2024-09-04T09:33:58,490 Created temporary directory: /tmp/pip-build-tracker-k37urg0g 2024-09-04T09:33:58,491 Initialized build tracking at /tmp/pip-build-tracker-k37urg0g 2024-09-04T09:33:58,492 Created build tracker: /tmp/pip-build-tracker-k37urg0g 2024-09-04T09:33:58,492 Entered build tracker: /tmp/pip-build-tracker-k37urg0g 2024-09-04T09:33:58,493 Created temporary directory: /tmp/pip-wheel-62mjppez 2024-09-04T09:33:58,497 Created temporary directory: /tmp/pip-ephem-wheel-cache-mz7tunfc 2024-09-04T09:33:58,541 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-09-04T09:33:58,544 2 location(s) to search for versions of maginator: 2024-09-04T09:33:58,544 * https://pypi.org/simple/maginator/ 2024-09-04T09:33:58,544 * https://www.piwheels.org/simple/maginator/ 2024-09-04T09:33:58,545 Fetching project page and analyzing links: https://pypi.org/simple/maginator/ 2024-09-04T09:33:58,546 Getting page https://pypi.org/simple/maginator/ 2024-09-04T09:33:58,547 Found index url https://pypi.org/simple/ 2024-09-04T09:33:58,764 Fetched page https://pypi.org/simple/maginator/ as application/vnd.pypi.simple.v1+json 2024-09-04T09:33:58,766 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/28/10/ecccd562aaffc3f6d204d7204aec58c58d9a9f6af3ade5cc175db4537a5b/maginator-0.1.8-py3.7.egg (from https://pypi.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,767 Found link https://files.pythonhosted.org/packages/b2/0e/e9f8fab4868fdbeac8e0d4e20739b76094430d0359620da63f5fae1ebb9d/maginator-0.1.8.tar.gz (from https://pypi.org/simple/maginator/) (requires-python:>=3.5), version: 0.1.8 2024-09-04T09:33:58,768 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/33/51/ffee33c05503c602c0583f3968e3e63cde50489be8d9a80e43f0a17d4d29/maginator-0.1.13-py3.10.egg (from https://pypi.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,769 Found link https://files.pythonhosted.org/packages/27/d1/d8b739151ffea3e1dec7103e89dd35113f0bf883897372ab3e92837495a7/maginator-0.1.13.tar.gz (from https://pypi.org/simple/maginator/) (requires-python:>=3.5), version: 0.1.13 2024-09-04T09:33:58,770 Found link https://files.pythonhosted.org/packages/c2/3a/bd37a8cd702b674447ca27c5ca1dc197a99f6be8aa53040d244a065517c6/maginator-0.1.17.tar.gz (from https://pypi.org/simple/maginator/) (requires-python:>=3.5), version: 0.1.17 2024-09-04T09:33:58,771 Skipping link: No binaries permitted for maginator: https://files.pythonhosted.org/packages/c5/43/3eb04ddfd26ab3354a5c5f932f35c600b8bcd92271c1410115a08bf91fd8/maginator-0.1.18-py3-none-any.whl (from https://pypi.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,772 Found link https://files.pythonhosted.org/packages/34/a6/760a35922ab75b39d27477cc808a5eb9dfe02817dc51bd2fbaf5b2a7d0c6/maginator-0.1.18.tar.gz (from https://pypi.org/simple/maginator/) (requires-python:>=3.5), version: 0.1.18 2024-09-04T09:33:58,773 Found link https://files.pythonhosted.org/packages/08/d6/37a1f51d0f7bd4de9ad96f2aa17121470f0a4efd9274573400bca68368f4/maginator-0.1.19.tar.gz (from https://pypi.org/simple/maginator/) (requires-python:>=3.5), version: 0.1.19 2024-09-04T09:33:58,774 Found link https://files.pythonhosted.org/packages/db/be/89e247ebfc09de9774f240da16fdabc55260117c404371245cfb552a7f9d/maginator-0.1.20.tar.gz (from https://pypi.org/simple/maginator/) (requires-python:>=3.5), version: 0.1.20 2024-09-04T09:33:58,775 Found link https://files.pythonhosted.org/packages/38/21/0f7aea47151de305c773e61586e7b9ddd65c01e064fdf7e3b3841e59c4ea/maginator-1.0.0.tar.gz (from https://pypi.org/simple/maginator/) (requires-python:>=3.5), version: 1.0.0 2024-09-04T09:33:58,776 Fetching project page and analyzing links: https://www.piwheels.org/simple/maginator/ 2024-09-04T09:33:58,776 Getting page https://www.piwheels.org/simple/maginator/ 2024-09-04T09:33:58,778 Found index url https://www.piwheels.org/simple/ 2024-09-04T09:33:58,939 Fetched page https://www.piwheels.org/simple/maginator/ as text/html 2024-09-04T09:33:58,942 Skipping link: No binaries permitted for maginator: https://www.piwheels.org/simple/maginator/maginator-0.1.20-py3-none-any.whl#sha256=82ef40fdd5f9dcea92009b50c2f9b24f6af582e7b91f5d48da634b0149542ee6 (from https://www.piwheels.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,943 Skipping link: No binaries permitted for maginator: https://www.piwheels.org/simple/maginator/maginator-0.1.19-py3-none-any.whl#sha256=6b4a26f0b7d95994e9567bf0abb33337bdeb307e8448ea1067c2ec9dfccba91e (from https://www.piwheels.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,944 Skipping link: No binaries permitted for maginator: https://www.piwheels.org/simple/maginator/maginator-0.1.18-py3-none-any.whl#sha256=0114e0d1fe603c8a8422259d735ba660898badb22a1a55852879dd7e245a0bf6 (from https://www.piwheels.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,944 Skipping link: No binaries permitted for maginator: https://www.piwheels.org/simple/maginator/maginator-0.1.17-py3-none-any.whl#sha256=c32d9436f952d95cdff5c8d474120637206df09332600e133f13419537cbd806 (from https://www.piwheels.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,945 Skipping link: No binaries permitted for maginator: https://www.piwheels.org/simple/maginator/maginator-0.1.13-py3-none-any.whl#sha256=bd4768ce02f00c01217d7adf241aad0ee1e1cc23c8f69a5a89be3d521b65b505 (from https://www.piwheels.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,945 Skipping link: No binaries permitted for maginator: https://www.piwheels.org/simple/maginator/maginator-0.1.8-py3-none-any.whl#sha256=cb0efbdc1f46362c03b97cd18b7dd860d2dcc0f4ad09fc15f7d688be7194ff51 (from https://www.piwheels.org/simple/maginator/) (requires-python:>=3.5) 2024-09-04T09:33:58,946 Skipping link: not a file: https://www.piwheels.org/simple/maginator/ 2024-09-04T09:33:58,946 Skipping link: not a file: https://pypi.org/simple/maginator/ 2024-09-04T09:33:58,966 Given no hashes to check 1 links for project 'maginator': discarding no candidates 2024-09-04T09:33:58,968 Collecting maginator==1.0.0 2024-09-04T09:33:58,970 Created temporary directory: /tmp/pip-unpack-z0py1zie 2024-09-04T09:33:59,103 Downloading maginator-1.0.0.tar.gz (57 kB) 2024-09-04T09:33:59,261 Added maginator==1.0.0 from https://files.pythonhosted.org/packages/38/21/0f7aea47151de305c773e61586e7b9ddd65c01e064fdf7e3b3841e59c4ea/maginator-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-k37urg0g' 2024-09-04T09:33:59,263 Running setup.py (path:/tmp/pip-wheel-62mjppez/maginator_27b60513f1eb4b889e0d410237228808/setup.py) egg_info for package maginator 2024-09-04T09:33:59,264 Created temporary directory: /tmp/pip-pip-egg-info-u15o065n 2024-09-04T09:33:59,264 Preparing metadata (setup.py): started 2024-09-04T09:33:59,266 Running command python setup.py egg_info 2024-09-04T09:34:00,358 running egg_info 2024-09-04T09:34:00,359 creating /tmp/pip-pip-egg-info-u15o065n/maginator.egg-info 2024-09-04T09:34:00,387 writing /tmp/pip-pip-egg-info-u15o065n/maginator.egg-info/PKG-INFO 2024-09-04T09:34:00,391 writing dependency_links to /tmp/pip-pip-egg-info-u15o065n/maginator.egg-info/dependency_links.txt 2024-09-04T09:34:00,392 writing entry points to /tmp/pip-pip-egg-info-u15o065n/maginator.egg-info/entry_points.txt 2024-09-04T09:34:00,394 writing requirements to /tmp/pip-pip-egg-info-u15o065n/maginator.egg-info/requires.txt 2024-09-04T09:34:00,395 writing top-level names to /tmp/pip-pip-egg-info-u15o065n/maginator.egg-info/top_level.txt 2024-09-04T09:34:00,396 writing manifest file '/tmp/pip-pip-egg-info-u15o065n/maginator.egg-info/SOURCES.txt' 2024-09-04T09:34:00,486 reading manifest file '/tmp/pip-pip-egg-info-u15o065n/maginator.egg-info/SOURCES.txt' 2024-09-04T09:34:00,488 reading manifest template 'MANIFEST.in' 2024-09-04T09:34:00,505 adding license file 'LICENSE' 2024-09-04T09:34:00,508 writing manifest file '/tmp/pip-pip-egg-info-u15o065n/maginator.egg-info/SOURCES.txt' 2024-09-04T09:34:00,621 Preparing metadata (setup.py): finished with status 'done' 2024-09-04T09:34:00,625 Source in /tmp/pip-wheel-62mjppez/maginator_27b60513f1eb4b889e0d410237228808 has version 1.0.0, which satisfies requirement maginator==1.0.0 from https://files.pythonhosted.org/packages/38/21/0f7aea47151de305c773e61586e7b9ddd65c01e064fdf7e3b3841e59c4ea/maginator-1.0.0.tar.gz 2024-09-04T09:34:00,626 Removed maginator==1.0.0 from https://files.pythonhosted.org/packages/38/21/0f7aea47151de305c773e61586e7b9ddd65c01e064fdf7e3b3841e59c4ea/maginator-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-k37urg0g' 2024-09-04T09:34:00,633 Created temporary directory: /tmp/pip-unpack-svm5prnv 2024-09-04T09:34:00,634 Created temporary directory: /tmp/pip-unpack-eub2ln2a 2024-09-04T09:34:00,634 Building wheels for collected packages: maginator 2024-09-04T09:34:00,638 Created temporary directory: /tmp/pip-wheel-8lwk6dmy 2024-09-04T09:34:00,639 Building wheel for maginator (setup.py): started 2024-09-04T09:34:00,640 Destination directory: /tmp/pip-wheel-8lwk6dmy 2024-09-04T09:34:00,641 Running command python setup.py bdist_wheel 2024-09-04T09:34:01,684 running bdist_wheel 2024-09-04T09:34:01,823 running build 2024-09-04T09:34:01,823 running build_py 2024-09-04T09:34:01,855 creating build 2024-09-04T09:34:01,856 creating build/lib 2024-09-04T09:34:01,856 creating build/lib/maginator 2024-09-04T09:34:01,858 copying maginator/controller.py -> build/lib/maginator 2024-09-04T09:34:01,860 copying maginator/__init__.py -> build/lib/maginator 2024-09-04T09:34:01,861 copying maginator/messages.py -> build/lib/maginator 2024-09-04T09:34:01,863 copying maginator/workflow.py -> build/lib/maginator 2024-09-04T09:34:01,865 copying maginator/main.py -> build/lib/maginator 2024-09-04T09:34:01,867 running egg_info 2024-09-04T09:34:01,894 writing maginator.egg-info/PKG-INFO 2024-09-04T09:34:01,897 writing dependency_links to maginator.egg-info/dependency_links.txt 2024-09-04T09:34:01,899 writing entry points to maginator.egg-info/entry_points.txt 2024-09-04T09:34:01,900 writing requirements to maginator.egg-info/requires.txt 2024-09-04T09:34:01,901 writing top-level names to maginator.egg-info/top_level.txt 2024-09-04T09:34:01,932 reading manifest file 'maginator.egg-info/SOURCES.txt' 2024-09-04T09:34:01,937 reading manifest template 'MANIFEST.in' 2024-09-04T09:34:01,956 adding license file 'LICENSE' 2024-09-04T09:34:01,960 writing manifest file 'maginator.egg-info/SOURCES.txt' 2024-09-04T09:34:01,962 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'maginator.workflow' is absent from the `packages` configuration. 2024-09-04T09:34:01,963 !! 2024-09-04T09:34:01,964 ******************************************************************************** 2024-09-04T09:34:01,964 ############################ 2024-09-04T09:34:01,965 # Package would be ignored # 2024-09-04T09:34:01,965 ############################ 2024-09-04T09:34:01,966 Python recognizes 'maginator.workflow' as an importable package[^1], 2024-09-04T09:34:01,966 but it is absent from setuptools' `packages` configuration. 2024-09-04T09:34:01,967 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-04T09:34:01,968 package, please make sure that 'maginator.workflow' is explicitly added 2024-09-04T09:34:01,969 to the `packages` configuration field. 2024-09-04T09:34:01,970 Alternatively, you can also rely on setuptools' discovery methods 2024-09-04T09:34:01,970 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-04T09:34:01,970 instead of `find_packages(...)`/`find:`). 2024-09-04T09:34:01,971 You can read more about "package discovery" on setuptools documentation page: 2024-09-04T09:34:01,973 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-04T09:34:01,974 If you don't want 'maginator.workflow' to be distributed and are 2024-09-04T09:34:01,974 already explicitly excluding 'maginator.workflow' via 2024-09-04T09:34:01,975 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-04T09:34:01,975 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-04T09:34:01,976 combination with a more fine grained `package-data` configuration. 2024-09-04T09:34:01,977 You can read more about "package data files" on setuptools documentation page: 2024-09-04T09:34:01,977 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-04T09:34:01,978 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-04T09:34:01,979 even if it does not contain any `.py` files. 2024-09-04T09:34:01,979 On the other hand, currently there is no concept of package data 2024-09-04T09:34:01,980 directory, all directories are treated like packages. 2024-09-04T09:34:01,980 ******************************************************************************** 2024-09-04T09:34:01,981 !! 2024-09-04T09:34:01,981 check.warn(importable) 2024-09-04T09:34:01,982 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'maginator.workflow.envs' is absent from the `packages` configuration. 2024-09-04T09:34:01,982 !! 2024-09-04T09:34:01,983 ******************************************************************************** 2024-09-04T09:34:01,984 ############################ 2024-09-04T09:34:01,984 # Package would be ignored # 2024-09-04T09:34:01,985 ############################ 2024-09-04T09:34:01,985 Python recognizes 'maginator.workflow.envs' as an importable package[^1], 2024-09-04T09:34:01,986 but it is absent from setuptools' `packages` configuration. 2024-09-04T09:34:01,987 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-04T09:34:01,987 package, please make sure that 'maginator.workflow.envs' is explicitly added 2024-09-04T09:34:01,988 to the `packages` configuration field. 2024-09-04T09:34:01,989 Alternatively, you can also rely on setuptools' discovery methods 2024-09-04T09:34:01,990 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-04T09:34:01,990 instead of `find_packages(...)`/`find:`). 2024-09-04T09:34:01,991 You can read more about "package discovery" on setuptools documentation page: 2024-09-04T09:34:01,992 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-04T09:34:01,993 If you don't want 'maginator.workflow.envs' to be distributed and are 2024-09-04T09:34:01,994 already explicitly excluding 'maginator.workflow.envs' via 2024-09-04T09:34:01,994 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-04T09:34:01,995 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-04T09:34:01,995 combination with a more fine grained `package-data` configuration. 2024-09-04T09:34:01,996 You can read more about "package data files" on setuptools documentation page: 2024-09-04T09:34:01,997 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-04T09:34:01,998 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-04T09:34:01,999 even if it does not contain any `.py` files. 2024-09-04T09:34:02,000 On the other hand, currently there is no concept of package data 2024-09-04T09:34:02,000 directory, all directories are treated like packages. 2024-09-04T09:34:02,001 ******************************************************************************** 2024-09-04T09:34:02,002 !! 2024-09-04T09:34:02,002 check.warn(importable) 2024-09-04T09:34:02,003 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:215: _Warning: Package 'maginator.workflow.scripts' is absent from the `packages` configuration. 2024-09-04T09:34:02,003 !! 2024-09-04T09:34:02,004 ******************************************************************************** 2024-09-04T09:34:02,005 ############################ 2024-09-04T09:34:02,005 # Package would be ignored # 2024-09-04T09:34:02,005 ############################ 2024-09-04T09:34:02,006 Python recognizes 'maginator.workflow.scripts' as an importable package[^1], 2024-09-04T09:34:02,006 but it is absent from setuptools' `packages` configuration. 2024-09-04T09:34:02,007 This leads to an ambiguous overall configuration. If you want to distribute this 2024-09-04T09:34:02,008 package, please make sure that 'maginator.workflow.scripts' is explicitly added 2024-09-04T09:34:02,009 to the `packages` configuration field. 2024-09-04T09:34:02,010 Alternatively, you can also rely on setuptools' discovery methods 2024-09-04T09:34:02,011 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-09-04T09:34:02,011 instead of `find_packages(...)`/`find:`). 2024-09-04T09:34:02,012 You can read more about "package discovery" on setuptools documentation page: 2024-09-04T09:34:02,013 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-09-04T09:34:02,015 If you don't want 'maginator.workflow.scripts' to be distributed and are 2024-09-04T09:34:02,016 already explicitly excluding 'maginator.workflow.scripts' via 2024-09-04T09:34:02,016 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-09-04T09:34:02,017 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-09-04T09:34:02,018 combination with a more fine grained `package-data` configuration. 2024-09-04T09:34:02,019 You can read more about "package data files" on setuptools documentation page: 2024-09-04T09:34:02,020 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-09-04T09:34:02,022 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-09-04T09:34:02,023 even if it does not contain any `.py` files. 2024-09-04T09:34:02,023 On the other hand, currently there is no concept of package data 2024-09-04T09:34:02,024 directory, all directories are treated like packages. 2024-09-04T09:34:02,025 ******************************************************************************** 2024-09-04T09:34:02,026 !! 2024-09-04T09:34:02,027 check.warn(importable) 2024-09-04T09:34:02,027 creating build/lib/maginator/workflow 2024-09-04T09:34:02,028 copying maginator/workflow/alignment.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,029 copying maginator/workflow/benchmark.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,030 copying maginator/workflow/filter.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,031 copying maginator/workflow/filter_geneclusters.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,031 copying maginator/workflow/functional.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,032 copying maginator/workflow/gene_count_mat.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,033 copying maginator/workflow/gene_tax.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,033 copying maginator/workflow/gtdbtk.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,034 copying maginator/workflow/outgroup.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,035 copying maginator/workflow/parse_gtdbtk.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,035 copying maginator/workflow/phylo.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,036 copying maginator/workflow/pileup.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,037 copying maginator/workflow/pileup_parse.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,038 copying maginator/workflow/prescreening_genes.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,039 copying maginator/workflow/reads_to_bins.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,039 copying maginator/workflow/signature_genes.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,039 copying maginator/workflow/signature_reads.Snakefile -> build/lib/maginator/workflow 2024-09-04T09:34:02,040 creating build/lib/maginator/workflow/envs 2024-09-04T09:34:02,040 copying maginator/workflow/envs/filter_geneclusters.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,041 copying maginator/workflow/envs/filter_geneclusters.yaml.BACKUP.6404.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,042 copying maginator/workflow/envs/filter_geneclusters.yaml.BASE.6404.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,043 copying maginator/workflow/envs/filter_geneclusters.yaml.LOCAL.6404.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,043 copying maginator/workflow/envs/filter_geneclusters.yaml.REMOTE.6404.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,044 copying maginator/workflow/envs/filter_gtdbtk.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,045 copying maginator/workflow/envs/phylo.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,046 copying maginator/workflow/envs/signature_genes.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,046 copying maginator/workflow/envs/signature_reads.yaml -> build/lib/maginator/workflow/envs 2024-09-04T09:34:02,047 creating build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,047 copying maginator/workflow/scripts/Functions_v4.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,048 copying maginator/workflow/scripts/MGS_counts.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,049 copying maginator/workflow/scripts/SG_refinement.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,051 copying maginator/workflow/scripts/abundance_profiles.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,054 copying maginator/workflow/scripts/allele_frequency_mat.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,056 copying maginator/workflow/scripts/benchmark.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,058 copying maginator/workflow/scripts/concat.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,061 copying maginator/workflow/scripts/extract_coverage.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,063 copying maginator/workflow/scripts/filter.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,065 copying maginator/workflow/scripts/functional_profiling.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,067 copying maginator/workflow/scripts/gene_cluster2tax.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,069 copying maginator/workflow/scripts/gene_refinement_plots.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,072 copying maginator/workflow/scripts/marker_genes.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,074 copying maginator/workflow/scripts/matrix2SG_formatconversion.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,076 copying maginator/workflow/scripts/modify_gene_count_matrix.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,078 copying maginator/workflow/scripts/mpileup.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,081 copying maginator/workflow/scripts/parse_gtdbtk.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,083 copying maginator/workflow/scripts/prescreening_genes.R -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,085 copying maginator/workflow/scripts/sort_gene_mat.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,087 copying maginator/workflow/scripts/species_collections.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,089 copying maginator/workflow/scripts/synteny.py -> build/lib/maginator/workflow/scripts 2024-09-04T09:34:02,118 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-09-04T09:34:02,119 !! 2024-09-04T09:34:02,120 ******************************************************************************** 2024-09-04T09:34:02,120 Please avoid running ``setup.py`` directly. 2024-09-04T09:34:02,121 Instead, use pypa/build, pypa/installer or other 2024-09-04T09:34:02,121 standards-based tools. 2024-09-04T09:34:02,122 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-09-04T09:34:02,123 ******************************************************************************** 2024-09-04T09:34:02,124 !! 2024-09-04T09:34:02,124 self.initialize_options() 2024-09-04T09:34:02,147 installing to build/bdist.linux-armv7l/wheel 2024-09-04T09:34:02,147 running install 2024-09-04T09:34:02,172 running install_lib 2024-09-04T09:34:02,199 creating build/bdist.linux-armv7l 2024-09-04T09:34:02,200 creating build/bdist.linux-armv7l/wheel 2024-09-04T09:34:02,201 creating build/bdist.linux-armv7l/wheel/maginator 2024-09-04T09:34:02,202 copying build/lib/maginator/controller.py -> build/bdist.linux-armv7l/wheel/./maginator 2024-09-04T09:34:02,205 copying build/lib/maginator/__init__.py -> build/bdist.linux-armv7l/wheel/./maginator 2024-09-04T09:34:02,207 creating build/bdist.linux-armv7l/wheel/maginator/workflow 2024-09-04T09:34:02,208 copying build/lib/maginator/workflow/parse_gtdbtk.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,210 copying build/lib/maginator/workflow/gene_tax.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,213 creating build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-09-04T09:34:02,214 copying build/lib/maginator/workflow/scripts/sort_gene_mat.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,216 copying build/lib/maginator/workflow/scripts/filter.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,218 copying build/lib/maginator/workflow/scripts/benchmark.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,220 copying build/lib/maginator/workflow/scripts/species_collections.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,222 copying build/lib/maginator/workflow/scripts/marker_genes.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,224 copying build/lib/maginator/workflow/scripts/modify_gene_count_matrix.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,226 copying build/lib/maginator/workflow/scripts/matrix2SG_formatconversion.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,228 copying build/lib/maginator/workflow/scripts/parse_gtdbtk.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,230 copying build/lib/maginator/workflow/scripts/allele_frequency_mat.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,232 copying build/lib/maginator/workflow/scripts/gene_refinement_plots.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,234 copying build/lib/maginator/workflow/scripts/mpileup.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,237 copying build/lib/maginator/workflow/scripts/gene_cluster2tax.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,239 copying build/lib/maginator/workflow/scripts/synteny.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,241 copying build/lib/maginator/workflow/scripts/Functions_v4.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,243 copying build/lib/maginator/workflow/scripts/prescreening_genes.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,245 copying build/lib/maginator/workflow/scripts/extract_coverage.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,246 copying build/lib/maginator/workflow/scripts/SG_refinement.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,249 copying build/lib/maginator/workflow/scripts/functional_profiling.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,250 copying build/lib/maginator/workflow/scripts/concat.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,253 copying build/lib/maginator/workflow/scripts/MGS_counts.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,254 copying build/lib/maginator/workflow/scripts/abundance_profiles.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2024-09-04T09:34:02,257 copying build/lib/maginator/workflow/filter.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,259 creating build/bdist.linux-armv7l/wheel/maginator/workflow/envs 2024-09-04T09:34:02,259 copying build/lib/maginator/workflow/envs/filter_gtdbtk.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,261 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml.LOCAL.6404.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,263 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml.BASE.6404.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,265 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml.REMOTE.6404.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,267 copying build/lib/maginator/workflow/envs/signature_genes.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,268 copying build/lib/maginator/workflow/envs/signature_reads.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,270 copying build/lib/maginator/workflow/envs/phylo.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,272 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,274 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml.BACKUP.6404.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2024-09-04T09:34:02,275 copying build/lib/maginator/workflow/pileup_parse.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,277 copying build/lib/maginator/workflow/benchmark.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,279 copying build/lib/maginator/workflow/functional.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,281 copying build/lib/maginator/workflow/prescreening_genes.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,283 copying build/lib/maginator/workflow/outgroup.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,285 copying build/lib/maginator/workflow/pileup.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,286 copying build/lib/maginator/workflow/gtdbtk.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,288 copying build/lib/maginator/workflow/signature_genes.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,290 copying build/lib/maginator/workflow/phylo.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,292 copying build/lib/maginator/workflow/filter_geneclusters.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,294 copying build/lib/maginator/workflow/gene_count_mat.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,296 copying build/lib/maginator/workflow/alignment.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,298 copying build/lib/maginator/workflow/reads_to_bins.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,300 copying build/lib/maginator/workflow/signature_reads.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2024-09-04T09:34:02,302 copying build/lib/maginator/messages.py -> build/bdist.linux-armv7l/wheel/./maginator 2024-09-04T09:34:02,304 copying build/lib/maginator/workflow.py -> build/bdist.linux-armv7l/wheel/./maginator 2024-09-04T09:34:02,306 copying build/lib/maginator/main.py -> build/bdist.linux-armv7l/wheel/./maginator 2024-09-04T09:34:02,308 running install_egg_info 2024-09-04T09:34:02,340 Copying maginator.egg-info to build/bdist.linux-armv7l/wheel/./maginator-1.0.0-py3.11.egg-info 2024-09-04T09:34:02,354 running install_scripts 2024-09-04T09:34:02,370 creating build/bdist.linux-armv7l/wheel/maginator-1.0.0.dist-info/WHEEL 2024-09-04T09:34:02,372 creating '/tmp/pip-wheel-8lwk6dmy/maginator-1.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-09-04T09:34:02,374 adding 'maginator/__init__.py' 2024-09-04T09:34:02,376 adding 'maginator/controller.py' 2024-09-04T09:34:02,378 adding 'maginator/main.py' 2024-09-04T09:34:02,379 adding 'maginator/messages.py' 2024-09-04T09:34:02,381 adding 'maginator/workflow.py' 2024-09-04T09:34:02,383 adding 'maginator/workflow/alignment.Snakefile' 2024-09-04T09:34:02,384 adding 'maginator/workflow/benchmark.Snakefile' 2024-09-04T09:34:02,385 adding 'maginator/workflow/filter.Snakefile' 2024-09-04T09:34:02,387 adding 'maginator/workflow/filter_geneclusters.Snakefile' 2024-09-04T09:34:02,388 adding 'maginator/workflow/functional.Snakefile' 2024-09-04T09:34:02,389 adding 'maginator/workflow/gene_count_mat.Snakefile' 2024-09-04T09:34:02,391 adding 'maginator/workflow/gene_tax.Snakefile' 2024-09-04T09:34:02,392 adding 'maginator/workflow/gtdbtk.Snakefile' 2024-09-04T09:34:02,393 adding 'maginator/workflow/outgroup.Snakefile' 2024-09-04T09:34:02,395 adding 'maginator/workflow/parse_gtdbtk.Snakefile' 2024-09-04T09:34:02,396 adding 'maginator/workflow/phylo.Snakefile' 2024-09-04T09:34:02,397 adding 'maginator/workflow/pileup.Snakefile' 2024-09-04T09:34:02,398 adding 'maginator/workflow/pileup_parse.Snakefile' 2024-09-04T09:34:02,400 adding 'maginator/workflow/prescreening_genes.Snakefile' 2024-09-04T09:34:02,402 adding 'maginator/workflow/reads_to_bins.Snakefile' 2024-09-04T09:34:02,403 adding 'maginator/workflow/signature_genes.Snakefile' 2024-09-04T09:34:02,405 adding 'maginator/workflow/signature_reads.Snakefile' 2024-09-04T09:34:02,406 adding 'maginator/workflow/envs/filter_geneclusters.yaml' 2024-09-04T09:34:02,408 adding 'maginator/workflow/envs/filter_geneclusters.yaml.BACKUP.6404.yaml' 2024-09-04T09:34:02,409 adding 'maginator/workflow/envs/filter_geneclusters.yaml.BASE.6404.yaml' 2024-09-04T09:34:02,410 adding 'maginator/workflow/envs/filter_geneclusters.yaml.LOCAL.6404.yaml' 2024-09-04T09:34:02,411 adding 'maginator/workflow/envs/filter_geneclusters.yaml.REMOTE.6404.yaml' 2024-09-04T09:34:02,412 adding 'maginator/workflow/envs/filter_gtdbtk.yaml' 2024-09-04T09:34:02,413 adding 'maginator/workflow/envs/phylo.yaml' 2024-09-04T09:34:02,414 adding 'maginator/workflow/envs/signature_genes.yaml' 2024-09-04T09:34:02,416 adding 'maginator/workflow/envs/signature_reads.yaml' 2024-09-04T09:34:02,418 adding 'maginator/workflow/scripts/Functions_v4.R' 2024-09-04T09:34:02,419 adding 'maginator/workflow/scripts/MGS_counts.R' 2024-09-04T09:34:02,421 adding 'maginator/workflow/scripts/SG_refinement.R' 2024-09-04T09:34:02,423 adding 'maginator/workflow/scripts/abundance_profiles.R' 2024-09-04T09:34:02,424 adding 'maginator/workflow/scripts/allele_frequency_mat.R' 2024-09-04T09:34:02,425 adding 'maginator/workflow/scripts/benchmark.py' 2024-09-04T09:34:02,427 adding 'maginator/workflow/scripts/concat.py' 2024-09-04T09:34:02,428 adding 'maginator/workflow/scripts/extract_coverage.py' 2024-09-04T09:34:02,429 adding 'maginator/workflow/scripts/filter.py' 2024-09-04T09:34:02,430 adding 'maginator/workflow/scripts/functional_profiling.R' 2024-09-04T09:34:02,431 adding 'maginator/workflow/scripts/gene_cluster2tax.py' 2024-09-04T09:34:02,433 adding 'maginator/workflow/scripts/gene_refinement_plots.R' 2024-09-04T09:34:02,435 adding 'maginator/workflow/scripts/marker_genes.py' 2024-09-04T09:34:02,436 adding 'maginator/workflow/scripts/matrix2SG_formatconversion.R' 2024-09-04T09:34:02,437 adding 'maginator/workflow/scripts/modify_gene_count_matrix.R' 2024-09-04T09:34:02,440 adding 'maginator/workflow/scripts/mpileup.py' 2024-09-04T09:34:02,441 adding 'maginator/workflow/scripts/parse_gtdbtk.py' 2024-09-04T09:34:02,443 adding 'maginator/workflow/scripts/prescreening_genes.R' 2024-09-04T09:34:02,444 adding 'maginator/workflow/scripts/sort_gene_mat.py' 2024-09-04T09:34:02,445 adding 'maginator/workflow/scripts/species_collections.py' 2024-09-04T09:34:02,447 adding 'maginator/workflow/scripts/synteny.py' 2024-09-04T09:34:02,449 adding 'maginator-1.0.0.dist-info/LICENSE' 2024-09-04T09:34:02,451 adding 'maginator-1.0.0.dist-info/METADATA' 2024-09-04T09:34:02,452 adding 'maginator-1.0.0.dist-info/WHEEL' 2024-09-04T09:34:02,453 adding 'maginator-1.0.0.dist-info/entry_points.txt' 2024-09-04T09:34:02,453 adding 'maginator-1.0.0.dist-info/top_level.txt' 2024-09-04T09:34:02,455 adding 'maginator-1.0.0.dist-info/RECORD' 2024-09-04T09:34:02,457 removing build/bdist.linux-armv7l/wheel 2024-09-04T09:34:02,584 Building wheel for maginator (setup.py): finished with status 'done' 2024-09-04T09:34:02,588 Created wheel for maginator: filename=maginator-1.0.0-py3-none-any.whl size=71447 sha256=9d5bb09be370ddd74b0dc695731e4f44a35f7982a3bad6bf2206569a943c2733 2024-09-04T09:34:02,589 Stored in directory: /tmp/pip-ephem-wheel-cache-mz7tunfc/wheels/dc/bc/e5/cc4e9cdf3388ceafc6204f98b06edb5c57d846355c6e084c09 2024-09-04T09:34:02,602 Successfully built maginator 2024-09-04T09:34:02,607 Removed build tracker: '/tmp/pip-build-tracker-k37urg0g'