2024-04-12T10:11:42,181 Created temporary directory: /tmp/pip-build-tracker-reyjonkt 2024-04-12T10:11:42,183 Initialized build tracking at /tmp/pip-build-tracker-reyjonkt 2024-04-12T10:11:42,183 Created build tracker: /tmp/pip-build-tracker-reyjonkt 2024-04-12T10:11:42,184 Entered build tracker: /tmp/pip-build-tracker-reyjonkt 2024-04-12T10:11:42,185 Created temporary directory: /tmp/pip-wheel-bcxbgtf4 2024-04-12T10:11:42,188 Created temporary directory: /tmp/pip-ephem-wheel-cache-2n_i798e 2024-04-12T10:11:42,213 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2024-04-12T10:11:42,217 2 location(s) to search for versions of maginator: 2024-04-12T10:11:42,217 * https://pypi.org/simple/maginator/ 2024-04-12T10:11:42,217 * https://www.piwheels.org/simple/maginator/ 2024-04-12T10:11:42,218 Fetching project page and analyzing links: https://pypi.org/simple/maginator/ 2024-04-12T10:11:42,218 Getting page https://pypi.org/simple/maginator/ 2024-04-12T10:11:42,220 Found index url https://pypi.org/simple/ 2024-04-12T10:11:42,441 Fetched page https://pypi.org/simple/maginator/ as application/vnd.pypi.simple.v1+json 2024-04-12T10:11:42,443 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) 2024-04-12T10:11:42,444 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 2024-04-12T10:11:42,445 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) 2024-04-12T10:11:42,446 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 2024-04-12T10:11:42,447 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 2024-04-12T10:11:42,448 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) 2024-04-12T10:11:42,449 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 2024-04-12T10:11:42,450 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 2024-04-12T10:11:42,451 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 2024-04-12T10:11:42,452 Fetching project page and analyzing links: https://www.piwheels.org/simple/maginator/ 2024-04-12T10:11:42,453 Getting page https://www.piwheels.org/simple/maginator/ 2024-04-12T10:11:42,455 Found index url https://www.piwheels.org/simple/ 2024-04-12T10:11:42,812 Fetched page https://www.piwheels.org/simple/maginator/ as text/html 2024-04-12T10:11:42,815 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) 2024-04-12T10:11:42,816 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) 2024-04-12T10:11:42,817 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) 2024-04-12T10:11:42,818 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) 2024-04-12T10:11:42,818 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) 2024-04-12T10:11:42,819 Skipping link: not a file: https://www.piwheels.org/simple/maginator/ 2024-04-12T10:11:42,819 Skipping link: not a file: https://pypi.org/simple/maginator/ 2024-04-12T10:11:42,839 Given no hashes to check 1 links for project 'maginator': discarding no candidates 2024-04-12T10:11:42,857 Collecting maginator==0.1.20 2024-04-12T10:11:42,859 Created temporary directory: /tmp/pip-unpack-9ly9_529 2024-04-12T10:11:43,077 Downloading maginator-0.1.20.tar.gz (49 kB) 2024-04-12T10:11:43,215 Added maginator==0.1.20 from https://files.pythonhosted.org/packages/db/be/89e247ebfc09de9774f240da16fdabc55260117c404371245cfb552a7f9d/maginator-0.1.20.tar.gz to build tracker '/tmp/pip-build-tracker-reyjonkt' 2024-04-12T10:11:43,217 Running setup.py (path:/tmp/pip-wheel-bcxbgtf4/maginator_113899e98d0c49d998908d273e8a8efa/setup.py) egg_info for package maginator 2024-04-12T10:11:43,218 Created temporary directory: /tmp/pip-pip-egg-info-g4zv3uyc 2024-04-12T10:11:43,218 Preparing metadata (setup.py): started 2024-04-12T10:11:43,220 Running command python setup.py egg_info 2024-04-12T10:11:44,275 running egg_info 2024-04-12T10:11:44,277 creating /tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info 2024-04-12T10:11:44,303 writing /tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info/PKG-INFO 2024-04-12T10:11:44,307 writing dependency_links to /tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info/dependency_links.txt 2024-04-12T10:11:44,309 writing entry points to /tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info/entry_points.txt 2024-04-12T10:11:44,311 writing requirements to /tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info/requires.txt 2024-04-12T10:11:44,312 writing top-level names to /tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info/top_level.txt 2024-04-12T10:11:44,314 writing manifest file '/tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info/SOURCES.txt' 2024-04-12T10:11:44,398 reading manifest file '/tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info/SOURCES.txt' 2024-04-12T10:11:44,400 reading manifest template 'MANIFEST.in' 2024-04-12T10:11:44,641 writing manifest file '/tmp/pip-pip-egg-info-g4zv3uyc/maginator.egg-info/SOURCES.txt' 2024-04-12T10:11:44,749 Preparing metadata (setup.py): finished with status 'done' 2024-04-12T10:11:44,753 Source in /tmp/pip-wheel-bcxbgtf4/maginator_113899e98d0c49d998908d273e8a8efa has version 0.1.20, which satisfies requirement maginator==0.1.20 from https://files.pythonhosted.org/packages/db/be/89e247ebfc09de9774f240da16fdabc55260117c404371245cfb552a7f9d/maginator-0.1.20.tar.gz 2024-04-12T10:11:44,754 Removed maginator==0.1.20 from https://files.pythonhosted.org/packages/db/be/89e247ebfc09de9774f240da16fdabc55260117c404371245cfb552a7f9d/maginator-0.1.20.tar.gz from build tracker '/tmp/pip-build-tracker-reyjonkt' 2024-04-12T10:11:44,761 Created temporary directory: /tmp/pip-unpack-k0wygef_ 2024-04-12T10:11:44,763 Created temporary directory: /tmp/pip-unpack-j4w5pahp 2024-04-12T10:11:44,768 Building wheels for collected packages: maginator 2024-04-12T10:11:44,773 Created temporary directory: /tmp/pip-wheel-twkqurwo 2024-04-12T10:11:44,774 Building wheel for maginator (setup.py): started 2024-04-12T10:11:44,775 Destination directory: /tmp/pip-wheel-twkqurwo 2024-04-12T10:11:44,775 Running command python setup.py bdist_wheel 2024-04-12T10:11:45,823 running bdist_wheel 2024-04-12T10:11:45,925 running build 2024-04-12T10:11:45,925 running build_py 2024-04-12T10:11:45,954 creating build 2024-04-12T10:11:45,954 creating build/lib 2024-04-12T10:11:45,955 creating build/lib/maginator 2024-04-12T10:11:45,957 copying maginator/workflow.py -> build/lib/maginator 2024-04-12T10:11:45,959 copying maginator/main.py -> build/lib/maginator 2024-04-12T10:11:45,962 copying maginator/messages.py -> build/lib/maginator 2024-04-12T10:11:45,964 copying maginator/__init__.py -> build/lib/maginator 2024-04-12T10:11:45,966 copying maginator/controller.py -> build/lib/maginator 2024-04-12T10:11:45,967 running egg_info 2024-04-12T10:11:46,026 writing maginator.egg-info/PKG-INFO 2024-04-12T10:11:46,030 writing dependency_links to maginator.egg-info/dependency_links.txt 2024-04-12T10:11:46,032 writing entry points to maginator.egg-info/entry_points.txt 2024-04-12T10:11:46,033 writing requirements to maginator.egg-info/requires.txt 2024-04-12T10:11:46,034 writing top-level names to maginator.egg-info/top_level.txt 2024-04-12T10:11:46,063 reading manifest file 'maginator.egg-info/SOURCES.txt' 2024-04-12T10:11:46,067 reading manifest template 'MANIFEST.in' 2024-04-12T10:11:46,086 writing manifest file 'maginator.egg-info/SOURCES.txt' 2024-04-12T10:11:46,088 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'maginator.workflow' is absent from the `packages` configuration. 2024-04-12T10:11:46,089 !! 2024-04-12T10:11:46,090 ******************************************************************************** 2024-04-12T10:11:46,091 ############################ 2024-04-12T10:11:46,091 # Package would be ignored # 2024-04-12T10:11:46,092 ############################ 2024-04-12T10:11:46,092 Python recognizes 'maginator.workflow' as an importable package[^1], 2024-04-12T10:11:46,093 but it is absent from setuptools' `packages` configuration. 2024-04-12T10:11:46,094 This leads to an ambiguous overall configuration. If you want to distribute this 2024-04-12T10:11:46,095 package, please make sure that 'maginator.workflow' is explicitly added 2024-04-12T10:11:46,095 to the `packages` configuration field. 2024-04-12T10:11:46,096 Alternatively, you can also rely on setuptools' discovery methods 2024-04-12T10:11:46,097 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-04-12T10:11:46,097 instead of `find_packages(...)`/`find:`). 2024-04-12T10:11:46,099 You can read more about "package discovery" on setuptools documentation page: 2024-04-12T10:11:46,100 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-04-12T10:11:46,101 If you don't want 'maginator.workflow' to be distributed and are 2024-04-12T10:11:46,102 already explicitly excluding 'maginator.workflow' via 2024-04-12T10:11:46,102 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-04-12T10:11:46,103 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-04-12T10:11:46,103 combination with a more fine grained `package-data` configuration. 2024-04-12T10:11:46,105 You can read more about "package data files" on setuptools documentation page: 2024-04-12T10:11:46,106 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-04-12T10:11:46,108 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-04-12T10:11:46,109 even if it does not contain any `.py` files. 2024-04-12T10:11:46,110 On the other hand, currently there is no concept of package data 2024-04-12T10:11:46,111 directory, all directories are treated like packages. 2024-04-12T10:11:46,111 ******************************************************************************** 2024-04-12T10:11:46,113 !! 2024-04-12T10:11:46,113 check.warn(importable) 2024-04-12T10:11:46,114 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'maginator.workflow.envs' is absent from the `packages` configuration. 2024-04-12T10:11:46,115 !! 2024-04-12T10:11:46,116 ******************************************************************************** 2024-04-12T10:11:46,117 ############################ 2024-04-12T10:11:46,117 # Package would be ignored # 2024-04-12T10:11:46,118 ############################ 2024-04-12T10:11:46,119 Python recognizes 'maginator.workflow.envs' as an importable package[^1], 2024-04-12T10:11:46,120 but it is absent from setuptools' `packages` configuration. 2024-04-12T10:11:46,121 This leads to an ambiguous overall configuration. If you want to distribute this 2024-04-12T10:11:46,122 package, please make sure that 'maginator.workflow.envs' is explicitly added 2024-04-12T10:11:46,123 to the `packages` configuration field. 2024-04-12T10:11:46,124 Alternatively, you can also rely on setuptools' discovery methods 2024-04-12T10:11:46,125 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-04-12T10:11:46,126 instead of `find_packages(...)`/`find:`). 2024-04-12T10:11:46,127 You can read more about "package discovery" on setuptools documentation page: 2024-04-12T10:11:46,128 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-04-12T10:11:46,129 If you don't want 'maginator.workflow.envs' to be distributed and are 2024-04-12T10:11:46,130 already explicitly excluding 'maginator.workflow.envs' via 2024-04-12T10:11:46,130 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-04-12T10:11:46,131 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-04-12T10:11:46,132 combination with a more fine grained `package-data` configuration. 2024-04-12T10:11:46,133 You can read more about "package data files" on setuptools documentation page: 2024-04-12T10:11:46,135 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-04-12T10:11:46,137 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-04-12T10:11:46,137 even if it does not contain any `.py` files. 2024-04-12T10:11:46,138 On the other hand, currently there is no concept of package data 2024-04-12T10:11:46,139 directory, all directories are treated like packages. 2024-04-12T10:11:46,139 ******************************************************************************** 2024-04-12T10:11:46,140 !! 2024-04-12T10:11:46,141 check.warn(importable) 2024-04-12T10:11:46,141 /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'maginator.workflow.scripts' is absent from the `packages` configuration. 2024-04-12T10:11:46,142 !! 2024-04-12T10:11:46,143 ******************************************************************************** 2024-04-12T10:11:46,144 ############################ 2024-04-12T10:11:46,144 # Package would be ignored # 2024-04-12T10:11:46,145 ############################ 2024-04-12T10:11:46,145 Python recognizes 'maginator.workflow.scripts' as an importable package[^1], 2024-04-12T10:11:46,146 but it is absent from setuptools' `packages` configuration. 2024-04-12T10:11:46,147 This leads to an ambiguous overall configuration. If you want to distribute this 2024-04-12T10:11:46,148 package, please make sure that 'maginator.workflow.scripts' is explicitly added 2024-04-12T10:11:46,148 to the `packages` configuration field. 2024-04-12T10:11:46,149 Alternatively, you can also rely on setuptools' discovery methods 2024-04-12T10:11:46,150 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2024-04-12T10:11:46,151 instead of `find_packages(...)`/`find:`). 2024-04-12T10:11:46,152 You can read more about "package discovery" on setuptools documentation page: 2024-04-12T10:11:46,153 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2024-04-12T10:11:46,154 If you don't want 'maginator.workflow.scripts' to be distributed and are 2024-04-12T10:11:46,154 already explicitly excluding 'maginator.workflow.scripts' via 2024-04-12T10:11:46,155 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2024-04-12T10:11:46,155 you can try to use `exclude_package_data`, or `include-package-data=False` in 2024-04-12T10:11:46,156 combination with a more fine grained `package-data` configuration. 2024-04-12T10:11:46,157 You can read more about "package data files" on setuptools documentation page: 2024-04-12T10:11:46,159 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2024-04-12T10:11:46,161 [^1]: For Python, any directory (with suitable naming) can be imported, 2024-04-12T10:11:46,162 even if it does not contain any `.py` files. 2024-04-12T10:11:46,163 On the other hand, currently there is no concept of package data 2024-04-12T10:11:46,163 directory, all directories are treated like packages. 2024-04-12T10:11:46,164 ******************************************************************************** 2024-04-12T10:11:46,166 !! 2024-04-12T10:11:46,166 check.warn(importable) 2024-04-12T10:11:46,166 creating build/lib/maginator/workflow 2024-04-12T10:11:46,167 copying maginator/workflow/alignment.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,168 copying maginator/workflow/filter.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,168 copying maginator/workflow/filter_geneclusters.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,169 copying maginator/workflow/gene_count_mat.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,169 copying maginator/workflow/gene_tax.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,170 copying maginator/workflow/gtdbtk.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,170 copying maginator/workflow/outgroup.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,171 copying maginator/workflow/parse_gtdbtk.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,171 copying maginator/workflow/phylo.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,172 copying maginator/workflow/pileup.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,172 copying maginator/workflow/pileup_parse.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,173 copying maginator/workflow/prescreening_genes.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,173 copying maginator/workflow/reads_to_bins.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,174 copying maginator/workflow/signature_genes.Snakefile -> build/lib/maginator/workflow 2024-04-12T10:11:46,174 creating build/lib/maginator/workflow/envs 2024-04-12T10:11:46,175 copying maginator/workflow/envs/filter_geneclusters.yaml -> build/lib/maginator/workflow/envs 2024-04-12T10:11:46,176 copying maginator/workflow/envs/filter_gtdbtk.yaml -> build/lib/maginator/workflow/envs 2024-04-12T10:11:46,176 copying maginator/workflow/envs/phylo.yaml -> build/lib/maginator/workflow/envs 2024-04-12T10:11:46,177 copying maginator/workflow/envs/signature_genes.yaml -> build/lib/maginator/workflow/envs 2024-04-12T10:11:46,178 creating build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,178 copying maginator/workflow/scripts/Functions_v4.R -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,178 copying maginator/workflow/scripts/MGS_counts.R -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,179 copying maginator/workflow/scripts/SG_refinement.R -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,179 copying maginator/workflow/scripts/abundance_profiles.R -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,180 copying maginator/workflow/scripts/allele_frequency_mat.R -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,181 copying maginator/workflow/scripts/concat.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,181 copying maginator/workflow/scripts/filter.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,182 copying maginator/workflow/scripts/gene_cluster2tax.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,182 copying maginator/workflow/scripts/gene_refinement_plots.R -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,185 copying maginator/workflow/scripts/marker_genes.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,189 copying maginator/workflow/scripts/matrix2SG_formatconversion.R -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,191 copying maginator/workflow/scripts/mpileup.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,194 copying maginator/workflow/scripts/parse_gtdbtk.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,197 copying maginator/workflow/scripts/prescreening_genes.R -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,199 copying maginator/workflow/scripts/sort_gene_mat.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,201 copying maginator/workflow/scripts/species_collections.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,203 copying maginator/workflow/scripts/synteny.py -> build/lib/maginator/workflow/scripts 2024-04-12T10:11:46,231 /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2024-04-12T10:11:46,232 !! 2024-04-12T10:11:46,233 ******************************************************************************** 2024-04-12T10:11:46,233 Please avoid running ``setup.py`` directly. 2024-04-12T10:11:46,234 Instead, use pypa/build, pypa/installer or other 2024-04-12T10:11:46,235 standards-based tools. 2024-04-12T10:11:46,236 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2024-04-12T10:11:46,236 ******************************************************************************** 2024-04-12T10:11:46,238 !! 2024-04-12T10:11:46,238 self.initialize_options() 2024-04-12T10:11:46,258 installing to build/bdist.linux-armv7l/wheel 2024-04-12T10:11:46,258 running install 2024-04-12T10:11:46,282 running install_lib 2024-04-12T10:11:46,308 creating build/bdist.linux-armv7l 2024-04-12T10:11:46,309 creating build/bdist.linux-armv7l/wheel 2024-04-12T10:11:46,311 creating build/bdist.linux-armv7l/wheel/maginator 2024-04-12T10:11:46,312 copying build/lib/maginator/workflow.py -> build/bdist.linux-armv7l/wheel/maginator 2024-04-12T10:11:46,314 copying build/lib/maginator/main.py -> build/bdist.linux-armv7l/wheel/maginator 2024-04-12T10:11:46,316 copying build/lib/maginator/messages.py -> build/bdist.linux-armv7l/wheel/maginator 2024-04-12T10:11:46,319 copying build/lib/maginator/__init__.py -> build/bdist.linux-armv7l/wheel/maginator 2024-04-12T10:11:46,321 copying build/lib/maginator/controller.py -> build/bdist.linux-armv7l/wheel/maginator 2024-04-12T10:11:46,324 creating build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,325 creating build/bdist.linux-armv7l/wheel/maginator/workflow/envs 2024-04-12T10:11:46,327 copying build/lib/maginator/workflow/envs/phylo.yaml -> build/bdist.linux-armv7l/wheel/maginator/workflow/envs 2024-04-12T10:11:46,329 copying build/lib/maginator/workflow/envs/filter_gtdbtk.yaml -> build/bdist.linux-armv7l/wheel/maginator/workflow/envs 2024-04-12T10:11:46,332 copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml -> build/bdist.linux-armv7l/wheel/maginator/workflow/envs 2024-04-12T10:11:46,334 copying build/lib/maginator/workflow/envs/signature_genes.yaml -> build/bdist.linux-armv7l/wheel/maginator/workflow/envs 2024-04-12T10:11:46,337 creating build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,338 copying build/lib/maginator/workflow/scripts/abundance_profiles.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,341 copying build/lib/maginator/workflow/scripts/mpileup.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,345 copying build/lib/maginator/workflow/scripts/marker_genes.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,348 copying build/lib/maginator/workflow/scripts/synteny.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,351 copying build/lib/maginator/workflow/scripts/concat.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,354 copying build/lib/maginator/workflow/scripts/parse_gtdbtk.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,357 copying build/lib/maginator/workflow/scripts/matrix2SG_formatconversion.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,359 copying build/lib/maginator/workflow/scripts/prescreening_genes.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,362 copying build/lib/maginator/workflow/scripts/gene_refinement_plots.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,365 copying build/lib/maginator/workflow/scripts/Functions_v4.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,368 copying build/lib/maginator/workflow/scripts/species_collections.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,371 copying build/lib/maginator/workflow/scripts/allele_frequency_mat.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,374 copying build/lib/maginator/workflow/scripts/sort_gene_mat.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,377 copying build/lib/maginator/workflow/scripts/MGS_counts.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,379 copying build/lib/maginator/workflow/scripts/filter.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,382 copying build/lib/maginator/workflow/scripts/SG_refinement.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,386 copying build/lib/maginator/workflow/scripts/gene_cluster2tax.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts 2024-04-12T10:11:46,390 copying build/lib/maginator/workflow/filter_geneclusters.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,393 copying build/lib/maginator/workflow/gtdbtk.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,396 copying build/lib/maginator/workflow/signature_genes.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,399 copying build/lib/maginator/workflow/filter.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,402 copying build/lib/maginator/workflow/parse_gtdbtk.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,404 copying build/lib/maginator/workflow/outgroup.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,407 copying build/lib/maginator/workflow/phylo.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,409 copying build/lib/maginator/workflow/reads_to_bins.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,412 copying build/lib/maginator/workflow/pileup_parse.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,415 copying build/lib/maginator/workflow/gene_count_mat.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,417 copying build/lib/maginator/workflow/pileup.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,419 copying build/lib/maginator/workflow/gene_tax.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,421 copying build/lib/maginator/workflow/prescreening_genes.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,423 copying build/lib/maginator/workflow/alignment.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow 2024-04-12T10:11:46,425 running install_egg_info 2024-04-12T10:11:46,457 Copying maginator.egg-info to build/bdist.linux-armv7l/wheel/maginator-0.1.20-py3.11.egg-info 2024-04-12T10:11:46,480 running install_scripts 2024-04-12T10:11:46,498 creating build/bdist.linux-armv7l/wheel/maginator-0.1.20.dist-info/WHEEL 2024-04-12T10:11:46,502 creating '/tmp/pip-wheel-twkqurwo/maginator-0.1.20-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2024-04-12T10:11:46,505 adding 'maginator/__init__.py' 2024-04-12T10:11:46,507 adding 'maginator/controller.py' 2024-04-12T10:11:46,509 adding 'maginator/main.py' 2024-04-12T10:11:46,511 adding 'maginator/messages.py' 2024-04-12T10:11:46,513 adding 'maginator/workflow.py' 2024-04-12T10:11:46,515 adding 'maginator/workflow/alignment.Snakefile' 2024-04-12T10:11:46,517 adding 'maginator/workflow/filter.Snakefile' 2024-04-12T10:11:46,518 adding 'maginator/workflow/filter_geneclusters.Snakefile' 2024-04-12T10:11:46,520 adding 'maginator/workflow/gene_count_mat.Snakefile' 2024-04-12T10:11:46,522 adding 'maginator/workflow/gene_tax.Snakefile' 2024-04-12T10:11:46,523 adding 'maginator/workflow/gtdbtk.Snakefile' 2024-04-12T10:11:46,525 adding 'maginator/workflow/outgroup.Snakefile' 2024-04-12T10:11:46,527 adding 'maginator/workflow/parse_gtdbtk.Snakefile' 2024-04-12T10:11:46,528 adding 'maginator/workflow/phylo.Snakefile' 2024-04-12T10:11:46,530 adding 'maginator/workflow/pileup.Snakefile' 2024-04-12T10:11:46,531 adding 'maginator/workflow/pileup_parse.Snakefile' 2024-04-12T10:11:46,533 adding 'maginator/workflow/prescreening_genes.Snakefile' 2024-04-12T10:11:46,535 adding 'maginator/workflow/reads_to_bins.Snakefile' 2024-04-12T10:11:46,537 adding 'maginator/workflow/signature_genes.Snakefile' 2024-04-12T10:11:46,540 adding 'maginator/workflow/envs/filter_geneclusters.yaml' 2024-04-12T10:11:46,541 adding 'maginator/workflow/envs/filter_gtdbtk.yaml' 2024-04-12T10:11:46,543 adding 'maginator/workflow/envs/phylo.yaml' 2024-04-12T10:11:46,545 adding 'maginator/workflow/envs/signature_genes.yaml' 2024-04-12T10:11:46,548 adding 'maginator/workflow/scripts/Functions_v4.R' 2024-04-12T10:11:46,549 adding 'maginator/workflow/scripts/MGS_counts.R' 2024-04-12T10:11:46,552 adding 'maginator/workflow/scripts/SG_refinement.R' 2024-04-12T10:11:46,554 adding 'maginator/workflow/scripts/abundance_profiles.R' 2024-04-12T10:11:46,556 adding 'maginator/workflow/scripts/allele_frequency_mat.R' 2024-04-12T10:11:46,558 adding 'maginator/workflow/scripts/concat.py' 2024-04-12T10:11:46,559 adding 'maginator/workflow/scripts/filter.py' 2024-04-12T10:11:46,561 adding 'maginator/workflow/scripts/gene_cluster2tax.py' 2024-04-12T10:11:46,563 adding 'maginator/workflow/scripts/gene_refinement_plots.R' 2024-04-12T10:11:46,566 adding 'maginator/workflow/scripts/marker_genes.py' 2024-04-12T10:11:46,567 adding 'maginator/workflow/scripts/matrix2SG_formatconversion.R' 2024-04-12T10:11:46,571 adding 'maginator/workflow/scripts/mpileup.py' 2024-04-12T10:11:46,573 adding 'maginator/workflow/scripts/parse_gtdbtk.py' 2024-04-12T10:11:46,575 adding 'maginator/workflow/scripts/prescreening_genes.R' 2024-04-12T10:11:46,576 adding 'maginator/workflow/scripts/sort_gene_mat.py' 2024-04-12T10:11:46,578 adding 'maginator/workflow/scripts/species_collections.py' 2024-04-12T10:11:46,580 adding 'maginator/workflow/scripts/synteny.py' 2024-04-12T10:11:46,584 adding 'maginator-0.1.20.dist-info/METADATA' 2024-04-12T10:11:46,585 adding 'maginator-0.1.20.dist-info/WHEEL' 2024-04-12T10:11:46,587 adding 'maginator-0.1.20.dist-info/entry_points.txt' 2024-04-12T10:11:46,588 adding 'maginator-0.1.20.dist-info/top_level.txt' 2024-04-12T10:11:46,590 adding 'maginator-0.1.20.dist-info/RECORD' 2024-04-12T10:11:46,593 removing build/bdist.linux-armv7l/wheel 2024-04-12T10:11:46,718 Building wheel for maginator (setup.py): finished with status 'done' 2024-04-12T10:11:46,721 Created wheel for maginator: filename=maginator-0.1.20-py3-none-any.whl size=61756 sha256=82ef40fdd5f9dcea92009b50c2f9b24f6af582e7b91f5d48da634b0149542ee6 2024-04-12T10:11:46,722 Stored in directory: /tmp/pip-ephem-wheel-cache-2n_i798e/wheels/46/c9/5a/8298cd5949ccb266b4a4a390a9e2f8f3900a4b249e97513257 2024-04-12T10:11:46,734 Successfully built maginator 2024-04-12T10:11:46,742 Removed build tracker: '/tmp/pip-build-tracker-reyjonkt'