2025-01-09T14:37:28,117 Created temporary directory: /tmp/pip-build-tracker-j_lmkkts 2025-01-09T14:37:28,119 Initialized build tracking at /tmp/pip-build-tracker-j_lmkkts 2025-01-09T14:37:28,119 Created build tracker: /tmp/pip-build-tracker-j_lmkkts 2025-01-09T14:37:28,120 Entered build tracker: /tmp/pip-build-tracker-j_lmkkts 2025-01-09T14:37:28,121 Created temporary directory: /tmp/pip-wheel-ghr7h0of 2025-01-09T14:37:28,125 Created temporary directory: /tmp/pip-ephem-wheel-cache-d3ash4x4 2025-01-09T14:37:28,169 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-01-09T14:37:28,172 2 location(s) to search for versions of maginator: 2025-01-09T14:37:28,172 * https://pypi.org/simple/maginator/ 2025-01-09T14:37:28,172 * https://www.piwheels.org/simple/maginator/ 2025-01-09T14:37:28,173 Fetching project page and analyzing links: https://pypi.org/simple/maginator/ 2025-01-09T14:37:28,174 Getting page https://pypi.org/simple/maginator/ 2025-01-09T14:37:28,175 Found index url https://pypi.org/simple/ 2025-01-09T14:37:28,396 Fetched page https://pypi.org/simple/maginator/ as application/vnd.pypi.simple.v1+json 2025-01-09T14:37:28,399 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) 2025-01-09T14:37:28,400 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 2025-01-09T14:37:28,401 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) 2025-01-09T14:37:28,402 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 2025-01-09T14:37:28,403 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 2025-01-09T14:37:28,404 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) 2025-01-09T14:37:28,405 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 2025-01-09T14:37:28,406 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 2025-01-09T14:37:28,407 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 2025-01-09T14:37:28,408 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 2025-01-09T14:37:28,408 Skipping link: No binaries permitted for maginator: https://files.pythonhosted.org/packages/4d/a8/c0447e0df0e063e58d248f02fa0ef6a26129aa41475bce4d4bf1d415a33c/maginator-1.0.1-py3-none-any.whl (from https://pypi.org/simple/maginator/) (requires-python:>=3.5) 2025-01-09T14:37:28,409 Found link https://files.pythonhosted.org/packages/8e/df/2e97b6dee2f87c5b8ae7184aeecfb0ca049aec4976d702e30c69f5059b1b/maginator-1.0.1.tar.gz (from https://pypi.org/simple/maginator/) (requires-python:>=3.5), version: 1.0.1 2025-01-09T14:37:28,410 Fetching project page and analyzing links: https://www.piwheels.org/simple/maginator/ 2025-01-09T14:37:28,411 Getting page https://www.piwheels.org/simple/maginator/ 2025-01-09T14:37:28,413 Found index url https://www.piwheels.org/simple/ 2025-01-09T14:37:28,586 Fetched page https://www.piwheels.org/simple/maginator/ as text/html 2025-01-09T14:37:28,589 Skipping link: No binaries permitted for maginator: https://www.piwheels.org/simple/maginator/maginator-1.0.0-py3-none-any.whl#sha256=9d5bb09be370ddd74b0dc695731e4f44a35f7982a3bad6bf2206569a943c2733 (from https://www.piwheels.org/simple/maginator/) (requires-python:>=3.5) 2025-01-09T14:37:28,590 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) 2025-01-09T14:37:28,591 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) 2025-01-09T14:37:28,591 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) 2025-01-09T14:37:28,591 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) 2025-01-09T14:37:28,592 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) 2025-01-09T14:37:28,593 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) 2025-01-09T14:37:28,593 Skipping link: not a file: https://www.piwheels.org/simple/maginator/ 2025-01-09T14:37:28,594 Skipping link: not a file: https://pypi.org/simple/maginator/ 2025-01-09T14:37:28,614 Given no hashes to check 1 links for project 'maginator': discarding no candidates 2025-01-09T14:37:28,616 Collecting maginator==1.0.1 2025-01-09T14:37:28,618 Created temporary directory: /tmp/pip-unpack-30k2urq4 2025-01-09T14:37:28,838 Downloading maginator-1.0.1.tar.gz (57 kB) 2025-01-09T14:37:29,005 Added maginator==1.0.1 from https://files.pythonhosted.org/packages/8e/df/2e97b6dee2f87c5b8ae7184aeecfb0ca049aec4976d702e30c69f5059b1b/maginator-1.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-j_lmkkts' 2025-01-09T14:37:29,007 Running setup.py (path:/tmp/pip-wheel-ghr7h0of/maginator_516cb0aeea654315bd93100bc311a997/setup.py) egg_info for package maginator 2025-01-09T14:37:29,008 Created temporary directory: /tmp/pip-pip-egg-info-xe6darfg 2025-01-09T14:37:29,009 Preparing metadata (setup.py): started 2025-01-09T14:37:29,010 Running command python setup.py egg_info 2025-01-09T14:37:30,107 running egg_info 2025-01-09T14:37:30,135 creating /tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info 2025-01-09T14:37:30,137 writing /tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info/PKG-INFO 2025-01-09T14:37:30,141 writing dependency_links to /tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info/dependency_links.txt 2025-01-09T14:37:30,143 writing entry points to /tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info/entry_points.txt 2025-01-09T14:37:30,145 writing requirements to /tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info/requires.txt 2025-01-09T14:37:30,146 writing top-level names to /tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info/top_level.txt 2025-01-09T14:37:30,148 writing manifest file '/tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info/SOURCES.txt' 2025-01-09T14:37:30,238 reading manifest file '/tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info/SOURCES.txt' 2025-01-09T14:37:30,240 reading manifest template 'MANIFEST.in' 2025-01-09T14:37:30,258 adding license file 'LICENSE' 2025-01-09T14:37:30,263 writing manifest file '/tmp/pip-pip-egg-info-xe6darfg/maginator.egg-info/SOURCES.txt' 2025-01-09T14:37:30,371 Preparing metadata (setup.py): finished with status 'done' 2025-01-09T14:37:30,376 Source in /tmp/pip-wheel-ghr7h0of/maginator_516cb0aeea654315bd93100bc311a997 has version 1.0.1, which satisfies requirement maginator==1.0.1 from https://files.pythonhosted.org/packages/8e/df/2e97b6dee2f87c5b8ae7184aeecfb0ca049aec4976d702e30c69f5059b1b/maginator-1.0.1.tar.gz 2025-01-09T14:37:30,377 Removed maginator==1.0.1 from https://files.pythonhosted.org/packages/8e/df/2e97b6dee2f87c5b8ae7184aeecfb0ca049aec4976d702e30c69f5059b1b/maginator-1.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-j_lmkkts' 2025-01-09T14:37:30,383 Created temporary directory: /tmp/pip-unpack-5hrvwoj5 2025-01-09T14:37:30,384 Created temporary directory: /tmp/pip-unpack-ow7u28m8 2025-01-09T14:37:30,385 Building wheels for collected packages: maginator 2025-01-09T14:37:30,389 Created temporary directory: /tmp/pip-wheel-4gae16k7 2025-01-09T14:37:30,389 Building wheel for maginator (setup.py): started 2025-01-09T14:37:30,391 Destination directory: /tmp/pip-wheel-4gae16k7 2025-01-09T14:37:30,391 Running command python setup.py bdist_wheel 2025-01-09T14:37:31,407 running bdist_wheel 2025-01-09T14:37:31,542 running build 2025-01-09T14:37:31,542 running build_py 2025-01-09T14:37:31,573 creating build/lib/maginator 2025-01-09T14:37:31,576 copying maginator/main.py -> build/lib/maginator 2025-01-09T14:37:31,579 copying maginator/controller.py -> build/lib/maginator 2025-01-09T14:37:31,581 copying maginator/messages.py -> build/lib/maginator 2025-01-09T14:37:31,583 copying maginator/workflow.py -> build/lib/maginator 2025-01-09T14:37:31,585 copying maginator/__init__.py -> build/lib/maginator 2025-01-09T14:37:31,587 running egg_info 2025-01-09T14:37:31,615 writing maginator.egg-info/PKG-INFO 2025-01-09T14:37:31,618 writing dependency_links to maginator.egg-info/dependency_links.txt 2025-01-09T14:37:31,620 writing entry points to maginator.egg-info/entry_points.txt 2025-01-09T14:37:31,621 writing requirements to maginator.egg-info/requires.txt 2025-01-09T14:37:31,622 writing top-level names to maginator.egg-info/top_level.txt 2025-01-09T14:37:31,654 reading manifest file 'maginator.egg-info/SOURCES.txt' 2025-01-09T14:37:31,659 reading manifest template 'MANIFEST.in' 2025-01-09T14:37:31,677 adding license file 'LICENSE' 2025-01-09T14:37:31,682 writing manifest file 'maginator.egg-info/SOURCES.txt' 2025-01-09T14:37:31,686 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'maginator.workflow' is absent from the `packages` configuration. 2025-01-09T14:37:31,686 !! 2025-01-09T14:37:31,687 ******************************************************************************** 2025-01-09T14:37:31,688 ############################ 2025-01-09T14:37:31,688 # Package would be ignored # 2025-01-09T14:37:31,689 ############################ 2025-01-09T14:37:31,690 Python recognizes 'maginator.workflow' as an importable package[^1], 2025-01-09T14:37:31,690 but it is absent from setuptools' `packages` configuration. 2025-01-09T14:37:31,691 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-09T14:37:31,692 package, please make sure that 'maginator.workflow' is explicitly added 2025-01-09T14:37:31,693 to the `packages` configuration field. 2025-01-09T14:37:31,694 Alternatively, you can also rely on setuptools' discovery methods 2025-01-09T14:37:31,695 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-09T14:37:31,695 instead of `find_packages(...)`/`find:`). 2025-01-09T14:37:31,696 You can read more about "package discovery" on setuptools documentation page: 2025-01-09T14:37:31,697 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-09T14:37:31,698 If you don't want 'maginator.workflow' to be distributed and are 2025-01-09T14:37:31,699 already explicitly excluding 'maginator.workflow' via 2025-01-09T14:37:31,699 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-09T14:37:31,700 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-09T14:37:31,700 combination with a more fine grained `package-data` configuration. 2025-01-09T14:37:31,701 You can read more about "package data files" on setuptools documentation page: 2025-01-09T14:37:31,702 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-09T14:37:31,704 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-09T14:37:31,705 even if it does not contain any `.py` files. 2025-01-09T14:37:31,705 On the other hand, currently there is no concept of package data 2025-01-09T14:37:31,706 directory, all directories are treated like packages. 2025-01-09T14:37:31,706 ******************************************************************************** 2025-01-09T14:37:31,707 !! 2025-01-09T14:37:31,708 check.warn(importable) 2025-01-09T14:37:31,708 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'maginator.workflow.envs' is absent from the `packages` configuration. 2025-01-09T14:37:31,709 !! 2025-01-09T14:37:31,710 ******************************************************************************** 2025-01-09T14:37:31,711 ############################ 2025-01-09T14:37:31,711 # Package would be ignored # 2025-01-09T14:37:31,712 ############################ 2025-01-09T14:37:31,713 Python recognizes 'maginator.workflow.envs' as an importable package[^1], 2025-01-09T14:37:31,713 but it is absent from setuptools' `packages` configuration. 2025-01-09T14:37:31,714 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-09T14:37:31,715 package, please make sure that 'maginator.workflow.envs' is explicitly added 2025-01-09T14:37:31,715 to the `packages` configuration field. 2025-01-09T14:37:31,717 Alternatively, you can also rely on setuptools' discovery methods 2025-01-09T14:37:31,717 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-09T14:37:31,718 instead of `find_packages(...)`/`find:`). 2025-01-09T14:37:31,719 You can read more about "package discovery" on setuptools documentation page: 2025-01-09T14:37:31,720 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-09T14:37:31,721 If you don't want 'maginator.workflow.envs' to be distributed and are 2025-01-09T14:37:31,722 already explicitly excluding 'maginator.workflow.envs' via 2025-01-09T14:37:31,722 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-09T14:37:31,723 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-09T14:37:31,723 combination with a more fine grained `package-data` configuration. 2025-01-09T14:37:31,724 You can read more about "package data files" on setuptools documentation page: 2025-01-09T14:37:31,725 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-09T14:37:31,727 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-09T14:37:31,727 even if it does not contain any `.py` files. 2025-01-09T14:37:31,728 On the other hand, currently there is no concept of package data 2025-01-09T14:37:31,728 directory, all directories are treated like packages. 2025-01-09T14:37:31,728 ******************************************************************************** 2025-01-09T14:37:31,729 !! 2025-01-09T14:37:31,730 check.warn(importable) 2025-01-09T14:37:31,730 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:220: _Warning: Package 'maginator.workflow.scripts' is absent from the `packages` configuration. 2025-01-09T14:37:31,731 !! 2025-01-09T14:37:31,731 ******************************************************************************** 2025-01-09T14:37:31,732 ############################ 2025-01-09T14:37:31,732 # Package would be ignored # 2025-01-09T14:37:31,733 ############################ 2025-01-09T14:37:31,733 Python recognizes 'maginator.workflow.scripts' as an importable package[^1], 2025-01-09T14:37:31,734 but it is absent from setuptools' `packages` configuration. 2025-01-09T14:37:31,735 This leads to an ambiguous overall configuration. If you want to distribute this 2025-01-09T14:37:31,735 package, please make sure that 'maginator.workflow.scripts' is explicitly added 2025-01-09T14:37:31,736 to the `packages` configuration field. 2025-01-09T14:37:31,737 Alternatively, you can also rely on setuptools' discovery methods 2025-01-09T14:37:31,738 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-01-09T14:37:31,738 instead of `find_packages(...)`/`find:`). 2025-01-09T14:37:31,739 You can read more about "package discovery" on setuptools documentation page: 2025-01-09T14:37:31,740 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-01-09T14:37:31,741 If you don't want 'maginator.workflow.scripts' to be distributed and are 2025-01-09T14:37:31,742 already explicitly excluding 'maginator.workflow.scripts' via 2025-01-09T14:37:31,742 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-01-09T14:37:31,743 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-01-09T14:37:31,744 combination with a more fine grained `package-data` configuration. 2025-01-09T14:37:31,745 You can read more about "package data files" on setuptools documentation page: 2025-01-09T14:37:31,746 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-01-09T14:37:31,747 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-01-09T14:37:31,748 even if it does not contain any `.py` files. 2025-01-09T14:37:31,749 On the other hand, currently there is no concept of package data 2025-01-09T14:37:31,750 directory, all directories are treated like packages. 2025-01-09T14:37:31,750 ******************************************************************************** 2025-01-09T14:37:31,751 !! 2025-01-09T14:37:31,752 check.warn(importable) 2025-01-09T14:37:31,752 creating build/lib/maginator/workflow 2025-01-09T14:37:31,753 copying maginator/workflow/alignment.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,753 copying maginator/workflow/benchmark.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,754 copying maginator/workflow/filter.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,754 copying maginator/workflow/filter_geneclusters.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,755 copying maginator/workflow/functional.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,756 copying maginator/workflow/gene_count_mat.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,756 copying maginator/workflow/gene_tax.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,757 copying maginator/workflow/gtdbtk.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,757 copying maginator/workflow/outgroup.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,758 copying maginator/workflow/parse_gtdbtk.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,758 copying maginator/workflow/phylo.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,759 copying maginator/workflow/pileup.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,759 copying maginator/workflow/pileup_parse.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,760 copying maginator/workflow/prescreening_genes.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,760 copying maginator/workflow/reads_to_bins.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,761 copying maginator/workflow/signature_genes.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,761 copying maginator/workflow/signature_reads.Snakefile -> build/lib/maginator/workflow 2025-01-09T14:37:31,762 creating build/lib/maginator/workflow/envs 2025-01-09T14:37:31,762 copying maginator/workflow/envs/filter_geneclusters.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,763 copying maginator/workflow/envs/filter_geneclusters.yaml.BACKUP.6404.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,763 copying maginator/workflow/envs/filter_geneclusters.yaml.BASE.6404.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,764 copying maginator/workflow/envs/filter_geneclusters.yaml.LOCAL.6404.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,764 copying maginator/workflow/envs/filter_geneclusters.yaml.REMOTE.6404.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,765 copying maginator/workflow/envs/filter_gtdbtk.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,765 copying maginator/workflow/envs/phylo.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,766 copying maginator/workflow/envs/signature_genes.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,768 copying maginator/workflow/envs/signature_reads.yaml -> build/lib/maginator/workflow/envs 2025-01-09T14:37:31,770 creating build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,771 copying maginator/workflow/scripts/Functions_v4.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,774 copying maginator/workflow/scripts/MGS_counts.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,776 copying maginator/workflow/scripts/SG_refinement.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,779 copying maginator/workflow/scripts/abundance_profiles.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,782 copying maginator/workflow/scripts/allele_frequency_mat.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,785 copying maginator/workflow/scripts/benchmark.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,787 copying maginator/workflow/scripts/concat.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,790 copying maginator/workflow/scripts/extract_coverage.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,792 copying maginator/workflow/scripts/filter.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,795 copying maginator/workflow/scripts/functional_profiling.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,797 copying maginator/workflow/scripts/gene_cluster2tax.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,800 copying maginator/workflow/scripts/gene_refinement_plots.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,803 copying maginator/workflow/scripts/marker_genes.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,806 copying maginator/workflow/scripts/matrix2SG_formatconversion.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,808 copying maginator/workflow/scripts/modify_gene_count_matrix.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,811 copying maginator/workflow/scripts/mpileup.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,814 copying maginator/workflow/scripts/parse_gtdbtk.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,817 copying maginator/workflow/scripts/prescreening_genes.R -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,820 copying maginator/workflow/scripts/sort_gene_mat.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,823 copying maginator/workflow/scripts/species_collections.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,825 copying maginator/workflow/scripts/synteny.py -> build/lib/maginator/workflow/scripts 2025-01-09T14:37:31,856 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-01-09T14:37:31,856 !! 2025-01-09T14:37:31,857 ******************************************************************************** 2025-01-09T14:37:31,858 Please avoid running ``setup.py`` directly. 2025-01-09T14:37:31,858 Instead, use pypa/build, pypa/installer or other 2025-01-09T14:37:31,859 standards-based tools. 2025-01-09T14:37:31,860 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-01-09T14:37:31,860 ******************************************************************************** 2025-01-09T14:37:31,861 !! 2025-01-09T14:37:31,862 self.initialize_options() 2025-01-09T14:37:31,886 installing to build/bdist.linux-armv7l/wheel 2025-01-09T14:37:31,887 running install 2025-01-09T14:37:31,911 running install_lib 2025-01-09T14:37:31,943 creating build/bdist.linux-armv7l/wheel 2025-01-09T14:37:31,945 creating build/bdist.linux-armv7l/wheel/maginator 2025-01-09T14:37:31,946 copying build/lib/maginator/main.py -> build/bdist.linux-armv7l/wheel/./maginator 2025-01-09T14:37:31,949 copying build/lib/maginator/controller.py -> build/bdist.linux-armv7l/wheel/./maginator 2025-01-09T14:37:31,951 copying build/lib/maginator/messages.py -> build/bdist.linux-armv7l/wheel/./maginator 2025-01-09T14:37:31,954 creating build/bdist.linux-armv7l/wheel/maginator/workflow 2025-01-09T14:37:31,956 creating build/bdist.linux-armv7l/wheel/maginator/workflow/envs 2025-01-09T14:37:31,958 copying build/lib/maginator/workflow/envs/filter_gtdbtk.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,960 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml.BASE.6404.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,962 copying build/lib/maginator/workflow/envs/signature_genes.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,964 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,966 copying build/lib/maginator/workflow/envs/phylo.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,967 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml.REMOTE.6404.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,969 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml.LOCAL.6404.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,971 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml.BACKUP.6404.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,973 copying build/lib/maginator/workflow/envs/signature_reads.yaml -> build/bdist.linux-armv7l/wheel/./maginator/workflow/envs 2025-01-09T14:37:31,975 copying build/lib/maginator/workflow/pileup_parse.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:31,977 copying build/lib/maginator/workflow/pileup.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:31,980 creating build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2025-01-09T14:37:31,981 copying build/lib/maginator/workflow/scripts/MGS_counts.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,983 copying build/lib/maginator/workflow/scripts/matrix2SG_formatconversion.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,984 copying build/lib/maginator/workflow/scripts/benchmark.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,986 copying build/lib/maginator/workflow/scripts/gene_refinement_plots.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,988 copying build/lib/maginator/workflow/scripts/species_collections.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,990 copying build/lib/maginator/workflow/scripts/SG_refinement.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,993 copying build/lib/maginator/workflow/scripts/concat.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,995 copying build/lib/maginator/workflow/scripts/gene_cluster2tax.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,997 copying build/lib/maginator/workflow/scripts/prescreening_genes.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:31,999 copying build/lib/maginator/workflow/scripts/extract_coverage.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,000 copying build/lib/maginator/workflow/scripts/Functions_v4.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,003 copying build/lib/maginator/workflow/scripts/modify_gene_count_matrix.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,005 copying build/lib/maginator/workflow/scripts/filter.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,006 copying build/lib/maginator/workflow/scripts/sort_gene_mat.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,008 copying build/lib/maginator/workflow/scripts/functional_profiling.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,010 copying build/lib/maginator/workflow/scripts/marker_genes.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,013 copying build/lib/maginator/workflow/scripts/mpileup.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,016 copying build/lib/maginator/workflow/scripts/allele_frequency_mat.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,017 copying build/lib/maginator/workflow/scripts/synteny.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,019 copying build/lib/maginator/workflow/scripts/parse_gtdbtk.py -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,022 copying build/lib/maginator/workflow/scripts/abundance_profiles.R -> build/bdist.linux-armv7l/wheel/./maginator/workflow/scripts 2025-01-09T14:37:32,024 copying build/lib/maginator/workflow/filter_geneclusters.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,026 copying build/lib/maginator/workflow/functional.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,028 copying build/lib/maginator/workflow/benchmark.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,030 copying build/lib/maginator/workflow/gtdbtk.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,032 copying build/lib/maginator/workflow/prescreening_genes.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,034 copying build/lib/maginator/workflow/signature_genes.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,036 copying build/lib/maginator/workflow/gene_tax.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,038 copying build/lib/maginator/workflow/reads_to_bins.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,041 copying build/lib/maginator/workflow/alignment.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,043 copying build/lib/maginator/workflow/filter.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,045 copying build/lib/maginator/workflow/phylo.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,046 copying build/lib/maginator/workflow/gene_count_mat.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,049 copying build/lib/maginator/workflow/outgroup.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,051 copying build/lib/maginator/workflow/signature_reads.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,053 copying build/lib/maginator/workflow/parse_gtdbtk.Snakefile -> build/bdist.linux-armv7l/wheel/./maginator/workflow 2025-01-09T14:37:32,055 copying build/lib/maginator/workflow.py -> build/bdist.linux-armv7l/wheel/./maginator 2025-01-09T14:37:32,057 copying build/lib/maginator/__init__.py -> build/bdist.linux-armv7l/wheel/./maginator 2025-01-09T14:37:32,059 running install_egg_info 2025-01-09T14:37:32,093 Copying maginator.egg-info to build/bdist.linux-armv7l/wheel/./maginator-1.0.1-py3.11.egg-info 2025-01-09T14:37:32,108 running install_scripts 2025-01-09T14:37:32,124 creating build/bdist.linux-armv7l/wheel/maginator-1.0.1.dist-info/WHEEL 2025-01-09T14:37:32,127 creating '/tmp/pip-wheel-4gae16k7/maginator-1.0.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-01-09T14:37:32,129 adding 'maginator/__init__.py' 2025-01-09T14:37:32,131 adding 'maginator/controller.py' 2025-01-09T14:37:32,133 adding 'maginator/main.py' 2025-01-09T14:37:32,134 adding 'maginator/messages.py' 2025-01-09T14:37:32,136 adding 'maginator/workflow.py' 2025-01-09T14:37:32,138 adding 'maginator/workflow/alignment.Snakefile' 2025-01-09T14:37:32,140 adding 'maginator/workflow/benchmark.Snakefile' 2025-01-09T14:37:32,141 adding 'maginator/workflow/filter.Snakefile' 2025-01-09T14:37:32,143 adding 'maginator/workflow/filter_geneclusters.Snakefile' 2025-01-09T14:37:32,144 adding 'maginator/workflow/functional.Snakefile' 2025-01-09T14:37:32,146 adding 'maginator/workflow/gene_count_mat.Snakefile' 2025-01-09T14:37:32,147 adding 'maginator/workflow/gene_tax.Snakefile' 2025-01-09T14:37:32,149 adding 'maginator/workflow/gtdbtk.Snakefile' 2025-01-09T14:37:32,151 adding 'maginator/workflow/outgroup.Snakefile' 2025-01-09T14:37:32,152 adding 'maginator/workflow/parse_gtdbtk.Snakefile' 2025-01-09T14:37:32,154 adding 'maginator/workflow/phylo.Snakefile' 2025-01-09T14:37:32,155 adding 'maginator/workflow/pileup.Snakefile' 2025-01-09T14:37:32,157 adding 'maginator/workflow/pileup_parse.Snakefile' 2025-01-09T14:37:32,158 adding 'maginator/workflow/prescreening_genes.Snakefile' 2025-01-09T14:37:32,161 adding 'maginator/workflow/reads_to_bins.Snakefile' 2025-01-09T14:37:32,162 adding 'maginator/workflow/signature_genes.Snakefile' 2025-01-09T14:37:32,164 adding 'maginator/workflow/signature_reads.Snakefile' 2025-01-09T14:37:32,166 adding 'maginator/workflow/envs/filter_geneclusters.yaml' 2025-01-09T14:37:32,168 adding 'maginator/workflow/envs/filter_geneclusters.yaml.BACKUP.6404.yaml' 2025-01-09T14:37:32,169 adding 'maginator/workflow/envs/filter_geneclusters.yaml.BASE.6404.yaml' 2025-01-09T14:37:32,171 adding 'maginator/workflow/envs/filter_geneclusters.yaml.LOCAL.6404.yaml' 2025-01-09T14:37:32,172 adding 'maginator/workflow/envs/filter_geneclusters.yaml.REMOTE.6404.yaml' 2025-01-09T14:37:32,173 adding 'maginator/workflow/envs/filter_gtdbtk.yaml' 2025-01-09T14:37:32,175 adding 'maginator/workflow/envs/phylo.yaml' 2025-01-09T14:37:32,176 adding 'maginator/workflow/envs/signature_genes.yaml' 2025-01-09T14:37:32,177 adding 'maginator/workflow/envs/signature_reads.yaml' 2025-01-09T14:37:32,180 adding 'maginator/workflow/scripts/Functions_v4.R' 2025-01-09T14:37:32,181 adding 'maginator/workflow/scripts/MGS_counts.R' 2025-01-09T14:37:32,183 adding 'maginator/workflow/scripts/SG_refinement.R' 2025-01-09T14:37:32,185 adding 'maginator/workflow/scripts/abundance_profiles.R' 2025-01-09T14:37:32,187 adding 'maginator/workflow/scripts/allele_frequency_mat.R' 2025-01-09T14:37:32,188 adding 'maginator/workflow/scripts/benchmark.py' 2025-01-09T14:37:32,189 adding 'maginator/workflow/scripts/concat.py' 2025-01-09T14:37:32,191 adding 'maginator/workflow/scripts/extract_coverage.py' 2025-01-09T14:37:32,192 adding 'maginator/workflow/scripts/filter.py' 2025-01-09T14:37:32,193 adding 'maginator/workflow/scripts/functional_profiling.R' 2025-01-09T14:37:32,194 adding 'maginator/workflow/scripts/gene_cluster2tax.py' 2025-01-09T14:37:32,196 adding 'maginator/workflow/scripts/gene_refinement_plots.R' 2025-01-09T14:37:32,198 adding 'maginator/workflow/scripts/marker_genes.py' 2025-01-09T14:37:32,200 adding 'maginator/workflow/scripts/matrix2SG_formatconversion.R' 2025-01-09T14:37:32,201 adding 'maginator/workflow/scripts/modify_gene_count_matrix.R' 2025-01-09T14:37:32,204 adding 'maginator/workflow/scripts/mpileup.py' 2025-01-09T14:37:32,206 adding 'maginator/workflow/scripts/parse_gtdbtk.py' 2025-01-09T14:37:32,207 adding 'maginator/workflow/scripts/prescreening_genes.R' 2025-01-09T14:37:32,208 adding 'maginator/workflow/scripts/sort_gene_mat.py' 2025-01-09T14:37:32,210 adding 'maginator/workflow/scripts/species_collections.py' 2025-01-09T14:37:32,211 adding 'maginator/workflow/scripts/synteny.py' 2025-01-09T14:37:32,213 adding 'maginator-1.0.1.dist-info/LICENSE' 2025-01-09T14:37:32,216 adding 'maginator-1.0.1.dist-info/METADATA' 2025-01-09T14:37:32,217 adding 'maginator-1.0.1.dist-info/WHEEL' 2025-01-09T14:37:32,218 adding 'maginator-1.0.1.dist-info/entry_points.txt' 2025-01-09T14:37:32,219 adding 'maginator-1.0.1.dist-info/top_level.txt' 2025-01-09T14:37:32,220 adding 'maginator-1.0.1.dist-info/RECORD' 2025-01-09T14:37:32,223 removing build/bdist.linux-armv7l/wheel 2025-01-09T14:37:32,352 Building wheel for maginator (setup.py): finished with status 'done' 2025-01-09T14:37:32,355 Created wheel for maginator: filename=maginator-1.0.1-py3-none-any.whl size=71775 sha256=340d26368f5cfec759796f9e4d064d17d834eb1a95ae0bf41082adce55b7daea 2025-01-09T14:37:32,357 Stored in directory: /tmp/pip-ephem-wheel-cache-d3ash4x4/wheels/48/94/fc/4ad540812f0aa0533763b325a2a59c1c307ee33ec706643eac 2025-01-09T14:37:32,370 Successfully built maginator 2025-01-09T14:37:32,375 Removed build tracker: '/tmp/pip-build-tracker-j_lmkkts'