:51,633 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:51,812 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:51,874 package, please make sure that 'hecatomb.snakemake.workflow.rules.annotation' is explicitly added 2024-02-01T05:18:52,456 to the `packages` configuration field. 2024-02-01T05:18:52,681 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:52,746 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:52,789 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:53,289 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:53,329 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:53,332 If you don't want 'hecatomb.snakemake.workflow.rules.annotation' to be distributed and are 2024-02-01T05:18:53,333 already explicitly excluding 'hecatomb.snakemake.workflow.rules.annotation' via 2024-02-01T05:18:53,333 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:53,334 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:53,335 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:53,337 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:53,339 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:53,342 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:53,343 even if it does not contain any `.py` files. 2024-02-01T05:18:53,344 On the other hand, currently there is no concept of package data 2024-02-01T05:18:53,345 directory, all directories are treated like packages. 2024-02-01T05:18:53,346 ******************************************************************************** 2024-02-01T05:18:53,348 !! 2024-02-01T05:18:53,349 check.warn(importable) 2024-02-01T05:18:53,350 /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. 2024-02-01T05:18:53,351 !! 2024-02-01T05:18:53,353 ******************************************************************************** 2024-02-01T05:18:53,354 ############################ 2024-02-01T05:18:53,355 # Package would be ignored # 2024-02-01T05:18:53,355 ############################ 2024-02-01T05:18:53,356 Python recognizes 'hecatomb.snakemake.workflow.rules.assembly' as an importable package[^1], 2024-02-01T05:18:53,357 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:53,359 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:53,360 package, please make sure that 'hecatomb.snakemake.workflow.rules.assembly' is explicitly added 2024-02-01T05:18:53,361 to the `packages` configuration field. 2024-02-01T05:18:53,363 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:53,364 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:53,365 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:53,367 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:53,369 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:53,371 If you don't want 'hecatomb.snakemake.workflow.rules.assembly' to be distributed and are 2024-02-01T05:18:53,372 already explicitly excluding 'hecatomb.snakemake.workflow.rules.assembly' via 2024-02-01T05:18:53,373 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:53,374 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:53,375 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:53,377 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:53,379 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:53,382 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:53,383 even if it does not contain any `.py` files. 2024-02-01T05:18:53,384 On the other hand, currently there is no concept of package data 2024-02-01T05:18:53,385 directory, all directories are treated like packages. 2024-02-01T05:18:53,387 ******************************************************************************** 2024-02-01T05:18:53,388 !! 2024-02-01T05:18:53,389 check.warn(importable) 2024-02-01T05:18:53,390 /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. 2024-02-01T05:18:53,391 !! 2024-02-01T05:18:53,393 ******************************************************************************** 2024-02-01T05:18:53,394 ############################ 2024-02-01T05:18:53,395 # Package would be ignored # 2024-02-01T05:18:53,396 ############################ 2024-02-01T05:18:53,397 Python recognizes 'hecatomb.snakemake.workflow.rules.preflight' as an importable package[^1], 2024-02-01T05:18:53,398 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:53,400 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:53,401 package, please make sure that 'hecatomb.snakemake.workflow.rules.preflight' is explicitly added 2024-02-01T05:18:53,401 to the `packages` configuration field. 2024-02-01T05:18:53,403 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:53,404 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:53,405 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:53,407 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:53,408 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:53,410 If you don't want 'hecatomb.snakemake.workflow.rules.preflight' to be distributed and are 2024-02-01T05:18:53,411 already explicitly excluding 'hecatomb.snakemake.workflow.rules.preflight' via 2024-02-01T05:18:53,411 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:53,412 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:53,413 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:53,415 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:53,416 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:53,418 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:53,419 even if it does not contain any `.py` files. 2024-02-01T05:18:53,420 On the other hand, currently there is no concept of package data 2024-02-01T05:18:53,421 directory, all directories are treated like packages. 2024-02-01T05:18:53,421 ******************************************************************************** 2024-02-01T05:18:53,423 !! 2024-02-01T05:18:53,423 check.warn(importable) 2024-02-01T05:18:53,424 /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. 2024-02-01T05:18:53,425 !! 2024-02-01T05:18:53,427 ******************************************************************************** 2024-02-01T05:18:53,427 ############################ 2024-02-01T05:18:53,428 # Package would be ignored # 2024-02-01T05:18:53,429 ############################ 2024-02-01T05:18:53,429 Python recognizes 'hecatomb.snakemake.workflow.rules.preprocessing' as an importable package[^1], 2024-02-01T05:18:53,430 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:53,432 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:53,432 package, please make sure that 'hecatomb.snakemake.workflow.rules.preprocessing' is explicitly added 2024-02-01T05:18:53,434 to the `packages` configuration field. 2024-02-01T05:18:53,435 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:53,436 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:53,436 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:53,438 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:53,440 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:53,442 If you don't want 'hecatomb.snakemake.workflow.rules.preprocessing' to be distributed and are 2024-02-01T05:18:53,443 already explicitly excluding 'hecatomb.snakemake.workflow.rules.preprocessing' via 2024-02-01T05:18:53,443 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:53,444 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:53,445 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:53,446 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:53,448 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:53,449 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:53,450 even if it does not contain any `.py` files. 2024-02-01T05:18:53,451 On the other hand, currently there is no concept of package data 2024-02-01T05:18:53,451 directory, all directories are treated like packages. 2024-02-01T05:18:53,452 ******************************************************************************** 2024-02-01T05:18:53,454 !! 2024-02-01T05:18:53,455 check.warn(importable) 2024-02-01T05:18:53,456 /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. 2024-02-01T05:18:53,457 !! 2024-02-01T05:18:53,458 ******************************************************************************** 2024-02-01T05:18:53,459 ############################ 2024-02-01T05:18:53,459 # Package would be ignored # 2024-02-01T05:18:53,460 ############################ 2024-02-01T05:18:53,461 Python recognizes 'hecatomb.snakemake.workflow.rules.reports' as an importable package[^1], 2024-02-01T05:18:53,461 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:53,463 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:53,464 package, please make sure that 'hecatomb.snakemake.workflow.rules.reports' is explicitly added 2024-02-01T05:18:53,465 to the `packages` configuration field. 2024-02-01T05:18:53,466 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:53,467 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:53,468 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:53,469 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:53,471 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:53,473 If you don't want 'hecatomb.snakemake.workflow.rules.reports' to be distributed and are 2024-02-01T05:18:53,473 already explicitly excluding 'hecatomb.snakemake.workflow.rules.reports' via 2024-02-01T05:18:53,474 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:53,475 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:53,476 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:53,477 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:53,479 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:53,480 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:53,481 even if it does not contain any `.py` files. 2024-02-01T05:18:53,482 On the other hand, currently there is no concept of package data 2024-02-01T05:18:53,483 directory, all directories are treated like packages. 2024-02-01T05:18:53,483 ******************************************************************************** 2024-02-01T05:18:53,484 !! 2024-02-01T05:18:53,485 check.warn(importable) 2024-02-01T05:18:53,486 /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. 2024-02-01T05:18:53,487 !! 2024-02-01T05:18:53,488 ******************************************************************************** 2024-02-01T05:18:53,488 ############################ 2024-02-01T05:18:53,489 # Package would be ignored # 2024-02-01T05:18:53,490 ############################ 2024-02-01T05:18:53,490 Python recognizes 'hecatomb.snakemake.workflow.scripts' as an importable package[^1], 2024-02-01T05:18:53,491 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:53,492 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:53,493 package, please make sure that 'hecatomb.snakemake.workflow.scripts' is explicitly added 2024-02-01T05:18:53,494 to the `packages` configuration field. 2024-02-01T05:18:53,495 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:53,496 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:53,496 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:53,498 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:53,499 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:53,501 If you don't want 'hecatomb.snakemake.workflow.scripts' to be distributed and are 2024-02-01T05:18:53,501 already explicitly excluding 'hecatomb.snakemake.workflow.scripts' via 2024-02-01T05:18:53,502 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:53,503 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:53,504 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:53,506 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:53,507 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:53,510 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:53,511 even if it does not contain any `.py` files. 2024-02-01T05:18:53,512 On the other hand, currently there is no concept of package data 2024-02-01T05:18:53,512 directory, all directories are treated like packages. 2024-02-01T05:18:53,513 ******************************************************************************** 2024-02-01T05:18:53,514 !! 2024-02-01T05:18:53,515 check.warn(importable) 2024-02-01T05:18:53,516 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'hecatomb.test_data' is absent from the `packages` configuration. 2024-02-01T05:18:53,517 !! 2024-02-01T05:18:53,518 ******************************************************************************** 2024-02-01T05:18:53,519 ############################ 2024-02-01T05:18:53,520 # Package would be ignored # 2024-02-01T05:18:53,520 ############################ 2024-02-01T05:18:53,521 Python recognizes 'hecatomb.test_data' as an importable package[^1], 2024-02-01T05:18:53,522 but it is absent from setuptools' `packages` configuration. 2024-02-01T05:18:53,523 This leads to an ambiguous overall configuration. If you want to distribute this 2024-02-01T05:18:53,524 package, please make sure that 'hecatomb.test_data' is explicitly added 2024-02-01T05:18:53,524 to the `packages` configuration field. 2024-02-01T05:18:53,526 Alternatively, you can also rely on setuptools' discovery methods 2024-02-01T05:18:53,527 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-02-01T05:18:53,528 instead of `find_packages(...)`/`find:`). 2024-02-01T05:18:53,530 You can read more about "package discovery" on setuptools documentation page: 2024-02-01T05:18:53,531 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-02-01T05:18:53,532 If you don't want 'hecatomb.test_data' to be distributed and are 2024-02-01T05:18:53,533 already explicitly excluding 'hecatomb.test_data' via 2024-02-01T05:18:53,534 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-02-01T05:18:53,534 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-02-01T05:18:53,535 combination with a more fine grained `package-data` configuration. 2024-02-01T05:18:53,536 You can read more about "package data files" on setuptools documentation page: 2024-02-01T05:18:53,538 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-02-01T05:18:53,540 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-02-01T05:18:53,541 even if it does not contain any `.py` files. 2024-02-01T05:18:53,542 On the other hand, currently there is no concept of package data 2024-02-01T05:18:53,542 directory, all directories are treated like packages. 2024-02-01T05:18:53,543 ******************************************************************************** 2024-02-01T05:18:53,544 !! 2024-02-01T05:18:53,545 check.warn(importable) 2024-02-01T05:18:53,546 copying hecatomb/hecatomb.CITATION -> build/lib/hecatomb 2024-02-01T05:18:53,546 copying hecatomb/hecatomb.LICENSE -> build/lib/hecatomb 2024-02-01T05:18:53,547 copying hecatomb/hecatomb.VERSION -> build/lib/hecatomb 2024-02-01T05:18:53,548 creating build/lib/hecatomb/snakemake 2024-02-01T05:18:53,548 creating build/lib/hecatomb/snakemake/config 2024-02-01T05:18:53,550 copying hecatomb/snakemake/config/config.yaml -> build/lib/hecatomb/snakemake/config 2024-02-01T05:18:53,551 copying hecatomb/snakemake/config/dbFiles.yaml -> build/lib/hecatomb/snakemake/config 2024-02-01T05:18:53,552 copying hecatomb/snakemake/config/immutable.yaml -> build/lib/hecatomb/snakemake/config 2024-02-01T05:18:53,552 creating build/lib/hecatomb/snakemake/profile 2024-02-01T05:18:53,553 creating build/lib/hecatomb/snakemake/profile/example_slurm 2024-02-01T05:18:53,554 copying hecatomb/snakemake/profile/example_slurm/config.yaml -> build/lib/hecatomb/snakemake/profile/example_slurm 2024-02-01T05:18:53,555 copying hecatomb/snakemake/profile/example_slurm/slurm-status.py -> build/lib/hecatomb/snakemake/profile/example_slurm 2024-02-01T05:18:53,556 creating build/lib/hecatomb/snakemake/workflow 2024-02-01T05:18:53,557 copying hecatomb/snakemake/workflow/AddHost.smk -> build/lib/hecatomb/snakemake/workflow 2024-02-01T05:18:53,558 copying hecatomb/snakemake/workflow/DownloadDB.smk -> build/lib/hecatomb/snakemake/workflow 2024-02-01T05:18:53,560 copying hecatomb/snakemake/workflow/Hecatomb.smk -> build/lib/hecatomb/snakemake/workflow 2024-02-01T05:18:53,560 copying hecatomb/snakemake/workflow/combineOutputs.smk -> build/lib/hecatomb/snakemake/workflow 2024-02-01T05:18:53,562 creating build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,562 copying hecatomb/snakemake/workflow/envs/bbmap.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,563 copying hecatomb/snakemake/workflow/envs/bedtools.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,563 copying hecatomb/snakemake/workflow/envs/canu.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,564 copying hecatomb/snakemake/workflow/envs/curl.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,565 copying hecatomb/snakemake/workflow/envs/koverage.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,566 copying hecatomb/snakemake/workflow/envs/krona.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,567 copying hecatomb/snakemake/workflow/envs/megahit.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,567 copying hecatomb/snakemake/workflow/envs/metaflye.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,568 copying hecatomb/snakemake/workflow/envs/minimap2.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,569 copying hecatomb/snakemake/workflow/envs/mmseqs2.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,569 copying hecatomb/snakemake/workflow/envs/pigz.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,570 copying hecatomb/snakemake/workflow/envs/pysam.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,571 copying hecatomb/snakemake/workflow/envs/samtools.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,572 copying hecatomb/snakemake/workflow/envs/seqkit.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,572 copying hecatomb/snakemake/workflow/envs/trimnami.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2024-02-01T05:18:53,573 creating build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,574 copying hecatomb/snakemake/workflow/report/host_removed_counts.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,575 copying hecatomb/snakemake/workflow/report/mapped_counts.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,575 copying hecatomb/snakemake/workflow/report/nucleotide_annotations.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,576 copying hecatomb/snakemake/workflow/report/protein_annotations.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,577 copying hecatomb/snakemake/workflow/report/raw_read_counts.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,578 copying hecatomb/snakemake/workflow/report/sankey.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,579 copying hecatomb/snakemake/workflow/report/step07.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,580 copying hecatomb/snakemake/workflow/report/step08.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,580 copying hecatomb/snakemake/workflow/report/step09.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,581 copying hecatomb/snakemake/workflow/report/step10.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,582 copying hecatomb/snakemake/workflow/report/step11.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,583 copying hecatomb/snakemake/workflow/report/step12.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,584 copying hecatomb/snakemake/workflow/report/step13.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,584 copying hecatomb/snakemake/workflow/report/summary_table.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,585 copying hecatomb/snakemake/workflow/report/tax_level_counts.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,586 copying hecatomb/snakemake/workflow/report/unclassified_seqtable.rst -> build/lib/hecatomb/snakemake/workflow/report 2024-02-01T05:18:53,587 creating build/lib/hecatomb/snakemake/workflow/rules 2024-02-01T05:18:53,588 creating build/lib/hecatomb/snakemake/workflow/rules/annotation 2024-02-01T05:18:53,588 copying hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation 2024-02-01T05:18:53,589 copying hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation 2024-02-01T05:18:53,589 copying hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation 2024-02-01T05:18:53,590 creating build/lib/hecatomb/snakemake/workflow/rules/assembly 2024-02-01T05:18:53,591 copying hecatomb/snakemake/workflow/rules/assembly/coverage.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly 2024-02-01T05:18:53,592 copying hecatomb/snakemake/workflow/rules/assembly/longreads.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly 2024-02-01T05:18:53,593 copying hecatomb/snakemake/workflow/rules/assembly/shortreads.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly 2024-02-01T05:18:53,593 creating build/lib/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:18:53,594 copying hecatomb/snakemake/workflow/rules/preflight/directories.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:18:53,595 copying hecatomb/snakemake/workflow/rules/preflight/functions.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:18:53,596 copying hecatomb/snakemake/workflow/rules/preflight/targets.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:18:53,597 copying hecatomb/snakemake/workflow/rules/preflight/validate.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:18:53,598 creating build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2024-02-01T05:18:53,598 copying hecatomb/snakemake/workflow/rules/preprocessing/preprocessing.smk -> build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2024-02-01T05:18:53,599 creating build/lib/hecatomb/snakemake/workflow/rules/reports 2024-02-01T05:18:53,599 copying hecatomb/snakemake/workflow/rules/reports/summaries.smk -> build/lib/hecatomb/snakemake/workflow/rules/reports 2024-02-01T05:18:53,601 copying hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk -> build/lib/hecatomb/snakemake/workflow/rules/reports 2024-02-01T05:18:53,601 creating build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,602 copying hecatomb/snakemake/workflow/scripts/__init__.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,603 copying hecatomb/snakemake/workflow/scripts/aaBigtable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,606 copying hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,607 copying hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,608 copying hecatomb/snakemake/workflow/scripts/contigCountTable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,609 copying hecatomb/snakemake/workflow/scripts/contigKronaText.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,610 copying hecatomb/snakemake/workflow/scripts/contigReadTaxon.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,611 copying hecatomb/snakemake/workflow/scripts/kronaText.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,611 copying hecatomb/snakemake/workflow/scripts/mergeSeqTable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,612 copying hecatomb/snakemake/workflow/scripts/ntBigtable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,616 copying hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,620 copying hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,624 copying hecatomb/snakemake/workflow/scripts/orfmFilt.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,628 copying hecatomb/snakemake/workflow/scripts/sankey.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,632 copying hecatomb/snakemake/workflow/scripts/seqPropertyTable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,639 copying hecatomb/snakemake/workflow/scripts/taxLevelCounts.py -> build/lib/hecatomb/snakemake/workflow/scripts 2024-02-01T05:18:53,642 creating build/lib/hecatomb/test_data 2024-02-01T05:18:53,643 copying hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:53,802 copying hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:53,963 copying hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:54,112 copying hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:54,228 copying hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:54,328 copying hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:54,481 copying hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:57,296 copying hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:57,472 copying hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:57,630 copying hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:57,751 copying hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:57,901 copying hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:18:58,030 copying hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:19:03,680 copying hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:19:03,825 copying hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:19:03,969 copying hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:19:08,299 copying hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:19:08,480 copying hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:19:11,260 copying hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:19:14,499 copying hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz -> build/lib/hecatomb/test_data 2024-02-01T05:19:14,693 copying hecatomb/test_data/test_config.yaml -> build/lib/hecatomb/test_data 2024-02-01T05:19:14,697 file hecatomb.py (for module hecatomb) not found 2024-02-01T05:19:14,738 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-02-01T05:19:14,739 !! 2024-02-01T05:19:14,740 ******************************************************************************** 2024-02-01T05:19:14,741 Please avoid running ``setup.py`` directly. 2024-02-01T05:19:14,742 Instead, use pypa/build, pypa/installer or other 2024-02-01T05:19:14,742 standards-based tools. 2024-02-01T05:19:14,744 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-02-01T05:19:14,745 ******************************************************************************** 2024-02-01T05:19:14,748 !! 2024-02-01T05:19:14,748 self.initialize_options() 2024-02-01T05:19:14,782 installing to build/bdist.linux-armv7l/wheel 2024-02-01T05:19:14,783 running install 2024-02-01T05:19:14,806 running install_lib 2024-02-01T05:19:14,847 creating build/bdist.linux-armv7l 2024-02-01T05:19:14,848 creating build/bdist.linux-armv7l/wheel 2024-02-01T05:19:14,851 creating build/bdist.linux-armv7l/wheel/hecatomb 2024-02-01T05:19:14,853 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake 2024-02-01T05:19:14,855 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile 2024-02-01T05:19:14,857 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm 2024-02-01T05:19:14,859 copying build/lib/hecatomb/snakemake/profile/example_slurm/config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm 2024-02-01T05:19:14,862 copying build/lib/hecatomb/snakemake/profile/example_slurm/slurm-status.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm 2024-02-01T05:19:14,866 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2024-02-01T05:19:14,868 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,870 copying build/lib/hecatomb/snakemake/workflow/envs/samtools.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,874 copying build/lib/hecatomb/snakemake/workflow/envs/megahit.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,878 copying build/lib/hecatomb/snakemake/workflow/envs/canu.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,882 copying build/lib/hecatomb/snakemake/workflow/envs/seqkit.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,884 copying build/lib/hecatomb/snakemake/workflow/envs/mmseqs2.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,887 copying build/lib/hecatomb/snakemake/workflow/envs/pysam.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,890 copying build/lib/hecatomb/snakemake/workflow/envs/krona.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,894 copying build/lib/hecatomb/snakemake/workflow/envs/pigz.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,897 copying build/lib/hecatomb/snakemake/workflow/envs/minimap2.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,900 copying build/lib/hecatomb/snakemake/workflow/envs/curl.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,902 copying build/lib/hecatomb/snakemake/workflow/envs/bedtools.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,906 copying build/lib/hecatomb/snakemake/workflow/envs/koverage.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,910 copying build/lib/hecatomb/snakemake/workflow/envs/bbmap.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,913 copying build/lib/hecatomb/snakemake/workflow/envs/metaflye.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,916 copying build/lib/hecatomb/snakemake/workflow/envs/trimnami.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2024-02-01T05:19:14,920 copying build/lib/hecatomb/snakemake/workflow/AddHost.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2024-02-01T05:19:16,328 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:16,977 copying build/lib/hecatomb/snakemake/workflow/report/nucleotide_annotations.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,123 copying build/lib/hecatomb/snakemake/workflow/report/protein_annotations.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,130 copying build/lib/hecatomb/snakemake/workflow/report/step13.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,136 copying build/lib/hecatomb/snakemake/workflow/report/summary_table.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,141 copying build/lib/hecatomb/snakemake/workflow/report/unclassified_seqtable.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,144 copying build/lib/hecatomb/snakemake/workflow/report/step10.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,148 copying build/lib/hecatomb/snakemake/workflow/report/tax_level_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,152 copying build/lib/hecatomb/snakemake/workflow/report/step11.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,162 copying build/lib/hecatomb/snakemake/workflow/report/step08.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,166 copying build/lib/hecatomb/snakemake/workflow/report/step12.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,170 copying build/lib/hecatomb/snakemake/workflow/report/raw_read_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,175 copying build/lib/hecatomb/snakemake/workflow/report/step07.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,179 copying build/lib/hecatomb/snakemake/workflow/report/host_removed_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,182 copying build/lib/hecatomb/snakemake/workflow/report/sankey.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,187 copying build/lib/hecatomb/snakemake/workflow/report/mapped_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,192 copying build/lib/hecatomb/snakemake/workflow/report/step09.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2024-02-01T05:19:17,197 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,199 copying build/lib/hecatomb/snakemake/workflow/scripts/ntBigtable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,204 copying build/lib/hecatomb/snakemake/workflow/scripts/contigCountTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,208 copying build/lib/hecatomb/snakemake/workflow/scripts/seqPropertyTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,212 copying build/lib/hecatomb/snakemake/workflow/scripts/mergeSeqTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,216 copying build/lib/hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,219 copying build/lib/hecatomb/snakemake/workflow/scripts/kronaText.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,223 copying build/lib/hecatomb/snakemake/workflow/scripts/orfmFilt.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,227 copying build/lib/hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,231 copying build/lib/hecatomb/snakemake/workflow/scripts/contigReadTaxon.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,243 copying build/lib/hecatomb/snakemake/workflow/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,246 copying build/lib/hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,251 copying build/lib/hecatomb/snakemake/workflow/scripts/aaBigtable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,258 copying build/lib/hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,260 copying build/lib/hecatomb/snakemake/workflow/scripts/sankey.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,265 copying build/lib/hecatomb/snakemake/workflow/scripts/contigKronaText.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,268 copying build/lib/hecatomb/snakemake/workflow/scripts/taxLevelCounts.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2024-02-01T05:19:17,276 copying build/lib/hecatomb/snakemake/workflow/DownloadDB.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2024-02-01T05:19:17,279 copying build/lib/hecatomb/snakemake/workflow/combineOutputs.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2024-02-01T05:19:17,284 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules 2024-02-01T05:19:17,286 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2024-02-01T05:19:17,290 copying build/lib/hecatomb/snakemake/workflow/rules/assembly/coverage.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2024-02-01T05:19:17,294 copying build/lib/hecatomb/snakemake/workflow/rules/assembly/shortreads.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2024-02-01T05:19:17,299 copying build/lib/hecatomb/snakemake/workflow/rules/assembly/longreads.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2024-02-01T05:19:17,302 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2024-02-01T05:19:17,304 copying build/lib/hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2024-02-01T05:19:17,308 copying build/lib/hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2024-02-01T05:19:17,311 copying build/lib/hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2024-02-01T05:19:17,317 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2024-02-01T05:19:17,318 copying build/lib/hecatomb/snakemake/workflow/rules/preprocessing/preprocessing.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2024-02-01T05:19:17,324 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:19:17,326 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/directories.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:19:17,330 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/validate.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:19:17,333 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/targets.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:19:17,338 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/functions.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2024-02-01T05:19:17,343 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports 2024-02-01T05:19:17,344 copying build/lib/hecatomb/snakemake/workflow/rules/reports/summaries.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports 2024-02-01T05:19:17,354 copying build/lib/hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports 2024-02-01T05:19:17,357 copying build/lib/hecatomb/snakemake/workflow/Hecatomb.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2024-02-01T05:19:17,361 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config 2024-02-01T05:19:17,363 copying build/lib/hecatomb/snakemake/config/immutable.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config 2024-02-01T05:19:17,366 copying build/lib/hecatomb/snakemake/config/config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config 2024-02-01T05:19:17,370 copying build/lib/hecatomb/snakemake/config/dbFiles.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config 2024-02-01T05:19:17,373 copying build/lib/hecatomb/__main__.py -> build/bdist.linux-armv7l/wheel/hecatomb 2024-02-01T05:19:17,379 copying build/lib/hecatomb/hecatomb.CITATION -> build/bdist.linux-armv7l/wheel/hecatomb 2024-02-01T05:19:17,382 copying build/lib/hecatomb/hecatomb.LICENSE -> build/bdist.linux-armv7l/wheel/hecatomb 2024-02-01T05:19:17,386 creating build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:17,388 copying build/lib/hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:17,541 copying build/lib/hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:17,674 copying build/lib/hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:17,808 copying build/lib/hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:17,961 copying build/lib/hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:18,107 copying build/lib/hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:18,250 copying build/lib/hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:22,837 copying build/lib/hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:24,907 copying build/lib/hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:25,085 copying build/lib/hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:25,556 copying build/lib/hecatomb/test_data/test_config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:25,565 copying build/lib/hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:27,672 copying build/lib/hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:27,834 copying build/lib/hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:27,967 copying build/lib/hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:28,100 copying build/lib/hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:28,260 copying build/lib/hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:28,373 copying build/lib/hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:28,497 copying build/lib/hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:28,620 copying build/lib/hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:28,870 copying build/lib/hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2024-02-01T05:19:28,990 copying build/lib/hecatomb/__init__.py -> build/bdist.linux-armv7l/wheel/hecatomb 2024-02-01T05:19:28,992 copying build/lib/hecatomb/hecatomb.VERSION -> build/bdist.linux-armv7l/wheel/hecatomb 2024-02-01T05:19:28,994 running install_data 2024-02-01T05:19:29,032 creating build/bdist.linux-armv7l/wheel/hecatomb-1.3.0.data 2024-02-01T05:19:29,032 creating build/bdist.linux-armv7l/wheel/hecatomb-1.3.0.data/data 2024-02-01T05:19:29,034 copying README.md -> build/bdist.linux-armv7l/wheel/hecatomb-1.3.0.data/data/. 2024-02-01T05:19:29,037 running install_egg_info 2024-02-01T05:19:29,081 Copying hecatomb.egg-info to build/bdist.linux-armv7l/wheel/hecatomb-1.3.0-py3.11.egg-info 2024-02-01T05:19:29,099 running install_scripts 2024-02-01T05:19:29,128 creating build/bdist.linux-armv7l/wheel/hecatomb-1.3.0.dist-info/WHEEL 2024-02-01T05:19:29,131 creating '/tmp/pip-wheel-pjzfwp00/hecatomb-1.3.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-02-01T05:19:29,134 adding 'hecatomb/__init__.py' 2024-02-01T05:19:29,136 adding 'hecatomb/__main__.py' 2024-02-01T05:19:29,138 adding 'hecatomb/hecatomb.CITATION' 2024-02-01T05:19:29,139 adding 'hecatomb/hecatomb.LICENSE' 2024-02-01T05:19:29,140 adding 'hecatomb/hecatomb.VERSION' 2024-02-01T05:19:29,143 adding 'hecatomb/snakemake/config/config.yaml' 2024-02-01T05:19:29,145 adding 'hecatomb/snakemake/config/dbFiles.yaml' 2024-02-01T05:19:29,146 adding 'hecatomb/snakemake/config/immutable.yaml' 2024-02-01T05:19:29,149 adding 'hecatomb/snakemake/profile/example_slurm/config.yaml' 2024-02-01T05:19:29,150 adding 'hecatomb/snakemake/profile/example_slurm/slurm-status.py' 2024-02-01T05:19:29,153 adding 'hecatomb/snakemake/workflow/AddHost.smk' 2024-02-01T05:19:29,154 adding 'hecatomb/snakemake/workflow/DownloadDB.smk' 2024-02-01T05:19:29,156 adding 'hecatomb/snakemake/workflow/Hecatomb.smk' 2024-02-01T05:19:29,158 adding 'hecatomb/snakemake/workflow/combineOutputs.smk' 2024-02-01T05:19:29,160 adding 'hecatomb/snakemake/workflow/envs/bbmap.yaml' 2024-02-01T05:19:29,161 adding 'hecatomb/snakemake/workflow/envs/bedtools.yaml' 2024-02-01T05:19:29,162 adding 'hecatomb/snakemake/workflow/envs/canu.yaml' 2024-02-01T05:19:29,164 adding 'hecatomb/snakemake/workflow/envs/curl.yaml' 2024-02-01T05:19:29,165 adding 'hecatomb/snakemake/workflow/envs/koverage.yaml' 2024-02-01T05:19:29,166 adding 'hecatomb/snakemake/workflow/envs/krona.yaml' 2024-02-01T05:19:29,168 adding 'hecatomb/snakemake/workflow/envs/megahit.yaml' 2024-02-01T05:19:29,170 adding 'hecatomb/snakemake/workflow/envs/metaflye.yaml' 2024-02-01T05:19:29,171 adding 'hecatomb/snakemake/workflow/envs/minimap2.yaml' 2024-02-01T05:19:29,173 adding 'hecatomb/snakemake/workflow/envs/mmseqs2.yaml' 2024-02-01T05:19:29,174 adding 'hecatomb/snakemake/workflow/envs/pigz.yaml' 2024-02-01T05:19:29,176 adding 'hecatomb/snakemake/workflow/envs/pysam.yaml' 2024-02-01T05:19:29,177 adding 'hecatomb/snakemake/workflow/envs/samtools.yaml' 2024-02-01T05:19:29,179 adding 'hecatomb/snakemake/workflow/envs/seqkit.yaml' 2024-02-01T05:19:29,180 adding 'hecatomb/snakemake/workflow/envs/trimnami.yaml' 2024-02-01T05:19:29,184 adding 'hecatomb/snakemake/workflow/report/host_removed_counts.rst' 2024-02-01T05:19:29,185 adding 'hecatomb/snakemake/workflow/report/mapped_counts.rst' 2024-02-01T05:19:29,187 adding 'hecatomb/snakemake/workflow/report/nucleotide_annotations.rst' 2024-02-01T05:19:29,188 adding 'hecatomb/snakemake/workflow/report/protein_annotations.rst' 2024-02-01T05:19:29,190 adding 'hecatomb/snakemake/workflow/report/raw_read_counts.rst' 2024-02-01T05:19:29,191 adding 'hecatomb/snakemake/workflow/report/sankey.rst' 2024-02-01T05:19:29,193 adding 'hecatomb/snakemake/workflow/report/step07.rst' 2024-02-01T05:19:29,194 adding 'hecatomb/snakemake/workflow/report/step08.rst' 2024-02-01T05:19:29,195 adding 'hecatomb/snakemake/workflow/report/step09.rst' 2024-02-01T05:19:29,196 adding 'hecatomb/snakemake/workflow/report/step10.rst' 2024-02-01T05:19:29,198 adding 'hecatomb/snakemake/workflow/report/step11.rst' 2024-02-01T05:19:29,199 adding 'hecatomb/snakemake/workflow/report/step12.rst' 2024-02-01T05:19:29,201 adding 'hecatomb/snakemake/workflow/report/step13.rst' 2024-02-01T05:19:29,202 adding 'hecatomb/snakemake/workflow/report/summary_table.rst' 2024-02-01T05:19:29,203 adding 'hecatomb/snakemake/workflow/report/tax_level_counts.rst' 2024-02-01T05:19:29,204 adding 'hecatomb/snakemake/workflow/report/unclassified_seqtable.rst' 2024-02-01T05:19:29,207 adding 'hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk' 2024-02-01T05:19:29,209 adding 'hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk' 2024-02-01T05:19:29,211 adding 'hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk' 2024-02-01T05:19:29,213 adding 'hecatomb/snakemake/workflow/rules/assembly/coverage.smk' 2024-02-01T05:19:29,215 adding 'hecatomb/snakemake/workflow/rules/assembly/longreads.smk' 2024-02-01T05:19:29,217 adding 'hecatomb/snakemake/workflow/rules/assembly/shortreads.smk' 2024-02-01T05:19:29,219 adding 'hecatomb/snakemake/workflow/rules/preflight/directories.smk' 2024-02-01T05:19:29,220 adding 'hecatomb/snakemake/workflow/rules/preflight/functions.smk' 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'hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz' 2024-02-01T05:19:31,262 adding 'hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz' 2024-02-01T05:19:31,889 adding 'hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz' 2024-02-01T05:19:32,699 adding 'hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz' 2024-02-01T05:19:33,819 adding 'hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz' 2024-02-01T05:19:34,359 adding 'hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz' 2024-02-01T05:19:34,944 adding 'hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz' 2024-02-01T05:19:35,496 adding 'hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz' 2024-02-01T05:19:36,105 adding 'hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz' 2024-02-01T05:19:36,628 adding 'hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz' 2024-02-01T05:19:37,711 adding 'hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz' 2024-02-01T05:19:45,122 adding 'hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz' 2024-02-01T05:19:45,660 adding 'hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz' 2024-02-01T05:19:46,197 adding 'hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz' 2024-02-01T05:19:47,084 adding 'hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz' 2024-02-01T05:19:48,544 adding 'hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz' 2024-02-01T05:19:49,354 adding 'hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz' 2024-02-01T05:19:49,874 adding 'hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz' 2024-02-01T05:19:50,754 adding 'hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz' 2024-02-01T05:19:51,314 adding 'hecatomb/test_data/test_config.yaml' 2024-02-01T05:19:51,679 adding 'hecatomb-1.3.0.data/data/README.md' 2024-02-01T05:19:51,683 adding 'hecatomb-1.3.0.dist-info/LICENSE' 2024-02-01T05:19:51,686 adding 'hecatomb-1.3.0.dist-info/METADATA' 2024-02-01T05:19:51,689 adding 'hecatomb-1.3.0.dist-info/WHEEL' 2024-02-01T05:19:51,691 adding 'hecatomb-1.3.0.dist-info/entry_points.txt' 2024-02-01T05:19:51,694 adding 'hecatomb-1.3.0.dist-info/top_level.txt' 2024-02-01T05:19:51,698 adding 'hecatomb-1.3.0.dist-info/RECORD' 2024-02-01T05:19:52,652 removing build/bdist.linux-armv7l/wheel 2024-02-01T05:19:54,142 Building wheel for hecatomb (setup.py): finished with status 'done' 2024-02-01T05:19:59,088 Created wheel for hecatomb: filename=hecatomb-1.3.0-py3-none-any.whl size=98564455 sha256=7c88ee5207d15214efcf06eab485fc2b867d86cc43648f88f8ca409228d62d42 2024-02-01T05:19:59,090 Stored in directory: /tmp/pip-ephem-wheel-cache-0tdhw68u/wheels/8f/b0/4c/c38640b25919b22f36e532be3fd3d76b8a967207a22a7743d9 2024-02-01T05:19:59,137 Successfully built hecatomb 2024-02-01T05:20:29,990 Removed build tracker: '/tmp/pip-build-tracker-n3403wvk'