2023-03-30T05:17:53,371 Created temporary directory: /tmp/pip-ephem-wheel-cache-jpv1uhms 2023-03-30T05:17:53,377 Created temporary directory: /tmp/pip-build-tracker-uo3kdbc9 2023-03-30T05:17:53,377 Initialized build tracking at /tmp/pip-build-tracker-uo3kdbc9 2023-03-30T05:17:53,378 Created build tracker: /tmp/pip-build-tracker-uo3kdbc9 2023-03-30T05:17:53,378 Entered build tracker: /tmp/pip-build-tracker-uo3kdbc9 2023-03-30T05:17:53,379 Created temporary directory: /tmp/pip-wheel-_63hwxdp 2023-03-30T05:17:53,389 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2023-03-30T05:17:53,395 Created temporary directory: /tmp/pip-ephem-wheel-cache-zcxogokz 2023-03-30T05:17:53,456 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-03-30T05:17:53,463 2 location(s) to search for versions of hecatomb: 2023-03-30T05:17:53,463 * https://pypi.org/simple/hecatomb/ 2023-03-30T05:17:53,463 * https://www.piwheels.org/simple/hecatomb/ 2023-03-30T05:17:53,464 Fetching project page and analyzing links: https://pypi.org/simple/hecatomb/ 2023-03-30T05:17:53,465 Getting page https://pypi.org/simple/hecatomb/ 2023-03-30T05:17:53,468 Found index url https://pypi.org/simple 2023-03-30T05:17:53,658 Fetched page https://pypi.org/simple/hecatomb/ as application/vnd.pypi.simple.v1+json 2023-03-30T05:17:53,661 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) 2023-03-30T05:17:53,662 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 2023-03-30T05:17:53,663 Fetching project page and analyzing links: https://www.piwheels.org/simple/hecatomb/ 2023-03-30T05:17:53,664 Getting page https://www.piwheels.org/simple/hecatomb/ 2023-03-30T05:17:53,666 Found index url https://www.piwheels.org/simple 2023-03-30T05:17:53,894 Fetched page https://www.piwheels.org/simple/hecatomb/ as text/html 2023-03-30T05:17:53,896 Skipping link: not a file: https://www.piwheels.org/simple/hecatomb/ 2023-03-30T05:17:53,897 Skipping link: not a file: https://pypi.org/simple/hecatomb/ 2023-03-30T05:17:53,930 Given no hashes to check 1 links for project 'hecatomb': discarding no candidates 2023-03-30T05:17:53,960 Collecting hecatomb==1.2.0 2023-03-30T05:17:53,964 Created temporary directory: /tmp/pip-unpack-o6lrvhzf 2023-03-30T05:17:54,559 Downloading hecatomb-1.2.0.tar.gz (98.6 MB) 2023-03-30T05:18:44,853 Added hecatomb==1.2.0 from https://files.pythonhosted.org/packages/e4/8a/60abbe18523fcf27f997b4b5e25499d58a76e6a17cb2343787c4853050f9/hecatomb-1.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-uo3kdbc9' 2023-03-30T05:18:44,857 Running setup.py (path:/tmp/pip-wheel-_63hwxdp/hecatomb_050aa2dcc5494408abb55836156d4987/setup.py) egg_info for package hecatomb 2023-03-30T05:18:44,858 Created temporary directory: /tmp/pip-pip-egg-info-2fubg8vj 2023-03-30T05:18:44,859 Preparing metadata (setup.py): started 2023-03-30T05:18:44,861 Running command python setup.py egg_info 2023-03-30T05:18:46,408 running egg_info 2023-03-30T05:18:46,411 creating /tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info 2023-03-30T05:18:46,477 writing /tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info/PKG-INFO 2023-03-30T05:18:46,482 writing dependency_links to /tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info/dependency_links.txt 2023-03-30T05:18:46,485 writing entry points to /tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info/entry_points.txt 2023-03-30T05:18:46,488 writing requirements to /tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info/requires.txt 2023-03-30T05:18:46,490 writing top-level names to /tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info/top_level.txt 2023-03-30T05:18:46,493 writing manifest file '/tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info/SOURCES.txt' 2023-03-30T05:18:46,633 /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:547: UserWarning: Normalizing 'v1.2.0' to '1.2.0' 2023-03-30T05:18:46,634 warnings.warn(tmpl.format(**locals())) 2023-03-30T05:18:46,634 file hecatomb.py (for module hecatomb) not found 2023-03-30T05:18:46,699 reading manifest file '/tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info/SOURCES.txt' 2023-03-30T05:18:46,703 reading manifest template 'MANIFEST.in' 2023-03-30T05:18:46,812 warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/conda/' 2023-03-30T05:18:46,814 warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/databases/' 2023-03-30T05:18:46,830 writing manifest file '/tmp/pip-pip-egg-info-2fubg8vj/hecatomb.egg-info/SOURCES.txt' 2023-03-30T05:18:46,949 Preparing metadata (setup.py): finished with status 'done' 2023-03-30T05:18:46,962 Source in /tmp/pip-wheel-_63hwxdp/hecatomb_050aa2dcc5494408abb55836156d4987 has version 1.2.0, which satisfies requirement hecatomb==1.2.0 from https://files.pythonhosted.org/packages/e4/8a/60abbe18523fcf27f997b4b5e25499d58a76e6a17cb2343787c4853050f9/hecatomb-1.2.0.tar.gz 2023-03-30T05:18:46,964 Removed hecatomb==1.2.0 from https://files.pythonhosted.org/packages/e4/8a/60abbe18523fcf27f997b4b5e25499d58a76e6a17cb2343787c4853050f9/hecatomb-1.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-uo3kdbc9' 2023-03-30T05:18:46,979 Created temporary directory: /tmp/pip-unpack-5c1e8cms 2023-03-30T05:18:46,980 Building wheels for collected packages: hecatomb 2023-03-30T05:18:46,990 Created temporary directory: /tmp/pip-wheel-5v8g_jjo 2023-03-30T05:18:46,990 Building wheel for hecatomb (setup.py): started 2023-03-30T05:18:46,992 Destination directory: /tmp/pip-wheel-5v8g_jjo 2023-03-30T05:18:46,993 Running command python setup.py bdist_wheel 2023-03-30T05:18:48,376 /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:547: UserWarning: Normalizing 'v1.2.0' to '1.2.0' 2023-03-30T05:18:48,378 warnings.warn(tmpl.format(**locals())) 2023-03-30T05:18:49,055 running bdist_wheel 2023-03-30T05:18:49,832 running build 2023-03-30T05:18:49,833 running build_py 2023-03-30T05:18:49,903 file hecatomb.py (for module hecatomb) not found 2023-03-30T05:18:49,907 creating build 2023-03-30T05:18:49,908 creating build/lib 2023-03-30T05:18:49,909 creating build/lib/hecatomb 2023-03-30T05:18:49,912 copying hecatomb/__init__.py -> build/lib/hecatomb 2023-03-30T05:18:49,915 copying hecatomb/__main__.py -> build/lib/hecatomb 2023-03-30T05:18:49,919 copying hecatomb/cli_util.py -> build/lib/hecatomb 2023-03-30T05:18:49,923 running egg_info 2023-03-30T05:18:50,080 writing hecatomb.egg-info/PKG-INFO 2023-03-30T05:18:50,084 writing dependency_links to hecatomb.egg-info/dependency_links.txt 2023-03-30T05:18:50,088 writing entry points to hecatomb.egg-info/entry_points.txt 2023-03-30T05:18:50,091 writing requirements to hecatomb.egg-info/requires.txt 2023-03-30T05:18:50,093 writing top-level names to hecatomb.egg-info/top_level.txt 2023-03-30T05:18:50,099 file hecatomb.py (for module hecatomb) not found 2023-03-30T05:18:50,166 reading manifest file 'hecatomb.egg-info/SOURCES.txt' 2023-03-30T05:18:50,179 reading manifest template 'MANIFEST.in' 2023-03-30T05:18:50,286 warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/conda/' 2023-03-30T05:18:50,288 warning: no previously-included files matching '*' found under directory 'hecatomb/snakemake/databases/' 2023-03-30T05:18:50,308 writing manifest file 'hecatomb.egg-info/SOURCES.txt' 2023-03-30T05:18:50,313 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.config' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,314 !! 2023-03-30T05:18:50,315 ############################ 2023-03-30T05:18:50,315 # Package would be ignored # 2023-03-30T05:18:50,315 ############################ 2023-03-30T05:18:50,316 Python recognizes 'hecatomb.snakemake.config' as an importable package, 2023-03-30T05:18:50,316 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,317 'hecatomb.snakemake.config' has been automatically added to the distribution only 2023-03-30T05:18:50,317 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,317 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,318 Please make sure that 'hecatomb.snakemake.config' is included as a package by using 2023-03-30T05:18:50,318 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,319 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,319 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,319 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,320 documentation page. 2023-03-30T05:18:50,321 !! 2023-03-30T05:18:50,321 check.warn(importable) 2023-03-30T05:18:50,322 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.profile.example_slurm' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,322 !! 2023-03-30T05:18:50,323 ############################ 2023-03-30T05:18:50,323 # Package would be ignored # 2023-03-30T05:18:50,323 ############################ 2023-03-30T05:18:50,324 Python recognizes 'hecatomb.snakemake.profile.example_slurm' as an importable package, 2023-03-30T05:18:50,324 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,325 'hecatomb.snakemake.profile.example_slurm' has been automatically added to the distribution only 2023-03-30T05:18:50,325 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,325 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,326 Please make sure that 'hecatomb.snakemake.profile.example_slurm' is included as a package by using 2023-03-30T05:18:50,326 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,326 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,327 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,327 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,328 documentation page. 2023-03-30T05:18:50,329 !! 2023-03-30T05:18:50,329 check.warn(importable) 2023-03-30T05:18:50,329 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,330 !! 2023-03-30T05:18:50,331 ############################ 2023-03-30T05:18:50,331 # Package would be ignored # 2023-03-30T05:18:50,331 ############################ 2023-03-30T05:18:50,332 Python recognizes 'hecatomb.snakemake.workflow' as an importable package, 2023-03-30T05:18:50,332 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,332 'hecatomb.snakemake.workflow' has been automatically added to the distribution only 2023-03-30T05:18:50,333 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,333 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,334 Please make sure that 'hecatomb.snakemake.workflow' is included as a package by using 2023-03-30T05:18:50,334 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,334 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,335 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,335 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,335 documentation page. 2023-03-30T05:18:50,336 !! 2023-03-30T05:18:50,337 check.warn(importable) 2023-03-30T05:18:50,337 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow.envs' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,338 !! 2023-03-30T05:18:50,339 ############################ 2023-03-30T05:18:50,339 # Package would be ignored # 2023-03-30T05:18:50,339 ############################ 2023-03-30T05:18:50,339 Python recognizes 'hecatomb.snakemake.workflow.envs' as an importable package, 2023-03-30T05:18:50,340 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,340 'hecatomb.snakemake.workflow.envs' has been automatically added to the distribution only 2023-03-30T05:18:50,341 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,341 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,341 Please make sure that 'hecatomb.snakemake.workflow.envs' is included as a package by using 2023-03-30T05:18:50,342 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,342 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,342 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,343 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,343 documentation page. 2023-03-30T05:18:50,344 !! 2023-03-30T05:18:50,345 check.warn(importable) 2023-03-30T05:18:50,345 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow.report' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,345 !! 2023-03-30T05:18:50,346 ############################ 2023-03-30T05:18:50,346 # Package would be ignored # 2023-03-30T05:18:50,347 ############################ 2023-03-30T05:18:50,347 Python recognizes 'hecatomb.snakemake.workflow.report' as an importable package, 2023-03-30T05:18:50,347 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,348 'hecatomb.snakemake.workflow.report' has been automatically added to the distribution only 2023-03-30T05:18:50,348 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,348 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,349 Please make sure that 'hecatomb.snakemake.workflow.report' is included as a package by using 2023-03-30T05:18:50,349 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,350 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,350 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,350 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,351 documentation page. 2023-03-30T05:18:50,352 !! 2023-03-30T05:18:50,352 check.warn(importable) 2023-03-30T05:18:50,353 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow.rules.annotation' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,353 !! 2023-03-30T05:18:50,354 ############################ 2023-03-30T05:18:50,354 # Package would be ignored # 2023-03-30T05:18:50,354 ############################ 2023-03-30T05:18:50,355 Python recognizes 'hecatomb.snakemake.workflow.rules.annotation' as an importable package, 2023-03-30T05:18:50,355 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,355 'hecatomb.snakemake.workflow.rules.annotation' has been automatically added to the distribution only 2023-03-30T05:18:50,356 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,356 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,357 Please make sure that 'hecatomb.snakemake.workflow.rules.annotation' is included as a package by using 2023-03-30T05:18:50,357 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,357 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,358 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,358 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,358 documentation page. 2023-03-30T05:18:50,359 !! 2023-03-30T05:18:50,360 check.warn(importable) 2023-03-30T05:18:50,360 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow.rules.assembly' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,361 !! 2023-03-30T05:18:50,361 ############################ 2023-03-30T05:18:50,362 # Package would be ignored # 2023-03-30T05:18:50,362 ############################ 2023-03-30T05:18:50,362 Python recognizes 'hecatomb.snakemake.workflow.rules.assembly' as an importable package, 2023-03-30T05:18:50,363 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,363 'hecatomb.snakemake.workflow.rules.assembly' has been automatically added to the distribution only 2023-03-30T05:18:50,363 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,364 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,364 Please make sure that 'hecatomb.snakemake.workflow.rules.assembly' is included as a package by using 2023-03-30T05:18:50,365 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,365 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,366 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,366 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,367 documentation page. 2023-03-30T05:18:50,368 !! 2023-03-30T05:18:50,368 check.warn(importable) 2023-03-30T05:18:50,369 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow.rules.preflight' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,369 !! 2023-03-30T05:18:50,370 ############################ 2023-03-30T05:18:50,371 # Package would be ignored # 2023-03-30T05:18:50,371 ############################ 2023-03-30T05:18:50,371 Python recognizes 'hecatomb.snakemake.workflow.rules.preflight' as an importable package, 2023-03-30T05:18:50,372 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,372 'hecatomb.snakemake.workflow.rules.preflight' has been automatically added to the distribution only 2023-03-30T05:18:50,373 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,373 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,374 Please make sure that 'hecatomb.snakemake.workflow.rules.preflight' is included as a package by using 2023-03-30T05:18:50,374 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,375 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,375 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,376 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,376 documentation page. 2023-03-30T05:18:50,377 !! 2023-03-30T05:18:50,378 check.warn(importable) 2023-03-30T05:18:50,378 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow.rules.preprocessing' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,378 !! 2023-03-30T05:18:50,379 ############################ 2023-03-30T05:18:50,380 # Package would be ignored # 2023-03-30T05:18:50,380 ############################ 2023-03-30T05:18:50,380 Python recognizes 'hecatomb.snakemake.workflow.rules.preprocessing' as an importable package, 2023-03-30T05:18:50,381 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,381 'hecatomb.snakemake.workflow.rules.preprocessing' has been automatically added to the distribution only 2023-03-30T05:18:50,382 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,382 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,383 Please make sure that 'hecatomb.snakemake.workflow.rules.preprocessing' is included as a package by using 2023-03-30T05:18:50,383 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,384 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,384 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,385 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,385 documentation page. 2023-03-30T05:18:50,386 !! 2023-03-30T05:18:50,387 check.warn(importable) 2023-03-30T05:18:50,387 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow.rules.reports' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,388 !! 2023-03-30T05:18:50,389 ############################ 2023-03-30T05:18:50,389 # Package would be ignored # 2023-03-30T05:18:50,389 ############################ 2023-03-30T05:18:50,390 Python recognizes 'hecatomb.snakemake.workflow.rules.reports' as an importable package, 2023-03-30T05:18:50,390 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,391 'hecatomb.snakemake.workflow.rules.reports' has been automatically added to the distribution only 2023-03-30T05:18:50,391 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,392 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,393 Please make sure that 'hecatomb.snakemake.workflow.rules.reports' is included as a package by using 2023-03-30T05:18:50,393 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,393 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,394 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,394 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,395 documentation page. 2023-03-30T05:18:50,396 !! 2023-03-30T05:18:50,396 check.warn(importable) 2023-03-30T05:18:50,397 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.snakemake.workflow.scripts' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,397 !! 2023-03-30T05:18:50,398 ############################ 2023-03-30T05:18:50,398 # Package would be ignored # 2023-03-30T05:18:50,399 ############################ 2023-03-30T05:18:50,399 Python recognizes 'hecatomb.snakemake.workflow.scripts' as an importable package, 2023-03-30T05:18:50,399 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,400 'hecatomb.snakemake.workflow.scripts' has been automatically added to the distribution only 2023-03-30T05:18:50,401 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,401 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,401 Please make sure that 'hecatomb.snakemake.workflow.scripts' is included as a package by using 2023-03-30T05:18:50,402 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,402 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,402 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,403 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,403 documentation page. 2023-03-30T05:18:50,404 !! 2023-03-30T05:18:50,405 check.warn(importable) 2023-03-30T05:18:50,406 /usr/local/lib/python3.7/dist-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'hecatomb.test_data' as data is deprecated, please list it in `packages`. 2023-03-30T05:18:50,406 !! 2023-03-30T05:18:50,407 ############################ 2023-03-30T05:18:50,407 # Package would be ignored # 2023-03-30T05:18:50,408 ############################ 2023-03-30T05:18:50,408 Python recognizes 'hecatomb.test_data' as an importable package, 2023-03-30T05:18:50,408 but it is not listed in the `packages` configuration of setuptools. 2023-03-30T05:18:50,409 'hecatomb.test_data' has been automatically added to the distribution only 2023-03-30T05:18:50,409 because it may contain data files, but this behavior is likely to change 2023-03-30T05:18:50,410 in future versions of setuptools (and therefore is considered deprecated). 2023-03-30T05:18:50,410 Please make sure that 'hecatomb.test_data' is included as a package by using 2023-03-30T05:18:50,411 the `packages` configuration field or the proper discovery methods 2023-03-30T05:18:50,411 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-03-30T05:18:50,412 instead of `find_packages(...)`/`find:`). 2023-03-30T05:18:50,412 You can read more about "package discovery" and "data files" on setuptools 2023-03-30T05:18:50,413 documentation page. 2023-03-30T05:18:50,414 !! 2023-03-30T05:18:50,414 check.warn(importable) 2023-03-30T05:18:50,415 copying hecatomb/hecatomb.CITATION -> build/lib/hecatomb 2023-03-30T05:18:50,415 copying hecatomb/hecatomb.LICENSE -> build/lib/hecatomb 2023-03-30T05:18:50,415 copying hecatomb/hecatomb.VERSION -> build/lib/hecatomb 2023-03-30T05:18:50,416 creating build/lib/hecatomb/snakemake 2023-03-30T05:18:50,416 creating build/lib/hecatomb/snakemake/config 2023-03-30T05:18:50,417 copying hecatomb/snakemake/config/config.yaml -> build/lib/hecatomb/snakemake/config 2023-03-30T05:18:50,417 copying hecatomb/snakemake/config/dbFiles.yaml -> build/lib/hecatomb/snakemake/config 2023-03-30T05:18:50,417 copying hecatomb/snakemake/config/immutable.yaml -> build/lib/hecatomb/snakemake/config 2023-03-30T05:18:50,418 creating build/lib/hecatomb/snakemake/profile 2023-03-30T05:18:50,418 creating build/lib/hecatomb/snakemake/profile/example_slurm 2023-03-30T05:18:50,418 copying hecatomb/snakemake/profile/example_slurm/config.yaml -> build/lib/hecatomb/snakemake/profile/example_slurm 2023-03-30T05:18:50,419 copying hecatomb/snakemake/profile/example_slurm/slurm-status.py -> build/lib/hecatomb/snakemake/profile/example_slurm 2023-03-30T05:18:50,419 creating build/lib/hecatomb/snakemake/workflow 2023-03-30T05:18:50,419 copying hecatomb/snakemake/workflow/AddHost.smk -> build/lib/hecatomb/snakemake/workflow 2023-03-30T05:18:50,420 copying hecatomb/snakemake/workflow/DownloadDB.smk -> build/lib/hecatomb/snakemake/workflow 2023-03-30T05:18:50,421 copying hecatomb/snakemake/workflow/Hecatomb.smk -> build/lib/hecatomb/snakemake/workflow 2023-03-30T05:18:50,423 copying hecatomb/snakemake/workflow/combineOutputs.smk -> build/lib/hecatomb/snakemake/workflow 2023-03-30T05:18:50,428 creating build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,430 copying hecatomb/snakemake/workflow/envs/bbmap.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,434 copying hecatomb/snakemake/workflow/envs/canu.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,439 copying hecatomb/snakemake/workflow/envs/curl.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,443 copying hecatomb/snakemake/workflow/envs/dependency_notes.txt -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,447 copying hecatomb/snakemake/workflow/envs/fastp.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,451 copying hecatomb/snakemake/workflow/envs/krona.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,455 copying hecatomb/snakemake/workflow/envs/megahit.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,460 copying hecatomb/snakemake/workflow/envs/metaflye.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,464 copying hecatomb/snakemake/workflow/envs/minimap2.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,468 copying hecatomb/snakemake/workflow/envs/mmseqs2.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,472 copying hecatomb/snakemake/workflow/envs/pigz.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,477 copying hecatomb/snakemake/workflow/envs/plotly.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,481 copying hecatomb/snakemake/workflow/envs/prinseqpp.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,485 copying hecatomb/snakemake/workflow/envs/pysam.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,489 copying hecatomb/snakemake/workflow/envs/samtools.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,493 copying hecatomb/snakemake/workflow/envs/seqkit.yaml -> build/lib/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:50,497 creating build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,499 copying hecatomb/snakemake/workflow/report/host_removed_counts.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,504 copying hecatomb/snakemake/workflow/report/mapped_counts.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,508 copying hecatomb/snakemake/workflow/report/nucleotide_annotations.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,512 copying hecatomb/snakemake/workflow/report/protein_annotations.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,516 copying hecatomb/snakemake/workflow/report/raw_read_counts.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,520 copying hecatomb/snakemake/workflow/report/sankey.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,524 copying hecatomb/snakemake/workflow/report/step07.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,528 copying hecatomb/snakemake/workflow/report/step08.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,532 copying hecatomb/snakemake/workflow/report/step09.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,536 copying hecatomb/snakemake/workflow/report/step10.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,541 copying hecatomb/snakemake/workflow/report/step11.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,545 copying hecatomb/snakemake/workflow/report/step12.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,549 copying hecatomb/snakemake/workflow/report/step13.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,553 copying hecatomb/snakemake/workflow/report/summary_table.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,557 copying hecatomb/snakemake/workflow/report/tax_level_counts.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,561 copying hecatomb/snakemake/workflow/report/unclassified_seqtable.rst -> build/lib/hecatomb/snakemake/workflow/report 2023-03-30T05:18:50,565 creating build/lib/hecatomb/snakemake/workflow/rules 2023-03-30T05:18:50,566 creating build/lib/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:50,569 copying hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:50,573 copying hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:50,578 copying hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:50,583 copying hecatomb/snakemake/workflow/rules/annotation/read_annotation_orfm.smk -> build/lib/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:50,589 creating build/lib/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:50,591 copying hecatomb/snakemake/workflow/rules/assembly/README.md -> build/lib/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:50,595 copying hecatomb/snakemake/workflow/rules/assembly/combine_sample_assemblies.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:50,599 copying hecatomb/snakemake/workflow/rules/assembly/longreads.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:50,604 copying hecatomb/snakemake/workflow/rules/assembly/paired_end.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:50,609 copying hecatomb/snakemake/workflow/rules/assembly/single_end.smk -> build/lib/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:50,614 creating build/lib/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:50,616 copying hecatomb/snakemake/workflow/rules/preflight/directories.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:50,621 copying hecatomb/snakemake/workflow/rules/preflight/functions.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:50,625 copying hecatomb/snakemake/workflow/rules/preflight/samples_pe.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:50,630 copying hecatomb/snakemake/workflow/rules/preflight/samples_se.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:50,634 copying hecatomb/snakemake/workflow/rules/preflight/targets.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:50,639 copying hecatomb/snakemake/workflow/rules/preflight/validate.smk -> build/lib/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:50,643 creating build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:50,644 copying hecatomb/snakemake/workflow/rules/preprocessing/README.md -> build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:50,649 copying hecatomb/snakemake/workflow/rules/preprocessing/cluster_seqs.smk -> build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:50,654 copying hecatomb/snakemake/workflow/rules/preprocessing/longreads.smk -> build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:50,658 copying hecatomb/snakemake/workflow/rules/preprocessing/paired_end.smk -> build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:50,663 copying hecatomb/snakemake/workflow/rules/preprocessing/roundAB.smk -> build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:50,668 copying hecatomb/snakemake/workflow/rules/preprocessing/single_end.smk -> build/lib/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:50,673 creating build/lib/hecatomb/snakemake/workflow/rules/reports 2023-03-30T05:18:50,675 copying hecatomb/snakemake/workflow/rules/reports/summaries.smk -> build/lib/hecatomb/snakemake/workflow/rules/reports 2023-03-30T05:18:50,679 copying hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk -> build/lib/hecatomb/snakemake/workflow/rules/reports 2023-03-30T05:18:50,684 creating build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,686 copying hecatomb/snakemake/workflow/scripts/__init__.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,690 copying hecatomb/snakemake/workflow/scripts/aaBigtable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,694 copying hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,698 copying hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,703 copying hecatomb/snakemake/workflow/scripts/contigCountTable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,707 copying hecatomb/snakemake/workflow/scripts/contigKronaText.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,712 copying hecatomb/snakemake/workflow/scripts/contigReadTaxon.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,716 copying hecatomb/snakemake/workflow/scripts/kronaText.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,720 copying hecatomb/snakemake/workflow/scripts/mergeSeqTable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,724 copying hecatomb/snakemake/workflow/scripts/ntBigtable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,728 copying hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,733 copying hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,737 copying hecatomb/snakemake/workflow/scripts/orfmFilt.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,741 copying hecatomb/snakemake/workflow/scripts/sankey.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,746 copying hecatomb/snakemake/workflow/scripts/seqPropertyTable.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,750 copying hecatomb/snakemake/workflow/scripts/taxLevelCounts.py -> build/lib/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:50,754 creating build/lib/hecatomb/test_data 2023-03-30T05:18:50,756 copying hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:51,066 copying hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:51,733 copying hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:51,998 copying hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:52,233 copying hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:52,482 copying hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:52,755 copying hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:52,953 copying hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:53,171 copying hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:53,383 copying hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:53,660 copying hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:53,844 copying hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:54,068 copying hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:54,290 copying hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:54,536 copying hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:54,776 copying hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:55,060 copying hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:55,301 copying hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:55,568 copying hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:55,790 copying hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz -> build/lib/hecatomb/test_data 2023-03-30T05:18:56,053 copying hecatomb/test_data/test_config.yaml -> build/lib/hecatomb/test_data 2023-03-30T05:18:56,057 file hecatomb.py (for module hecatomb) not found 2023-03-30T05:18:56,135 /usr/local/lib/python3.7/dist-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 2023-03-30T05:18:56,136 setuptools.SetuptoolsDeprecationWarning, 2023-03-30T05:18:56,204 installing to build/bdist.linux-armv7l/wheel 2023-03-30T05:18:56,205 running install 2023-03-30T05:18:56,264 running install_lib 2023-03-30T05:18:56,334 creating build/bdist.linux-armv7l 2023-03-30T05:18:56,335 creating build/bdist.linux-armv7l/wheel 2023-03-30T05:18:56,338 creating build/bdist.linux-armv7l/wheel/hecatomb 2023-03-30T05:18:56,340 copying build/lib/hecatomb/hecatomb.VERSION -> build/bdist.linux-armv7l/wheel/hecatomb 2023-03-30T05:18:56,345 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake 2023-03-30T05:18:56,348 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2023-03-30T05:18:56,350 copying build/lib/hecatomb/snakemake/workflow/DownloadDB.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2023-03-30T05:18:56,355 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,357 copying build/lib/hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,361 copying build/lib/hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,364 copying build/lib/hecatomb/snakemake/workflow/scripts/contigCountTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,368 copying build/lib/hecatomb/snakemake/workflow/scripts/mergeSeqTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,372 copying build/lib/hecatomb/snakemake/workflow/scripts/aaBigtable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,375 copying build/lib/hecatomb/snakemake/workflow/scripts/kronaText.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,379 copying build/lib/hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,382 copying build/lib/hecatomb/snakemake/workflow/scripts/sankey.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,387 copying build/lib/hecatomb/snakemake/workflow/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,390 copying build/lib/hecatomb/snakemake/workflow/scripts/seqPropertyTable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,394 copying build/lib/hecatomb/snakemake/workflow/scripts/ntBigtable.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,398 copying build/lib/hecatomb/snakemake/workflow/scripts/orfmFilt.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,401 copying build/lib/hecatomb/snakemake/workflow/scripts/contigKronaText.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,405 copying build/lib/hecatomb/snakemake/workflow/scripts/taxLevelCounts.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,409 copying build/lib/hecatomb/snakemake/workflow/scripts/contigReadTaxon.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,413 copying build/lib/hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/scripts 2023-03-30T05:18:56,418 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules 2023-03-30T05:18:56,421 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:56,423 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/directories.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:56,427 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/targets.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:56,431 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/validate.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:56,435 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/samples_se.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:56,439 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/functions.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:56,442 copying build/lib/hecatomb/snakemake/workflow/rules/preflight/samples_pe.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preflight 2023-03-30T05:18:56,448 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:56,450 copying build/lib/hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:56,455 copying build/lib/hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:56,460 copying build/lib/hecatomb/snakemake/workflow/rules/annotation/read_annotation_orfm.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:56,465 copying build/lib/hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/annotation 2023-03-30T05:18:56,471 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports 2023-03-30T05:18:56,472 copying build/lib/hecatomb/snakemake/workflow/rules/reports/summaries.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports 2023-03-30T05:18:56,476 copying build/lib/hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/reports 2023-03-30T05:18:56,483 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:56,485 copying build/lib/hecatomb/snakemake/workflow/rules/assembly/single_end.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:56,490 copying build/lib/hecatomb/snakemake/workflow/rules/assembly/combine_sample_assemblies.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:56,493 copying build/lib/hecatomb/snakemake/workflow/rules/assembly/README.md -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:56,497 copying build/lib/hecatomb/snakemake/workflow/rules/assembly/longreads.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:56,502 copying build/lib/hecatomb/snakemake/workflow/rules/assembly/paired_end.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/assembly 2023-03-30T05:18:56,508 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:56,510 copying build/lib/hecatomb/snakemake/workflow/rules/preprocessing/single_end.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:56,515 copying build/lib/hecatomb/snakemake/workflow/rules/preprocessing/roundAB.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:56,520 copying build/lib/hecatomb/snakemake/workflow/rules/preprocessing/cluster_seqs.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:56,524 copying build/lib/hecatomb/snakemake/workflow/rules/preprocessing/README.md -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:56,528 copying build/lib/hecatomb/snakemake/workflow/rules/preprocessing/longreads.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:56,532 copying build/lib/hecatomb/snakemake/workflow/rules/preprocessing/paired_end.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/rules/preprocessing 2023-03-30T05:18:56,536 copying build/lib/hecatomb/snakemake/workflow/combineOutputs.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2023-03-30T05:18:56,541 copying build/lib/hecatomb/snakemake/workflow/Hecatomb.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2023-03-30T05:18:56,546 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,548 copying build/lib/hecatomb/snakemake/workflow/envs/canu.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,551 copying build/lib/hecatomb/snakemake/workflow/envs/samtools.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,555 copying build/lib/hecatomb/snakemake/workflow/envs/bbmap.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,559 copying build/lib/hecatomb/snakemake/workflow/envs/plotly.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,562 copying build/lib/hecatomb/snakemake/workflow/envs/dependency_notes.txt -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,566 copying build/lib/hecatomb/snakemake/workflow/envs/megahit.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,569 copying build/lib/hecatomb/snakemake/workflow/envs/curl.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,573 copying build/lib/hecatomb/snakemake/workflow/envs/metaflye.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,576 copying build/lib/hecatomb/snakemake/workflow/envs/seqkit.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,580 copying build/lib/hecatomb/snakemake/workflow/envs/krona.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,584 copying build/lib/hecatomb/snakemake/workflow/envs/minimap2.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,587 copying build/lib/hecatomb/snakemake/workflow/envs/fastp.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,591 copying build/lib/hecatomb/snakemake/workflow/envs/pigz.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,594 copying build/lib/hecatomb/snakemake/workflow/envs/pysam.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,598 copying build/lib/hecatomb/snakemake/workflow/envs/prinseqpp.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,602 copying build/lib/hecatomb/snakemake/workflow/envs/mmseqs2.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/envs 2023-03-30T05:18:56,607 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,609 copying build/lib/hecatomb/snakemake/workflow/report/step10.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,613 copying build/lib/hecatomb/snakemake/workflow/report/host_removed_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,617 copying build/lib/hecatomb/snakemake/workflow/report/step09.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,621 copying build/lib/hecatomb/snakemake/workflow/report/step11.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,624 copying build/lib/hecatomb/snakemake/workflow/report/summary_table.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,628 copying build/lib/hecatomb/snakemake/workflow/report/step13.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,632 copying build/lib/hecatomb/snakemake/workflow/report/protein_annotations.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,635 copying build/lib/hecatomb/snakemake/workflow/report/mapped_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,640 copying build/lib/hecatomb/snakemake/workflow/report/nucleotide_annotations.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,643 copying build/lib/hecatomb/snakemake/workflow/report/raw_read_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,647 copying build/lib/hecatomb/snakemake/workflow/report/sankey.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,651 copying build/lib/hecatomb/snakemake/workflow/report/step08.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,654 copying build/lib/hecatomb/snakemake/workflow/report/step07.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,658 copying build/lib/hecatomb/snakemake/workflow/report/tax_level_counts.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,662 copying build/lib/hecatomb/snakemake/workflow/report/step12.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,665 copying build/lib/hecatomb/snakemake/workflow/report/unclassified_seqtable.rst -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow/report 2023-03-30T05:18:56,669 copying build/lib/hecatomb/snakemake/workflow/AddHost.smk -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/workflow 2023-03-30T05:18:56,674 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile 2023-03-30T05:18:56,677 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm 2023-03-30T05:18:56,679 copying build/lib/hecatomb/snakemake/profile/example_slurm/config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm 2023-03-30T05:18:56,683 copying build/lib/hecatomb/snakemake/profile/example_slurm/slurm-status.py -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/profile/example_slurm 2023-03-30T05:18:56,687 creating build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config 2023-03-30T05:18:56,689 copying build/lib/hecatomb/snakemake/config/dbFiles.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config 2023-03-30T05:18:56,693 copying build/lib/hecatomb/snakemake/config/immutable.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config 2023-03-30T05:18:56,697 copying build/lib/hecatomb/snakemake/config/config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/snakemake/config 2023-03-30T05:18:56,703 creating build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:56,705 copying build/lib/hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:56,938 copying build/lib/hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:57,157 copying build/lib/hecatomb/test_data/test_config.yaml -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:57,161 copying build/lib/hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:57,376 copying build/lib/hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:57,576 copying build/lib/hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:57,830 copying build/lib/hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:58,088 copying build/lib/hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:58,354 copying build/lib/hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:58,585 copying build/lib/hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:58,843 copying build/lib/hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:59,076 copying build/lib/hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:59,346 copying build/lib/hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:59,616 copying build/lib/hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:18:59,951 copying build/lib/hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:19:00,111 copying build/lib/hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:19:00,461 copying build/lib/hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:19:00,691 copying build/lib/hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:19:00,871 copying build/lib/hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:19:01,071 copying build/lib/hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:19:01,303 copying build/lib/hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz -> build/bdist.linux-armv7l/wheel/hecatomb/test_data 2023-03-30T05:19:01,546 copying build/lib/hecatomb/hecatomb.LICENSE -> build/bdist.linux-armv7l/wheel/hecatomb 2023-03-30T05:19:01,549 copying build/lib/hecatomb/__init__.py -> build/bdist.linux-armv7l/wheel/hecatomb 2023-03-30T05:19:01,552 copying build/lib/hecatomb/hecatomb.CITATION -> build/bdist.linux-armv7l/wheel/hecatomb 2023-03-30T05:19:01,555 copying build/lib/hecatomb/__main__.py -> build/bdist.linux-armv7l/wheel/hecatomb 2023-03-30T05:19:01,560 copying build/lib/hecatomb/cli_util.py -> build/bdist.linux-armv7l/wheel/hecatomb 2023-03-30T05:19:01,563 running install_data 2023-03-30T05:19:01,630 creating build/bdist.linux-armv7l/wheel/hecatomb-1.2.0.data 2023-03-30T05:19:01,631 creating build/bdist.linux-armv7l/wheel/hecatomb-1.2.0.data/data 2023-03-30T05:19:01,633 copying README.md -> build/bdist.linux-armv7l/wheel/hecatomb-1.2.0.data/data/. 2023-03-30T05:19:01,637 running install_egg_info 2023-03-30T05:19:01,719 Copying hecatomb.egg-info to build/bdist.linux-armv7l/wheel/hecatomb-1.2.0-py3.7.egg-info 2023-03-30T05:19:01,748 running install_scripts 2023-03-30T05:19:01,781 creating build/bdist.linux-armv7l/wheel/hecatomb-1.2.0.dist-info/WHEEL 2023-03-30T05:19:01,786 creating '/tmp/pip-wheel-5v8g_jjo/hecatomb-1.2.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-03-30T05:19:01,791 adding 'hecatomb/__init__.py' 2023-03-30T05:19:01,795 adding 'hecatomb/__main__.py' 2023-03-30T05:19:01,799 adding 'hecatomb/cli_util.py' 2023-03-30T05:19:01,801 adding 'hecatomb/hecatomb.CITATION' 2023-03-30T05:19:01,804 adding 'hecatomb/hecatomb.LICENSE' 2023-03-30T05:19:01,806 adding 'hecatomb/hecatomb.VERSION' 2023-03-30T05:19:01,811 adding 'hecatomb/snakemake/config/config.yaml' 2023-03-30T05:19:01,814 adding 'hecatomb/snakemake/config/dbFiles.yaml' 2023-03-30T05:19:01,817 adding 'hecatomb/snakemake/config/immutable.yaml' 2023-03-30T05:19:01,821 adding 'hecatomb/snakemake/profile/example_slurm/config.yaml' 2023-03-30T05:19:01,824 adding 'hecatomb/snakemake/profile/example_slurm/slurm-status.py' 2023-03-30T05:19:01,828 adding 'hecatomb/snakemake/workflow/AddHost.smk' 2023-03-30T05:19:01,830 adding 'hecatomb/snakemake/workflow/DownloadDB.smk' 2023-03-30T05:19:01,833 adding 'hecatomb/snakemake/workflow/Hecatomb.smk' 2023-03-30T05:19:01,836 adding 'hecatomb/snakemake/workflow/combineOutputs.smk' 2023-03-30T05:19:01,840 adding 'hecatomb/snakemake/workflow/envs/bbmap.yaml' 2023-03-30T05:19:01,842 adding 'hecatomb/snakemake/workflow/envs/canu.yaml' 2023-03-30T05:19:01,845 adding 'hecatomb/snakemake/workflow/envs/curl.yaml' 2023-03-30T05:19:01,847 adding 'hecatomb/snakemake/workflow/envs/dependency_notes.txt' 2023-03-30T05:19:01,849 adding 'hecatomb/snakemake/workflow/envs/fastp.yaml' 2023-03-30T05:19:01,852 adding 'hecatomb/snakemake/workflow/envs/krona.yaml' 2023-03-30T05:19:01,854 adding 'hecatomb/snakemake/workflow/envs/megahit.yaml' 2023-03-30T05:19:01,856 adding 'hecatomb/snakemake/workflow/envs/metaflye.yaml' 2023-03-30T05:19:01,859 adding 'hecatomb/snakemake/workflow/envs/minimap2.yaml' 2023-03-30T05:19:01,861 adding 'hecatomb/snakemake/workflow/envs/mmseqs2.yaml' 2023-03-30T05:19:01,863 adding 'hecatomb/snakemake/workflow/envs/pigz.yaml' 2023-03-30T05:19:01,865 adding 'hecatomb/snakemake/workflow/envs/plotly.yaml' 2023-03-30T05:19:01,868 adding 'hecatomb/snakemake/workflow/envs/prinseqpp.yaml' 2023-03-30T05:19:01,870 adding 'hecatomb/snakemake/workflow/envs/pysam.yaml' 2023-03-30T05:19:01,872 adding 'hecatomb/snakemake/workflow/envs/samtools.yaml' 2023-03-30T05:19:01,874 adding 'hecatomb/snakemake/workflow/envs/seqkit.yaml' 2023-03-30T05:19:01,878 adding 'hecatomb/snakemake/workflow/report/host_removed_counts.rst' 2023-03-30T05:19:01,880 adding 'hecatomb/snakemake/workflow/report/mapped_counts.rst' 2023-03-30T05:19:01,883 adding 'hecatomb/snakemake/workflow/report/nucleotide_annotations.rst' 2023-03-30T05:19:01,885 adding 'hecatomb/snakemake/workflow/report/protein_annotations.rst' 2023-03-30T05:19:01,887 adding 'hecatomb/snakemake/workflow/report/raw_read_counts.rst' 2023-03-30T05:19:01,889 adding 'hecatomb/snakemake/workflow/report/sankey.rst' 2023-03-30T05:19:01,892 adding 'hecatomb/snakemake/workflow/report/step07.rst' 2023-03-30T05:19:01,894 adding 'hecatomb/snakemake/workflow/report/step08.rst' 2023-03-30T05:19:01,896 adding 'hecatomb/snakemake/workflow/report/step09.rst' 2023-03-30T05:19:01,899 adding 'hecatomb/snakemake/workflow/report/step10.rst' 2023-03-30T05:19:01,901 adding 'hecatomb/snakemake/workflow/report/step11.rst' 2023-03-30T05:19:01,903 adding 'hecatomb/snakemake/workflow/report/step12.rst' 2023-03-30T05:19:01,905 adding 'hecatomb/snakemake/workflow/report/step13.rst' 2023-03-30T05:19:01,908 adding 'hecatomb/snakemake/workflow/report/summary_table.rst' 2023-03-30T05:19:01,910 adding 'hecatomb/snakemake/workflow/report/tax_level_counts.rst' 2023-03-30T05:19:01,912 adding 'hecatomb/snakemake/workflow/report/unclassified_seqtable.rst' 2023-03-30T05:19:01,917 adding 'hecatomb/snakemake/workflow/rules/annotation/contig_annotation.smk' 2023-03-30T05:19:01,920 adding 'hecatomb/snakemake/workflow/rules/annotation/contig_mapping.smk' 2023-03-30T05:19:01,925 adding 'hecatomb/snakemake/workflow/rules/annotation/read_annotation.smk' 2023-03-30T05:19:01,931 adding 'hecatomb/snakemake/workflow/rules/annotation/read_annotation_orfm.smk' 2023-03-30T05:19:01,935 adding 'hecatomb/snakemake/workflow/rules/assembly/README.md' 2023-03-30T05:19:01,938 adding 'hecatomb/snakemake/workflow/rules/assembly/combine_sample_assemblies.smk' 2023-03-30T05:19:01,941 adding 'hecatomb/snakemake/workflow/rules/assembly/longreads.smk' 2023-03-30T05:19:01,945 adding 'hecatomb/snakemake/workflow/rules/assembly/paired_end.smk' 2023-03-30T05:19:01,949 adding 'hecatomb/snakemake/workflow/rules/assembly/single_end.smk' 2023-03-30T05:19:01,953 adding 'hecatomb/snakemake/workflow/rules/preflight/directories.smk' 2023-03-30T05:19:01,956 adding 'hecatomb/snakemake/workflow/rules/preflight/functions.smk' 2023-03-30T05:19:01,960 adding 'hecatomb/snakemake/workflow/rules/preflight/samples_pe.smk' 2023-03-30T05:19:01,962 adding 'hecatomb/snakemake/workflow/rules/preflight/samples_se.smk' 2023-03-30T05:19:01,965 adding 'hecatomb/snakemake/workflow/rules/preflight/targets.smk' 2023-03-30T05:19:01,968 adding 'hecatomb/snakemake/workflow/rules/preflight/validate.smk' 2023-03-30T05:19:01,972 adding 'hecatomb/snakemake/workflow/rules/preprocessing/README.md' 2023-03-30T05:19:01,975 adding 'hecatomb/snakemake/workflow/rules/preprocessing/cluster_seqs.smk' 2023-03-30T05:19:01,977 adding 'hecatomb/snakemake/workflow/rules/preprocessing/longreads.smk' 2023-03-30T05:19:01,981 adding 'hecatomb/snakemake/workflow/rules/preprocessing/paired_end.smk' 2023-03-30T05:19:01,985 adding 'hecatomb/snakemake/workflow/rules/preprocessing/roundAB.smk' 2023-03-30T05:19:01,988 adding 'hecatomb/snakemake/workflow/rules/preprocessing/single_end.smk' 2023-03-30T05:19:01,992 adding 'hecatomb/snakemake/workflow/rules/reports/summaries.smk' 2023-03-30T05:19:01,995 adding 'hecatomb/snakemake/workflow/rules/reports/summaries_optional.smk' 2023-03-30T05:19:02,000 adding 'hecatomb/snakemake/workflow/scripts/__init__.py' 2023-03-30T05:19:02,002 adding 'hecatomb/snakemake/workflow/scripts/aaBigtable.py' 2023-03-30T05:19:02,005 adding 'hecatomb/snakemake/workflow/scripts/aaPrimaryParse.py' 2023-03-30T05:19:02,008 adding 'hecatomb/snakemake/workflow/scripts/aaSecondaryParse.py' 2023-03-30T05:19:02,010 adding 'hecatomb/snakemake/workflow/scripts/contigCountTable.py' 2023-03-30T05:19:02,013 adding 'hecatomb/snakemake/workflow/scripts/contigKronaText.py' 2023-03-30T05:19:02,015 adding 'hecatomb/snakemake/workflow/scripts/contigReadTaxon.py' 2023-03-30T05:19:02,018 adding 'hecatomb/snakemake/workflow/scripts/kronaText.py' 2023-03-30T05:19:02,021 adding 'hecatomb/snakemake/workflow/scripts/mergeSeqTable.py' 2023-03-30T05:19:02,023 adding 'hecatomb/snakemake/workflow/scripts/ntBigtable.py' 2023-03-30T05:19:02,026 adding 'hecatomb/snakemake/workflow/scripts/ntPrimaryParse.py' 2023-03-30T05:19:02,029 adding 'hecatomb/snakemake/workflow/scripts/ntSecondaryLca.py' 2023-03-30T05:19:02,031 adding 'hecatomb/snakemake/workflow/scripts/orfmFilt.py' 2023-03-30T05:19:02,034 adding 'hecatomb/snakemake/workflow/scripts/sankey.py' 2023-03-30T05:19:02,037 adding 'hecatomb/snakemake/workflow/scripts/seqPropertyTable.py' 2023-03-30T05:19:02,040 adding 'hecatomb/snakemake/workflow/scripts/taxLevelCounts.py' 2023-03-30T05:19:03,351 adding 'hecatomb/test_data/A13-04-182-06_TAGCTT_R1.fastq.gz' 2023-03-30T05:19:04,854 adding 'hecatomb/test_data/A13-04-182-06_TAGCTT_R2.fastq.gz' 2023-03-30T05:19:06,355 adding 'hecatomb/test_data/A13-12-250-06_GGCTAC_R1.fastq.gz' 2023-03-30T05:19:07,865 adding 'hecatomb/test_data/A13-12-250-06_GGCTAC_R2.fastq.gz' 2023-03-30T05:19:09,244 adding 'hecatomb/test_data/A13-135-177-06_AGTTCC_R1.fastq.gz' 2023-03-30T05:19:10,727 adding 'hecatomb/test_data/A13-135-177-06_AGTTCC_R2.fastq.gz' 2023-03-30T05:19:12,134 adding 'hecatomb/test_data/A13-151-169-06_ATGTCA_R1.fastq.gz' 2023-03-30T05:19:13,662 adding 'hecatomb/test_data/A13-151-169-06_ATGTCA_R2.fastq.gz' 2023-03-30T05:19:15,107 adding 'hecatomb/test_data/A13-252-114-06_CCGTCC_R1.fastq.gz' 2023-03-30T05:19:16,701 adding 'hecatomb/test_data/A13-252-114-06_CCGTCC_R2.fastq.gz' 2023-03-30T05:19:18,049 adding 'hecatomb/test_data/A13-253-140-06_GTCCGC_R1.fastq.gz' 2023-03-30T05:19:19,562 adding 'hecatomb/test_data/A13-253-140-06_GTCCGC_R2.fastq.gz' 2023-03-30T05:19:21,205 adding 'hecatomb/test_data/A13-255-183-06_GTGGCC_R1.fastq.gz' 2023-03-30T05:19:22,632 adding 'hecatomb/test_data/A13-255-183-06_GTGGCC_R2.fastq.gz' 2023-03-30T05:19:24,375 adding 'hecatomb/test_data/A13-256-115-06_GTTTCG_R1.fastq.gz' 2023-03-30T05:19:25,971 adding 'hecatomb/test_data/A13-256-115-06_GTTTCG_R2.fastq.gz' 2023-03-30T05:19:27,487 adding 'hecatomb/test_data/A13-256-117-06_ACTGAT_R1.fastq.gz' 2023-03-30T05:19:30,530 adding 'hecatomb/test_data/A13-256-117-06_ACTGAT_R2.fastq.gz' 2023-03-30T05:19:31,878 adding 'hecatomb/test_data/A13-258-124-06_CGTACG_R1.fastq.gz' 2023-03-30T05:19:33,440 adding 'hecatomb/test_data/A13-258-124-06_CGTACG_R2.fastq.gz' 2023-03-30T05:19:33,550 adding 'hecatomb/test_data/test_config.yaml' 2023-03-30T05:19:33,556 adding 'hecatomb-1.2.0.data/data/README.md' 2023-03-30T05:19:33,562 adding 'hecatomb-1.2.0.dist-info/METADATA' 2023-03-30T05:19:33,564 adding 'hecatomb-1.2.0.dist-info/WHEEL' 2023-03-30T05:19:33,566 adding 'hecatomb-1.2.0.dist-info/entry_points.txt' 2023-03-30T05:19:33,568 adding 'hecatomb-1.2.0.dist-info/top_level.txt' 2023-03-30T05:19:33,573 adding 'hecatomb-1.2.0.dist-info/RECORD' 2023-03-30T05:19:33,983 removing build/bdist.linux-armv7l/wheel 2023-03-30T05:19:34,293 Building wheel for hecatomb (setup.py): finished with status 'done' 2023-03-30T05:19:40,030 Created wheel for hecatomb: filename=hecatomb-1.2.0-py3-none-any.whl size=98585112 sha256=ad0eaa01aaa37d90124282fa20269ed0e9153ae6f03c8ab3f713b7245f58e98b 2023-03-30T05:19:40,032 Stored in directory: /tmp/pip-ephem-wheel-cache-zcxogokz/wheels/91/1b/0a/ce3153edd0d6bce9641a3e1511fc1fefe66013da2dbc30f74a 2023-03-30T05:19:40,188 Successfully built hecatomb 2023-03-30T05:19:46,438 Removed build tracker: '/tmp/pip-build-tracker-uo3kdbc9'