2026-01-13T07:19:28,724 Created temporary directory: /tmp/pip-ephem-wheel-cache-ys0yty9t 2026-01-13T07:19:28,726 Created temporary directory: /tmp/pip-build-tracker-ew2f6neu 2026-01-13T07:19:28,727 Initialized build tracking at /tmp/pip-build-tracker-ew2f6neu 2026-01-13T07:19:28,727 Created build tracker: /tmp/pip-build-tracker-ew2f6neu 2026-01-13T07:19:28,728 Entered build tracker: /tmp/pip-build-tracker-ew2f6neu 2026-01-13T07:19:28,729 Created temporary directory: /tmp/pip-wheel-q70o5n7z 2026-01-13T07:19:28,732 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-01-13T07:19:28,734 Created temporary directory: /tmp/pip-ephem-wheel-cache-qqv88s57 2026-01-13T07:19:28,759 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-13T07:19:28,762 2 location(s) to search for versions of biobuntu: 2026-01-13T07:19:28,762 * https://pypi.org/simple/biobuntu/ 2026-01-13T07:19:28,762 * https://www.piwheels.org/simple/biobuntu/ 2026-01-13T07:19:28,763 Fetching project page and analyzing links: https://pypi.org/simple/biobuntu/ 2026-01-13T07:19:28,764 Getting page https://pypi.org/simple/biobuntu/ 2026-01-13T07:19:28,765 Found index url https://pypi.org/simple 2026-01-13T07:19:28,980 Fetched page https://pypi.org/simple/biobuntu/ as application/vnd.pypi.simple.v1+json 2026-01-13T07:19:28,982 Skipping link: No binaries permitted for biobuntu: https://files.pythonhosted.org/packages/64/cf/4f21daa56026906df18253ea875635d40200b04c5398c2976cbe04bcf511/biobuntu-0.1.0-py3-none-any.whl (from https://pypi.org/simple/biobuntu/) (requires-python:>=3.8) 2026-01-13T07:19:28,983 Found link https://files.pythonhosted.org/packages/d9/11/4a6d8e68308234734e669afa1cd6b834cab4492099e5b846f9793c7360e2/biobuntu-0.1.0.tar.gz (from https://pypi.org/simple/biobuntu/) (requires-python:>=3.8), version: 0.1.0 2026-01-13T07:19:28,983 Fetching project page and analyzing links: https://www.piwheels.org/simple/biobuntu/ 2026-01-13T07:19:28,984 Getting page https://www.piwheels.org/simple/biobuntu/ 2026-01-13T07:19:28,986 Found index url https://www.piwheels.org/simple 2026-01-13T07:19:29,143 Fetched page https://www.piwheels.org/simple/biobuntu/ as text/html 2026-01-13T07:19:29,144 Skipping link: not a file: https://www.piwheels.org/simple/biobuntu/ 2026-01-13T07:19:29,145 Skipping link: not a file: https://pypi.org/simple/biobuntu/ 2026-01-13T07:19:29,166 Given no hashes to check 1 links for project 'biobuntu': discarding no candidates 2026-01-13T07:19:29,185 Collecting biobuntu==0.1.0 2026-01-13T07:19:29,188 Created temporary directory: /tmp/pip-unpack-h8_z7lut 2026-01-13T07:19:29,326 Downloading biobuntu-0.1.0.tar.gz (10 kB) 2026-01-13T07:19:29,394 Added biobuntu==0.1.0 from https://files.pythonhosted.org/packages/d9/11/4a6d8e68308234734e669afa1cd6b834cab4492099e5b846f9793c7360e2/biobuntu-0.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-ew2f6neu' 2026-01-13T07:19:29,399 Created temporary directory: /tmp/pip-build-env-tspp36y9 2026-01-13T07:19:29,404 Installing build dependencies: started 2026-01-13T07:19:29,405 Running command pip subprocess to install build dependencies 2026-01-13T07:19:30,527 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-01-13T07:19:31,187 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-01-13T07:19:31,210 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-13T07:19:32,935 Collecting setuptools 2026-01-13T07:19:33,031 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2026-01-13T07:19:33,301 Collecting wheel 2026-01-13T07:19:33,319 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2026-01-13T07:19:36,303 Installing collected packages: wheel, setuptools 2026-01-13T07:19:36,546 Creating /tmp/pip-build-env-tspp36y9/overlay/local/bin 2026-01-13T07:19:36,548 changing mode of /tmp/pip-build-env-tspp36y9/overlay/local/bin/wheel to 755 2026-01-13T07:19:40,144 Successfully installed setuptools-80.9.0 wheel-0.45.1 2026-01-13T07:19:40,417 Installing build dependencies: finished with status 'done' 2026-01-13T07:19:40,424 Getting requirements to build wheel: started 2026-01-13T07:19:40,425 Running command Getting requirements to build wheel 2026-01-13T07:19:41,104 /tmp/pip-build-env-tspp36y9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T07:19:41,105 !! 2026-01-13T07:19:41,106 ******************************************************************************** 2026-01-13T07:19:41,106 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T07:19:41,107 License :: OSI Approved :: MIT License 2026-01-13T07:19:41,108 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T07:19:41,109 ******************************************************************************** 2026-01-13T07:19:41,110 !! 2026-01-13T07:19:41,111 dist._finalize_license_expression() 2026-01-13T07:19:41,111 /tmp/pip-build-env-tspp36y9/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T07:19:41,112 !! 2026-01-13T07:19:41,113 ******************************************************************************** 2026-01-13T07:19:41,114 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T07:19:41,116 License :: OSI Approved :: MIT License 2026-01-13T07:19:41,117 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T07:19:41,117 ******************************************************************************** 2026-01-13T07:19:41,119 !! 2026-01-13T07:19:41,120 self._finalize_license_expression() 2026-01-13T07:19:41,120 running egg_info 2026-01-13T07:19:41,122 writing biobuntu.egg-info/PKG-INFO 2026-01-13T07:19:41,125 writing dependency_links to biobuntu.egg-info/dependency_links.txt 2026-01-13T07:19:41,127 writing entry points to biobuntu.egg-info/entry_points.txt 2026-01-13T07:19:41,129 writing requirements to biobuntu.egg-info/requires.txt 2026-01-13T07:19:41,130 writing top-level names to biobuntu.egg-info/top_level.txt 2026-01-13T07:19:41,155 reading manifest file 'biobuntu.egg-info/SOURCES.txt' 2026-01-13T07:19:41,158 adding license file 'LICENSE' 2026-01-13T07:19:41,162 writing manifest file 'biobuntu.egg-info/SOURCES.txt' 2026-01-13T07:19:41,259 Getting requirements to build wheel: finished with status 'done' 2026-01-13T07:19:41,263 Created temporary directory: /tmp/pip-modern-metadata-bexbkyih 2026-01-13T07:19:41,265 Preparing metadata (pyproject.toml): started 2026-01-13T07:19:41,267 Running command Preparing metadata (pyproject.toml) 2026-01-13T07:19:41,905 /tmp/pip-build-env-tspp36y9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T07:19:41,905 !! 2026-01-13T07:19:41,906 ******************************************************************************** 2026-01-13T07:19:41,907 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T07:19:41,908 License :: OSI Approved :: MIT License 2026-01-13T07:19:41,909 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T07:19:41,909 ******************************************************************************** 2026-01-13T07:19:41,910 !! 2026-01-13T07:19:41,911 dist._finalize_license_expression() 2026-01-13T07:19:41,912 /tmp/pip-build-env-tspp36y9/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T07:19:41,912 !! 2026-01-13T07:19:41,913 ******************************************************************************** 2026-01-13T07:19:41,913 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T07:19:41,914 License :: OSI Approved :: MIT License 2026-01-13T07:19:41,915 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T07:19:41,916 ******************************************************************************** 2026-01-13T07:19:41,917 !! 2026-01-13T07:19:41,917 self._finalize_license_expression() 2026-01-13T07:19:41,919 running dist_info 2026-01-13T07:19:41,932 creating /tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info 2026-01-13T07:19:41,933 writing /tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info/PKG-INFO 2026-01-13T07:19:41,936 writing dependency_links to /tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info/dependency_links.txt 2026-01-13T07:19:41,938 writing entry points to /tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info/entry_points.txt 2026-01-13T07:19:41,939 writing requirements to /tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info/requires.txt 2026-01-13T07:19:41,940 writing top-level names to /tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info/top_level.txt 2026-01-13T07:19:41,942 writing manifest file '/tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info/SOURCES.txt' 2026-01-13T07:19:41,965 reading manifest file '/tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info/SOURCES.txt' 2026-01-13T07:19:41,967 adding license file 'LICENSE' 2026-01-13T07:19:41,970 writing manifest file '/tmp/pip-modern-metadata-bexbkyih/biobuntu.egg-info/SOURCES.txt' 2026-01-13T07:19:41,971 creating '/tmp/pip-modern-metadata-bexbkyih/biobuntu-0.1.0.dist-info' 2026-01-13T07:19:42,097 Preparing metadata (pyproject.toml): finished with status 'done' 2026-01-13T07:19:42,102 Source in /tmp/pip-wheel-q70o5n7z/biobuntu_963f237c7eb74955a53c288bded262ce has version 0.1.0, which satisfies requirement biobuntu==0.1.0 from https://files.pythonhosted.org/packages/d9/11/4a6d8e68308234734e669afa1cd6b834cab4492099e5b846f9793c7360e2/biobuntu-0.1.0.tar.gz 2026-01-13T07:19:42,103 Removed biobuntu==0.1.0 from https://files.pythonhosted.org/packages/d9/11/4a6d8e68308234734e669afa1cd6b834cab4492099e5b846f9793c7360e2/biobuntu-0.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-ew2f6neu' 2026-01-13T07:19:42,110 Created temporary directory: /tmp/pip-unpack-iumvu41r 2026-01-13T07:19:42,111 Building wheels for collected packages: biobuntu 2026-01-13T07:19:42,115 Created temporary directory: /tmp/pip-wheel-rof0vlpi 2026-01-13T07:19:42,116 Destination directory: /tmp/pip-wheel-rof0vlpi 2026-01-13T07:19:42,118 Building wheel for biobuntu (pyproject.toml): started 2026-01-13T07:19:42,119 Running command Building wheel for biobuntu (pyproject.toml) 2026-01-13T07:19:42,765 /tmp/pip-build-env-tspp36y9/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:61: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T07:19:42,765 !! 2026-01-13T07:19:42,766 ******************************************************************************** 2026-01-13T07:19:42,767 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T07:19:42,769 License :: OSI Approved :: MIT License 2026-01-13T07:19:42,770 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T07:19:42,770 ******************************************************************************** 2026-01-13T07:19:42,771 !! 2026-01-13T07:19:42,772 dist._finalize_license_expression() 2026-01-13T07:19:42,772 /tmp/pip-build-env-tspp36y9/overlay/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2026-01-13T07:19:42,773 !! 2026-01-13T07:19:42,774 ******************************************************************************** 2026-01-13T07:19:42,774 Please consider removing the following classifiers in favor of a SPDX license expression: 2026-01-13T07:19:42,775 License :: OSI Approved :: MIT License 2026-01-13T07:19:42,776 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-01-13T07:19:42,777 ******************************************************************************** 2026-01-13T07:19:42,778 !! 2026-01-13T07:19:42,779 self._finalize_license_expression() 2026-01-13T07:19:42,779 running bdist_wheel 2026-01-13T07:19:42,793 running build 2026-01-13T07:19:42,794 running build_py 2026-01-13T07:19:42,801 creating build/lib/core 2026-01-13T07:19:42,803 copying core/project_manager.py -> build/lib/core 2026-01-13T07:19:42,805 copying core/__init__.py -> build/lib/core 2026-01-13T07:19:42,806 copying core/config.py -> build/lib/core 2026-01-13T07:19:42,808 copying core/utils.py -> build/lib/core 2026-01-13T07:19:42,810 copying core/file_manager.py -> build/lib/core 2026-01-13T07:19:42,812 copying core/engine.py -> build/lib/core 2026-01-13T07:19:42,815 copying core/logger.py -> build/lib/core 2026-01-13T07:19:42,816 copying core/runner.py -> build/lib/core 2026-01-13T07:19:42,819 creating build/lib/tools 2026-01-13T07:19:42,820 copying tools/samtools.py -> build/lib/tools 2026-01-13T07:19:42,822 copying tools/bwa.py -> build/lib/tools 2026-01-13T07:19:42,823 copying tools/fastqc.py -> build/lib/tools 2026-01-13T07:19:42,825 copying tools/hisat2.py -> build/lib/tools 2026-01-13T07:19:42,827 copying tools/gatk.py -> build/lib/tools 2026-01-13T07:19:42,829 creating build/lib/cli 2026-01-13T07:19:42,830 copying cli/__init__.py -> build/lib/cli 2026-01-13T07:19:42,832 copying cli/cli.py -> build/lib/cli 2026-01-13T07:19:42,834 creating build/lib/gui 2026-01-13T07:19:42,836 copying gui/__init__.py -> build/lib/gui 2026-01-13T07:19:42,837 copying gui/main.py -> build/lib/gui 2026-01-13T07:19:42,840 creating build/lib/web 2026-01-13T07:19:42,841 copying web/__init__.py -> build/lib/web 2026-01-13T07:19:42,842 copying web/api.py -> build/lib/web 2026-01-13T07:19:42,844 running egg_info 2026-01-13T07:19:42,855 writing biobuntu.egg-info/PKG-INFO 2026-01-13T07:19:42,858 writing dependency_links to biobuntu.egg-info/dependency_links.txt 2026-01-13T07:19:42,860 writing entry points to biobuntu.egg-info/entry_points.txt 2026-01-13T07:19:42,861 writing requirements to biobuntu.egg-info/requires.txt 2026-01-13T07:19:42,862 writing top-level names to biobuntu.egg-info/top_level.txt 2026-01-13T07:19:42,875 reading manifest file 'biobuntu.egg-info/SOURCES.txt' 2026-01-13T07:19:42,879 adding license file 'LICENSE' 2026-01-13T07:19:42,882 writing manifest file 'biobuntu.egg-info/SOURCES.txt' 2026-01-13T07:19:42,898 installing to build/bdist.linux-armv7l/wheel 2026-01-13T07:19:42,898 running install 2026-01-13T07:19:42,922 running install_lib 2026-01-13T07:19:42,929 creating build/bdist.linux-armv7l/wheel 2026-01-13T07:19:42,931 creating build/bdist.linux-armv7l/wheel/core 2026-01-13T07:19:42,932 copying build/lib/core/project_manager.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T07:19:42,935 copying build/lib/core/__init__.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T07:19:42,936 copying build/lib/core/config.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T07:19:42,938 copying build/lib/core/utils.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T07:19:42,940 copying build/lib/core/file_manager.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T07:19:42,941 copying build/lib/core/engine.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T07:19:42,943 copying build/lib/core/logger.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T07:19:42,945 copying build/lib/core/runner.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T07:19:42,947 creating build/bdist.linux-armv7l/wheel/tools 2026-01-13T07:19:42,948 copying build/lib/tools/samtools.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T07:19:42,950 copying build/lib/tools/bwa.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T07:19:42,952 copying build/lib/tools/fastqc.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T07:19:42,953 copying build/lib/tools/hisat2.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T07:19:42,955 copying build/lib/tools/gatk.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T07:19:42,957 creating build/bdist.linux-armv7l/wheel/cli 2026-01-13T07:19:42,958 copying build/lib/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./cli 2026-01-13T07:19:42,960 copying build/lib/cli/cli.py -> build/bdist.linux-armv7l/wheel/./cli 2026-01-13T07:19:42,962 creating build/bdist.linux-armv7l/wheel/gui 2026-01-13T07:19:42,963 copying build/lib/gui/__init__.py -> build/bdist.linux-armv7l/wheel/./gui 2026-01-13T07:19:42,964 copying build/lib/gui/main.py -> build/bdist.linux-armv7l/wheel/./gui 2026-01-13T07:19:42,966 creating build/bdist.linux-armv7l/wheel/web 2026-01-13T07:19:42,967 copying build/lib/web/__init__.py -> build/bdist.linux-armv7l/wheel/./web 2026-01-13T07:19:42,969 copying build/lib/web/api.py -> build/bdist.linux-armv7l/wheel/./web 2026-01-13T07:19:42,970 running install_egg_info 2026-01-13T07:19:42,976 Copying biobuntu.egg-info to build/bdist.linux-armv7l/wheel/./biobuntu-0.1.0-py3.11.egg-info 2026-01-13T07:19:42,987 running install_scripts 2026-01-13T07:19:42,998 creating build/bdist.linux-armv7l/wheel/biobuntu-0.1.0.dist-info/WHEEL 2026-01-13T07:19:43,001 creating '/tmp/pip-wheel-rof0vlpi/.tmp-5lvr4jh0/biobuntu-0.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-01-13T07:19:43,004 adding 'biobuntu-0.1.0.dist-info/licenses/LICENSE' 2026-01-13T07:19:43,006 adding 'cli/__init__.py' 2026-01-13T07:19:43,007 adding 'cli/cli.py' 2026-01-13T07:19:43,009 adding 'core/__init__.py' 2026-01-13T07:19:43,010 adding 'core/config.py' 2026-01-13T07:19:43,012 adding 'core/engine.py' 2026-01-13T07:19:43,013 adding 'core/file_manager.py' 2026-01-13T07:19:43,014 adding 'core/logger.py' 2026-01-13T07:19:43,016 adding 'core/project_manager.py' 2026-01-13T07:19:43,017 adding 'core/runner.py' 2026-01-13T07:19:43,018 adding 'core/utils.py' 2026-01-13T07:19:43,020 adding 'gui/__init__.py' 2026-01-13T07:19:43,021 adding 'gui/main.py' 2026-01-13T07:19:43,023 adding 'tools/bwa.py' 2026-01-13T07:19:43,024 adding 'tools/fastqc.py' 2026-01-13T07:19:43,025 adding 'tools/gatk.py' 2026-01-13T07:19:43,026 adding 'tools/hisat2.py' 2026-01-13T07:19:43,028 adding 'tools/samtools.py' 2026-01-13T07:19:43,029 adding 'web/__init__.py' 2026-01-13T07:19:43,031 adding 'web/api.py' 2026-01-13T07:19:43,032 adding 'biobuntu-0.1.0.dist-info/METADATA' 2026-01-13T07:19:43,033 adding 'biobuntu-0.1.0.dist-info/WHEEL' 2026-01-13T07:19:43,034 adding 'biobuntu-0.1.0.dist-info/entry_points.txt' 2026-01-13T07:19:43,035 adding 'biobuntu-0.1.0.dist-info/top_level.txt' 2026-01-13T07:19:43,036 adding 'biobuntu-0.1.0.dist-info/RECORD' 2026-01-13T07:19:43,038 removing build/bdist.linux-armv7l/wheel 2026-01-13T07:19:43,144 Building wheel for biobuntu (pyproject.toml): finished with status 'done' 2026-01-13T07:19:43,148 Created wheel for biobuntu: filename=biobuntu-0.1.0-py3-none-any.whl size=14087 sha256=68acacdc74787c20d7391575f834eae66ab68870d9d36e16e9da855efa5f3fad 2026-01-13T07:19:43,150 Stored in directory: /tmp/pip-ephem-wheel-cache-qqv88s57/wheels/6d/3c/f4/9b7d39f55a6afc0210535eb65cd469605c97e7393dcb102693 2026-01-13T07:19:43,162 Successfully built biobuntu 2026-01-13T07:19:43,165 Removed build tracker: '/tmp/pip-build-tracker-ew2f6neu'