2024-01-06T06:09:20,929 Created temporary directory: /tmp/pip-build-tracker-po94k8z1
2024-01-06T06:09:20,930 Initialized build tracking at /tmp/pip-build-tracker-po94k8z1
2024-01-06T06:09:20,931 Created build tracker: /tmp/pip-build-tracker-po94k8z1
2024-01-06T06:09:20,931 Entered build tracker: /tmp/pip-build-tracker-po94k8z1
2024-01-06T06:09:20,932 Created temporary directory: /tmp/pip-wheel-w0vgs8bo
2024-01-06T06:09:20,935 Created temporary directory: /tmp/pip-ephem-wheel-cache-4ecuy70s
2024-01-06T06:09:20,957 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-01-06T06:09:20,960 2 location(s) to search for versions of maginator:
2024-01-06T06:09:20,960 * https://pypi.org/simple/maginator/
2024-01-06T06:09:20,960 * https://www.piwheels.org/simple/maginator/
2024-01-06T06:09:20,961 Fetching project page and analyzing links: https://pypi.org/simple/maginator/
2024-01-06T06:09:20,962 Getting page https://pypi.org/simple/maginator/
2024-01-06T06:09:20,963 Found index url https://pypi.org/simple/
2024-01-06T06:09:21,181 Fetched page https://pypi.org/simple/maginator/ as application/vnd.pypi.simple.v1+json
2024-01-06T06:09:21,184   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)
2024-01-06T06:09:21,185   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
2024-01-06T06:09:21,185   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)
2024-01-06T06:09:21,186   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
2024-01-06T06:09:21,187   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
2024-01-06T06:09:21,188   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)
2024-01-06T06:09:21,189   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
2024-01-06T06:09:21,190   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
2024-01-06T06:09:21,191 Fetching project page and analyzing links: https://www.piwheels.org/simple/maginator/
2024-01-06T06:09:21,192 Getting page https://www.piwheels.org/simple/maginator/
2024-01-06T06:09:21,193 Found index url https://www.piwheels.org/simple/
2024-01-06T06:09:21,370 Fetched page https://www.piwheels.org/simple/maginator/ as text/html
2024-01-06T06:09:21,372   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)
2024-01-06T06:09:21,373   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)
2024-01-06T06:09:21,373   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)
2024-01-06T06:09:21,374   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)
2024-01-06T06:09:21,375 Skipping link: not a file: https://www.piwheels.org/simple/maginator/
2024-01-06T06:09:21,375 Skipping link: not a file: https://pypi.org/simple/maginator/
2024-01-06T06:09:21,394 Given no hashes to check 1 links for project 'maginator': discarding no candidates
2024-01-06T06:09:21,412 Collecting maginator==0.1.19
2024-01-06T06:09:21,415   Created temporary directory: /tmp/pip-unpack-vl1oq1qp
2024-01-06T06:09:21,624   Downloading maginator-0.1.19.tar.gz (49 kB)
2024-01-06T06:09:21,755   Added maginator==0.1.19 from https://files.pythonhosted.org/packages/08/d6/37a1f51d0f7bd4de9ad96f2aa17121470f0a4efd9274573400bca68368f4/maginator-0.1.19.tar.gz to build tracker '/tmp/pip-build-tracker-po94k8z1'
2024-01-06T06:09:21,757   Running setup.py (path:/tmp/pip-wheel-w0vgs8bo/maginator_c4de2d33df494c50bfba21ab351be058/setup.py) egg_info for package maginator
2024-01-06T06:09:21,758   Created temporary directory: /tmp/pip-pip-egg-info-1xm5kyrx
2024-01-06T06:09:21,758   Preparing metadata (setup.py): started
2024-01-06T06:09:21,760   Running command python setup.py egg_info
2024-01-06T06:09:22,745   running egg_info
2024-01-06T06:09:22,747   creating /tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info
2024-01-06T06:09:22,771   writing /tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info/PKG-INFO
2024-01-06T06:09:22,775   writing dependency_links to /tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info/dependency_links.txt
2024-01-06T06:09:22,777   writing entry points to /tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info/entry_points.txt
2024-01-06T06:09:22,778   writing requirements to /tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info/requires.txt
2024-01-06T06:09:22,779   writing top-level names to /tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info/top_level.txt
2024-01-06T06:09:22,781   writing manifest file '/tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info/SOURCES.txt'
2024-01-06T06:09:22,858   reading manifest file '/tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info/SOURCES.txt'
2024-01-06T06:09:22,860   reading manifest template 'MANIFEST.in'
2024-01-06T06:09:22,876   writing manifest file '/tmp/pip-pip-egg-info-1xm5kyrx/maginator.egg-info/SOURCES.txt'
2024-01-06T06:09:22,983   Preparing metadata (setup.py): finished with status 'done'
2024-01-06T06:09:22,987   Source in /tmp/pip-wheel-w0vgs8bo/maginator_c4de2d33df494c50bfba21ab351be058 has version 0.1.19, which satisfies requirement maginator==0.1.19 from https://files.pythonhosted.org/packages/08/d6/37a1f51d0f7bd4de9ad96f2aa17121470f0a4efd9274573400bca68368f4/maginator-0.1.19.tar.gz
2024-01-06T06:09:22,988   Removed maginator==0.1.19 from https://files.pythonhosted.org/packages/08/d6/37a1f51d0f7bd4de9ad96f2aa17121470f0a4efd9274573400bca68368f4/maginator-0.1.19.tar.gz from build tracker '/tmp/pip-build-tracker-po94k8z1'
2024-01-06T06:09:22,994 Created temporary directory: /tmp/pip-unpack-g2baqyh_
2024-01-06T06:09:22,995 Created temporary directory: /tmp/pip-unpack-8u4wdzl5
2024-01-06T06:09:23,000 Building wheels for collected packages: maginator
2024-01-06T06:09:23,005   Created temporary directory: /tmp/pip-wheel-vf2v9er8
2024-01-06T06:09:23,005   Building wheel for maginator (setup.py): started
2024-01-06T06:09:23,007   Destination directory: /tmp/pip-wheel-vf2v9er8
2024-01-06T06:09:23,007   Running command python setup.py bdist_wheel
2024-01-06T06:09:23,997   running bdist_wheel
2024-01-06T06:09:24,093   running build
2024-01-06T06:09:24,094   running build_py
2024-01-06T06:09:24,121   creating build
2024-01-06T06:09:24,121   creating build/lib
2024-01-06T06:09:24,122   creating build/lib/maginator
2024-01-06T06:09:24,123   copying maginator/main.py -> build/lib/maginator
2024-01-06T06:09:24,125   copying maginator/workflow.py -> build/lib/maginator
2024-01-06T06:09:24,127   copying maginator/__init__.py -> build/lib/maginator
2024-01-06T06:09:24,129   copying maginator/messages.py -> build/lib/maginator
2024-01-06T06:09:24,131   copying maginator/controller.py -> build/lib/maginator
2024-01-06T06:09:24,133   running egg_info
2024-01-06T06:09:24,188   writing maginator.egg-info/PKG-INFO
2024-01-06T06:09:24,191   writing dependency_links to maginator.egg-info/dependency_links.txt
2024-01-06T06:09:24,193   writing entry points to maginator.egg-info/entry_points.txt
2024-01-06T06:09:24,194   writing requirements to maginator.egg-info/requires.txt
2024-01-06T06:09:24,195   writing top-level names to maginator.egg-info/top_level.txt
2024-01-06T06:09:24,223   reading manifest file 'maginator.egg-info/SOURCES.txt'
2024-01-06T06:09:24,225   reading manifest template 'MANIFEST.in'
2024-01-06T06:09:24,241   writing manifest file 'maginator.egg-info/SOURCES.txt'
2024-01-06T06:09:24,244   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'maginator.workflow' is absent from the `packages` configuration.
2024-01-06T06:09:24,244   !!

2024-01-06T06:09:24,245           ********************************************************************************
2024-01-06T06:09:24,246           ############################
2024-01-06T06:09:24,246           # Package would be ignored #
2024-01-06T06:09:24,247           ############################
2024-01-06T06:09:24,247           Python recognizes 'maginator.workflow' as an importable package[^1],
2024-01-06T06:09:24,248           but it is absent from setuptools' `packages` configuration.

2024-01-06T06:09:24,249           This leads to an ambiguous overall configuration. If you want to distribute this
2024-01-06T06:09:24,249           package, please make sure that 'maginator.workflow' is explicitly added
2024-01-06T06:09:24,250           to the `packages` configuration field.

2024-01-06T06:09:24,251           Alternatively, you can also rely on setuptools' discovery methods
2024-01-06T06:09:24,251           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-01-06T06:09:24,252           instead of `find_packages(...)`/`find:`).

2024-01-06T06:09:24,253           You can read more about "package discovery" on setuptools documentation page:

2024-01-06T06:09:24,254           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-01-06T06:09:24,255           If you don't want 'maginator.workflow' to be distributed and are
2024-01-06T06:09:24,255           already explicitly excluding 'maginator.workflow' via
2024-01-06T06:09:24,256           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-01-06T06:09:24,256           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-01-06T06:09:24,257           combination with a more fine grained `package-data` configuration.

2024-01-06T06:09:24,258           You can read more about "package data files" on setuptools documentation page:

2024-01-06T06:09:24,259           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-01-06T06:09:24,260           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-01-06T06:09:24,261                 even if it does not contain any `.py` files.
2024-01-06T06:09:24,261                 On the other hand, currently there is no concept of package data
2024-01-06T06:09:24,262                 directory, all directories are treated like packages.
2024-01-06T06:09:24,263           ********************************************************************************

2024-01-06T06:09:24,264   !!
2024-01-06T06:09:24,264     check.warn(importable)
2024-01-06T06:09:24,265   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'maginator.workflow.envs' is absent from the `packages` configuration.
2024-01-06T06:09:24,265   !!

2024-01-06T06:09:24,266           ********************************************************************************
2024-01-06T06:09:24,267           ############################
2024-01-06T06:09:24,267           # Package would be ignored #
2024-01-06T06:09:24,268           ############################
2024-01-06T06:09:24,268           Python recognizes 'maginator.workflow.envs' as an importable package[^1],
2024-01-06T06:09:24,269           but it is absent from setuptools' `packages` configuration.

2024-01-06T06:09:24,270           This leads to an ambiguous overall configuration. If you want to distribute this
2024-01-06T06:09:24,270           package, please make sure that 'maginator.workflow.envs' is explicitly added
2024-01-06T06:09:24,270           to the `packages` configuration field.

2024-01-06T06:09:24,272           Alternatively, you can also rely on setuptools' discovery methods
2024-01-06T06:09:24,272           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-01-06T06:09:24,273           instead of `find_packages(...)`/`find:`).

2024-01-06T06:09:24,274           You can read more about "package discovery" on setuptools documentation page:

2024-01-06T06:09:24,275           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-01-06T06:09:24,275           If you don't want 'maginator.workflow.envs' to be distributed and are
2024-01-06T06:09:24,276           already explicitly excluding 'maginator.workflow.envs' via
2024-01-06T06:09:24,276           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-01-06T06:09:24,277           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-01-06T06:09:24,277           combination with a more fine grained `package-data` configuration.

2024-01-06T06:09:24,278           You can read more about "package data files" on setuptools documentation page:

2024-01-06T06:09:24,279           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-01-06T06:09:24,281           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-01-06T06:09:24,282                 even if it does not contain any `.py` files.
2024-01-06T06:09:24,282                 On the other hand, currently there is no concept of package data
2024-01-06T06:09:24,283                 directory, all directories are treated like packages.
2024-01-06T06:09:24,283           ********************************************************************************

2024-01-06T06:09:24,284   !!
2024-01-06T06:09:24,285     check.warn(importable)
2024-01-06T06:09:24,285   /usr/local/lib/python3.11/dist-packages/setuptools/command/build_py.py:207: _Warning: Package 'maginator.workflow.scripts' is absent from the `packages` configuration.
2024-01-06T06:09:24,286   !!

2024-01-06T06:09:24,287           ********************************************************************************
2024-01-06T06:09:24,287           ############################
2024-01-06T06:09:24,288           # Package would be ignored #
2024-01-06T06:09:24,288           ############################
2024-01-06T06:09:24,289           Python recognizes 'maginator.workflow.scripts' as an importable package[^1],
2024-01-06T06:09:24,289           but it is absent from setuptools' `packages` configuration.

2024-01-06T06:09:24,290           This leads to an ambiguous overall configuration. If you want to distribute this
2024-01-06T06:09:24,291           package, please make sure that 'maginator.workflow.scripts' is explicitly added
2024-01-06T06:09:24,291           to the `packages` configuration field.

2024-01-06T06:09:24,292           Alternatively, you can also rely on setuptools' discovery methods
2024-01-06T06:09:24,293           (for example by using `find_namespace_packages(...)`/`find_namespace:`
2024-01-06T06:09:24,293           instead of `find_packages(...)`/`find:`).

2024-01-06T06:09:24,294           You can read more about "package discovery" on setuptools documentation page:

2024-01-06T06:09:24,295           - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html

2024-01-06T06:09:24,296           If you don't want 'maginator.workflow.scripts' to be distributed and are
2024-01-06T06:09:24,296           already explicitly excluding 'maginator.workflow.scripts' via
2024-01-06T06:09:24,297           `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
2024-01-06T06:09:24,297           you can try to use `exclude_package_data`, or `include-package-data=False` in
2024-01-06T06:09:24,297           combination with a more fine grained `package-data` configuration.

2024-01-06T06:09:24,299           You can read more about "package data files" on setuptools documentation page:

2024-01-06T06:09:24,299           - https://setuptools.pypa.io/en/latest/userguide/datafiles.html


2024-01-06T06:09:24,301           [^1]: For Python, any directory (with suitable naming) can be imported,
2024-01-06T06:09:24,301                 even if it does not contain any `.py` files.
2024-01-06T06:09:24,301                 On the other hand, currently there is no concept of package data
2024-01-06T06:09:24,302                 directory, all directories are treated like packages.
2024-01-06T06:09:24,302           ********************************************************************************

2024-01-06T06:09:24,303   !!
2024-01-06T06:09:24,303     check.warn(importable)
2024-01-06T06:09:24,304   creating build/lib/maginator/workflow
2024-01-06T06:09:24,304   copying maginator/workflow/alignment.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,305   copying maginator/workflow/filter.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,305   copying maginator/workflow/filter_geneclusters.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,306   copying maginator/workflow/gene_count_mat.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,306   copying maginator/workflow/gene_tax.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,307   copying maginator/workflow/gtdbtk.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,307   copying maginator/workflow/outgroup.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,308   copying maginator/workflow/parse_gtdbtk.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,308   copying maginator/workflow/phylo.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,309   copying maginator/workflow/pileup.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,309   copying maginator/workflow/pileup_parse.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,310   copying maginator/workflow/prescreening_genes.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,310   copying maginator/workflow/reads_to_bins.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,311   copying maginator/workflow/signature_genes.Snakefile -> build/lib/maginator/workflow
2024-01-06T06:09:24,311   creating build/lib/maginator/workflow/envs
2024-01-06T06:09:24,312   copying maginator/workflow/envs/filter_geneclusters.yaml -> build/lib/maginator/workflow/envs
2024-01-06T06:09:24,312   copying maginator/workflow/envs/filter_gtdbtk.yaml -> build/lib/maginator/workflow/envs
2024-01-06T06:09:24,313   copying maginator/workflow/envs/phylo.yaml -> build/lib/maginator/workflow/envs
2024-01-06T06:09:24,313   copying maginator/workflow/envs/signature_genes.yaml -> build/lib/maginator/workflow/envs
2024-01-06T06:09:24,314   creating build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,314   copying maginator/workflow/scripts/Functions_v4.R -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,315   copying maginator/workflow/scripts/MGS_counts.R -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,315   copying maginator/workflow/scripts/SG_refinement.R -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,316   copying maginator/workflow/scripts/abundance_profiles.R -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,316   copying maginator/workflow/scripts/concat.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,317   copying maginator/workflow/scripts/filter.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,317   copying maginator/workflow/scripts/gene_cluster2tax.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,318   copying maginator/workflow/scripts/gene_refinement_plots.R -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,319   copying maginator/workflow/scripts/marker_genes.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,321   copying maginator/workflow/scripts/matrix2SG_formatconversion.R -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,323   copying maginator/workflow/scripts/mpileup.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,326   copying maginator/workflow/scripts/parse_gtdbtk.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,328   copying maginator/workflow/scripts/prescreening_genes.R -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,330   copying maginator/workflow/scripts/sort_gene_mat.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,332   copying maginator/workflow/scripts/species_collections.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,334   copying maginator/workflow/scripts/synteny.py -> build/lib/maginator/workflow/scripts
2024-01-06T06:09:24,359   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-01-06T06:09:24,360   !!

2024-01-06T06:09:24,361           ********************************************************************************
2024-01-06T06:09:24,362           Please avoid running ``setup.py`` directly.
2024-01-06T06:09:24,362           Instead, use pypa/build, pypa/installer or other
2024-01-06T06:09:24,363           standards-based tools.

2024-01-06T06:09:24,364           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-01-06T06:09:24,364           ********************************************************************************

2024-01-06T06:09:24,366   !!
2024-01-06T06:09:24,366     self.initialize_options()
2024-01-06T06:09:24,385   installing to build/bdist.linux-armv7l/wheel
2024-01-06T06:09:24,386   running install
2024-01-06T06:09:24,409   running install_lib
2024-01-06T06:09:24,434   creating build/bdist.linux-armv7l
2024-01-06T06:09:24,435   creating build/bdist.linux-armv7l/wheel
2024-01-06T06:09:24,437   creating build/bdist.linux-armv7l/wheel/maginator
2024-01-06T06:09:24,439   creating build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,440   copying build/lib/maginator/workflow/pileup_parse.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,443   creating build/bdist.linux-armv7l/wheel/maginator/workflow/envs
2024-01-06T06:09:24,444   copying build/lib/maginator/workflow/envs/filter_gtdbtk.yaml -> build/bdist.linux-armv7l/wheel/maginator/workflow/envs
2024-01-06T06:09:24,446   copying build/lib/maginator/workflow/envs/signature_genes.yaml -> build/bdist.linux-armv7l/wheel/maginator/workflow/envs
2024-01-06T06:09:24,448   copying build/lib/maginator/workflow/envs/phylo.yaml -> build/bdist.linux-armv7l/wheel/maginator/workflow/envs
2024-01-06T06:09:24,450   copying build/lib/maginator/workflow/envs/filter_geneclusters.yaml -> build/bdist.linux-armv7l/wheel/maginator/workflow/envs
2024-01-06T06:09:24,452   copying build/lib/maginator/workflow/gtdbtk.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,453   copying build/lib/maginator/workflow/parse_gtdbtk.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,456   copying build/lib/maginator/workflow/prescreening_genes.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,458   copying build/lib/maginator/workflow/phylo.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,460   copying build/lib/maginator/workflow/gene_count_mat.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,462   copying build/lib/maginator/workflow/pileup.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,464   copying build/lib/maginator/workflow/filter.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,466   copying build/lib/maginator/workflow/gene_tax.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,468   copying build/lib/maginator/workflow/signature_genes.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,471   creating build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,472   copying build/lib/maginator/workflow/scripts/species_collections.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,474   copying build/lib/maginator/workflow/scripts/sort_gene_mat.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,476   copying build/lib/maginator/workflow/scripts/Functions_v4.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,479   copying build/lib/maginator/workflow/scripts/synteny.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,481   copying build/lib/maginator/workflow/scripts/prescreening_genes.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,483   copying build/lib/maginator/workflow/scripts/gene_cluster2tax.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,485   copying build/lib/maginator/workflow/scripts/abundance_profiles.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,487   copying build/lib/maginator/workflow/scripts/MGS_counts.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,490   copying build/lib/maginator/workflow/scripts/SG_refinement.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,492   copying build/lib/maginator/workflow/scripts/concat.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,494   copying build/lib/maginator/workflow/scripts/parse_gtdbtk.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,497   copying build/lib/maginator/workflow/scripts/mpileup.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,500   copying build/lib/maginator/workflow/scripts/marker_genes.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,502   copying build/lib/maginator/workflow/scripts/filter.py -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,504   copying build/lib/maginator/workflow/scripts/gene_refinement_plots.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,507   copying build/lib/maginator/workflow/scripts/matrix2SG_formatconversion.R -> build/bdist.linux-armv7l/wheel/maginator/workflow/scripts
2024-01-06T06:09:24,509   copying build/lib/maginator/workflow/alignment.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,511   copying build/lib/maginator/workflow/filter_geneclusters.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,513   copying build/lib/maginator/workflow/outgroup.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,516   copying build/lib/maginator/workflow/reads_to_bins.Snakefile -> build/bdist.linux-armv7l/wheel/maginator/workflow
2024-01-06T06:09:24,518   copying build/lib/maginator/main.py -> build/bdist.linux-armv7l/wheel/maginator
2024-01-06T06:09:24,521   copying build/lib/maginator/workflow.py -> build/bdist.linux-armv7l/wheel/maginator
2024-01-06T06:09:24,523   copying build/lib/maginator/__init__.py -> build/bdist.linux-armv7l/wheel/maginator
2024-01-06T06:09:24,525   copying build/lib/maginator/messages.py -> build/bdist.linux-armv7l/wheel/maginator
2024-01-06T06:09:24,527   copying build/lib/maginator/controller.py -> build/bdist.linux-armv7l/wheel/maginator
2024-01-06T06:09:24,529   running install_egg_info
2024-01-06T06:09:24,559   Copying maginator.egg-info to build/bdist.linux-armv7l/wheel/maginator-0.1.19-py3.11.egg-info
2024-01-06T06:09:24,572   running install_scripts
2024-01-06T06:09:24,586   creating build/bdist.linux-armv7l/wheel/maginator-0.1.19.dist-info/WHEEL
2024-01-06T06:09:24,588   creating '/tmp/pip-wheel-vf2v9er8/maginator-0.1.19-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-01-06T06:09:24,591   adding 'maginator/__init__.py'
2024-01-06T06:09:24,593   adding 'maginator/controller.py'
2024-01-06T06:09:24,595   adding 'maginator/main.py'
2024-01-06T06:09:24,597   adding 'maginator/messages.py'
2024-01-06T06:09:24,599   adding 'maginator/workflow.py'
2024-01-06T06:09:24,601   adding 'maginator/workflow/alignment.Snakefile'
2024-01-06T06:09:24,603   adding 'maginator/workflow/filter.Snakefile'
2024-01-06T06:09:24,605   adding 'maginator/workflow/filter_geneclusters.Snakefile'
2024-01-06T06:09:24,606   adding 'maginator/workflow/gene_count_mat.Snakefile'
2024-01-06T06:09:24,608   adding 'maginator/workflow/gene_tax.Snakefile'
2024-01-06T06:09:24,610   adding 'maginator/workflow/gtdbtk.Snakefile'
2024-01-06T06:09:24,612   adding 'maginator/workflow/outgroup.Snakefile'
2024-01-06T06:09:24,613   adding 'maginator/workflow/parse_gtdbtk.Snakefile'
2024-01-06T06:09:24,615   adding 'maginator/workflow/phylo.Snakefile'
2024-01-06T06:09:24,616   adding 'maginator/workflow/pileup.Snakefile'
2024-01-06T06:09:24,618   adding 'maginator/workflow/pileup_parse.Snakefile'
2024-01-06T06:09:24,620   adding 'maginator/workflow/prescreening_genes.Snakefile'
2024-01-06T06:09:24,622   adding 'maginator/workflow/reads_to_bins.Snakefile'
2024-01-06T06:09:24,624   adding 'maginator/workflow/signature_genes.Snakefile'
2024-01-06T06:09:24,626   adding 'maginator/workflow/envs/filter_geneclusters.yaml'
2024-01-06T06:09:24,627   adding 'maginator/workflow/envs/filter_gtdbtk.yaml'
2024-01-06T06:09:24,629   adding 'maginator/workflow/envs/phylo.yaml'
2024-01-06T06:09:24,630   adding 'maginator/workflow/envs/signature_genes.yaml'
2024-01-06T06:09:24,633   adding 'maginator/workflow/scripts/Functions_v4.R'
2024-01-06T06:09:24,635   adding 'maginator/workflow/scripts/MGS_counts.R'
2024-01-06T06:09:24,637   adding 'maginator/workflow/scripts/SG_refinement.R'
2024-01-06T06:09:24,639   adding 'maginator/workflow/scripts/abundance_profiles.R'
2024-01-06T06:09:24,641   adding 'maginator/workflow/scripts/concat.py'
2024-01-06T06:09:24,643   adding 'maginator/workflow/scripts/filter.py'
2024-01-06T06:09:24,645   adding 'maginator/workflow/scripts/gene_cluster2tax.py'
2024-01-06T06:09:24,646   adding 'maginator/workflow/scripts/gene_refinement_plots.R'
2024-01-06T06:09:24,649   adding 'maginator/workflow/scripts/marker_genes.py'
2024-01-06T06:09:24,651   adding 'maginator/workflow/scripts/matrix2SG_formatconversion.R'
2024-01-06T06:09:24,654   adding 'maginator/workflow/scripts/mpileup.py'
2024-01-06T06:09:24,656   adding 'maginator/workflow/scripts/parse_gtdbtk.py'
2024-01-06T06:09:24,657   adding 'maginator/workflow/scripts/prescreening_genes.R'
2024-01-06T06:09:24,659   adding 'maginator/workflow/scripts/sort_gene_mat.py'
2024-01-06T06:09:24,661   adding 'maginator/workflow/scripts/species_collections.py'
2024-01-06T06:09:24,663   adding 'maginator/workflow/scripts/synteny.py'
2024-01-06T06:09:24,666   adding 'maginator-0.1.19.dist-info/METADATA'
2024-01-06T06:09:24,667   adding 'maginator-0.1.19.dist-info/WHEEL'
2024-01-06T06:09:24,669   adding 'maginator-0.1.19.dist-info/entry_points.txt'
2024-01-06T06:09:24,670   adding 'maginator-0.1.19.dist-info/top_level.txt'
2024-01-06T06:09:24,672   adding 'maginator-0.1.19.dist-info/RECORD'
2024-01-06T06:09:24,675   removing build/bdist.linux-armv7l/wheel
2024-01-06T06:09:24,794   Building wheel for maginator (setup.py): finished with status 'done'
2024-01-06T06:09:24,797   Created wheel for maginator: filename=maginator-0.1.19-py3-none-any.whl size=60459 sha256=6b4a26f0b7d95994e9567bf0abb33337bdeb307e8448ea1067c2ec9dfccba91e
2024-01-06T06:09:24,798   Stored in directory: /tmp/pip-ephem-wheel-cache-4ecuy70s/wheels/f2/2e/5e/73e81bea87a048d0a599e1b0a1f58463af06a40dbb06b7d8a5
2024-01-06T06:09:24,811 Successfully built maginator
2024-01-06T06:09:24,816 Removed build tracker: '/tmp/pip-build-tracker-po94k8z1'