2026-01-13T11:52:55,484 Created temporary directory: /tmp/pip-ephem-wheel-cache-6pxfzx6v 2026-01-13T11:52:55,486 Created temporary directory: /tmp/pip-build-tracker-to6vrf0a 2026-01-13T11:52:55,487 Initialized build tracking at /tmp/pip-build-tracker-to6vrf0a 2026-01-13T11:52:55,487 Created build tracker: /tmp/pip-build-tracker-to6vrf0a 2026-01-13T11:52:55,487 Entered build tracker: /tmp/pip-build-tracker-to6vrf0a 2026-01-13T11:52:55,488 Created temporary directory: /tmp/pip-wheel-k8flp885 2026-01-13T11:52:55,491 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 2026-01-13T11:52:55,493 Created temporary directory: /tmp/pip-ephem-wheel-cache-r6ohpaph 2026-01-13T11:52:55,517 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-13T11:52:55,521 2 location(s) to search for versions of biobuntu: 2026-01-13T11:52:55,521 * https://pypi.org/simple/biobuntu/ 2026-01-13T11:52:55,521 * https://www.piwheels.org/simple/biobuntu/ 2026-01-13T11:52:55,521 Fetching project page and analyzing links: https://pypi.org/simple/biobuntu/ 2026-01-13T11:52:55,522 Getting page https://pypi.org/simple/biobuntu/ 2026-01-13T11:52:55,524 Found index url https://pypi.org/simple 2026-01-13T11:52:55,738 Fetched page https://pypi.org/simple/biobuntu/ as application/vnd.pypi.simple.v1+json 2026-01-13T11:52:55,740 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) 2026-01-13T11:52:55,741 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 2026-01-13T11:52:55,742 Skipping link: No binaries permitted for biobuntu: https://files.pythonhosted.org/packages/12/b6/c2041168299e2d3d34820729f2ed11126b6e622d4ffd706f61aea2bcbabf/biobuntu-1.0.0-py3-none-any.whl (from https://pypi.org/simple/biobuntu/) (requires-python:>=3.8) 2026-01-13T11:52:55,743 Found link https://files.pythonhosted.org/packages/46/17/5399b95835bd8fe691bc24d3b3d8d1f8ae0c02fe51c7d30699d796524bf8/biobuntu-1.0.0.tar.gz (from https://pypi.org/simple/biobuntu/) (requires-python:>=3.8), version: 1.0.0 2026-01-13T11:52:55,744 Skipping link: No binaries permitted for biobuntu: https://files.pythonhosted.org/packages/2c/d0/b96c035b568ccd5176db706d831560b6639908f1318f353018dab091536a/biobuntu-1.0.1-py3-none-any.whl (from https://pypi.org/simple/biobuntu/) (requires-python:>=3.8) 2026-01-13T11:52:55,744 Fetching project page and analyzing links: https://www.piwheels.org/simple/biobuntu/ 2026-01-13T11:52:55,745 Getting page https://www.piwheels.org/simple/biobuntu/ 2026-01-13T11:52:55,747 Found index url https://www.piwheels.org/simple 2026-01-13T11:52:55,981 Fetched page https://www.piwheels.org/simple/biobuntu/ as text/html 2026-01-13T11:52:55,983 Skipping link: No binaries permitted for biobuntu: https://www.piwheels.org/simple/biobuntu/biobuntu-0.1.0-py3-none-any.whl#sha256=68acacdc74787c20d7391575f834eae66ab68870d9d36e16e9da855efa5f3fad (from https://www.piwheels.org/simple/biobuntu/) (requires-python:>=3.8) 2026-01-13T11:52:55,983 Skipping link: not a file: https://www.piwheels.org/simple/biobuntu/ 2026-01-13T11:52:55,984 Skipping link: not a file: https://pypi.org/simple/biobuntu/ 2026-01-13T11:52:56,004 Given no hashes to check 1 links for project 'biobuntu': discarding no candidates 2026-01-13T11:52:56,023 Collecting biobuntu==1.0.0 2026-01-13T11:52:56,026 Created temporary directory: /tmp/pip-unpack-0jr3gb11 2026-01-13T11:52:56,236 Downloading biobuntu-1.0.0.tar.gz (11 kB) 2026-01-13T11:52:56,297 Added biobuntu==1.0.0 from https://files.pythonhosted.org/packages/46/17/5399b95835bd8fe691bc24d3b3d8d1f8ae0c02fe51c7d30699d796524bf8/biobuntu-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-to6vrf0a' 2026-01-13T11:52:56,302 Created temporary directory: /tmp/pip-build-env-yr0nmaru 2026-01-13T11:52:56,306 Installing build dependencies: started 2026-01-13T11:52:56,307 Running command pip subprocess to install build dependencies 2026-01-13T11:52:57,440 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-01-13T11:52:58,128 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 2026-01-13T11:52:58,152 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-01-13T11:52:59,866 Collecting setuptools 2026-01-13T11:53:00,117 Using cached https://www.piwheels.org/simple/setuptools/setuptools-80.9.0-py3-none-any.whl (1.2 MB) 2026-01-13T11:53:00,415 Collecting wheel 2026-01-13T11:53:00,433 Using cached https://www.piwheels.org/simple/wheel/wheel-0.45.1-py3-none-any.whl (72 kB) 2026-01-13T11:53:03,471 Installing collected packages: wheel, setuptools 2026-01-13T11:53:03,713 Creating /tmp/pip-build-env-yr0nmaru/overlay/local/bin 2026-01-13T11:53:03,716 changing mode of /tmp/pip-build-env-yr0nmaru/overlay/local/bin/wheel to 755 2026-01-13T11:53:07,284 Successfully installed setuptools-80.9.0 wheel-0.45.1 2026-01-13T11:53:07,556 Installing build dependencies: finished with status 'done' 2026-01-13T11:53:07,563 Getting requirements to build wheel: started 2026-01-13T11:53:07,564 Running command Getting requirements to build wheel 2026-01-13T11:53:08,271 running egg_info 2026-01-13T11:53:08,278 writing biobuntu.egg-info/PKG-INFO 2026-01-13T11:53:08,282 writing dependency_links to biobuntu.egg-info/dependency_links.txt 2026-01-13T11:53:08,284 writing entry points to biobuntu.egg-info/entry_points.txt 2026-01-13T11:53:08,286 writing requirements to biobuntu.egg-info/requires.txt 2026-01-13T11:53:08,287 writing top-level names to biobuntu.egg-info/top_level.txt 2026-01-13T11:53:08,312 reading manifest file 'biobuntu.egg-info/SOURCES.txt' 2026-01-13T11:53:08,316 adding license file 'LICENSE' 2026-01-13T11:53:08,319 writing manifest file 'biobuntu.egg-info/SOURCES.txt' 2026-01-13T11:53:08,416 Getting requirements to build wheel: finished with status 'done' 2026-01-13T11:53:08,420 Created temporary directory: /tmp/pip-modern-metadata-trile04x 2026-01-13T11:53:08,422 Preparing metadata (pyproject.toml): started 2026-01-13T11:53:08,424 Running command Preparing metadata (pyproject.toml) 2026-01-13T11:53:09,081 running dist_info 2026-01-13T11:53:09,093 creating /tmp/pip-modern-metadata-trile04x/biobuntu.egg-info 2026-01-13T11:53:09,094 writing /tmp/pip-modern-metadata-trile04x/biobuntu.egg-info/PKG-INFO 2026-01-13T11:53:09,098 writing dependency_links to /tmp/pip-modern-metadata-trile04x/biobuntu.egg-info/dependency_links.txt 2026-01-13T11:53:09,099 writing entry points to /tmp/pip-modern-metadata-trile04x/biobuntu.egg-info/entry_points.txt 2026-01-13T11:53:09,101 writing requirements to /tmp/pip-modern-metadata-trile04x/biobuntu.egg-info/requires.txt 2026-01-13T11:53:09,102 writing top-level names to /tmp/pip-modern-metadata-trile04x/biobuntu.egg-info/top_level.txt 2026-01-13T11:53:09,103 writing manifest file '/tmp/pip-modern-metadata-trile04x/biobuntu.egg-info/SOURCES.txt' 2026-01-13T11:53:09,126 reading manifest file '/tmp/pip-modern-metadata-trile04x/biobuntu.egg-info/SOURCES.txt' 2026-01-13T11:53:09,129 adding license file 'LICENSE' 2026-01-13T11:53:09,132 writing manifest file '/tmp/pip-modern-metadata-trile04x/biobuntu.egg-info/SOURCES.txt' 2026-01-13T11:53:09,133 creating '/tmp/pip-modern-metadata-trile04x/biobuntu-1.0.0.dist-info' 2026-01-13T11:53:09,259 Preparing metadata (pyproject.toml): finished with status 'done' 2026-01-13T11:53:09,264 Source in /tmp/pip-wheel-k8flp885/biobuntu_eadf0fc24f3e4a87a46174b450b2a8e8 has version 1.0.0, which satisfies requirement biobuntu==1.0.0 from https://files.pythonhosted.org/packages/46/17/5399b95835bd8fe691bc24d3b3d8d1f8ae0c02fe51c7d30699d796524bf8/biobuntu-1.0.0.tar.gz 2026-01-13T11:53:09,265 Removed biobuntu==1.0.0 from https://files.pythonhosted.org/packages/46/17/5399b95835bd8fe691bc24d3b3d8d1f8ae0c02fe51c7d30699d796524bf8/biobuntu-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-to6vrf0a' 2026-01-13T11:53:09,271 Created temporary directory: /tmp/pip-unpack-p1nkussv 2026-01-13T11:53:09,272 Building wheels for collected packages: biobuntu 2026-01-13T11:53:09,277 Created temporary directory: /tmp/pip-wheel-3131kw16 2026-01-13T11:53:09,277 Destination directory: /tmp/pip-wheel-3131kw16 2026-01-13T11:53:09,279 Building wheel for biobuntu (pyproject.toml): started 2026-01-13T11:53:09,281 Running command Building wheel for biobuntu (pyproject.toml) 2026-01-13T11:53:09,904 running bdist_wheel 2026-01-13T11:53:09,925 running build 2026-01-13T11:53:09,926 running build_py 2026-01-13T11:53:09,932 creating build/lib/core 2026-01-13T11:53:09,934 copying core/project_manager.py -> build/lib/core 2026-01-13T11:53:09,936 copying core/__init__.py -> build/lib/core 2026-01-13T11:53:09,938 copying core/config.py -> build/lib/core 2026-01-13T11:53:09,940 copying core/utils.py -> build/lib/core 2026-01-13T11:53:09,942 copying core/file_manager.py -> build/lib/core 2026-01-13T11:53:09,944 copying core/engine.py -> build/lib/core 2026-01-13T11:53:09,946 copying core/logger.py -> build/lib/core 2026-01-13T11:53:09,948 copying core/runner.py -> build/lib/core 2026-01-13T11:53:09,950 creating build/lib/tools 2026-01-13T11:53:09,951 copying tools/samtools.py -> build/lib/tools 2026-01-13T11:53:09,953 copying tools/bwa.py -> build/lib/tools 2026-01-13T11:53:09,955 copying tools/fastqc.py -> build/lib/tools 2026-01-13T11:53:09,957 copying tools/hisat2.py -> build/lib/tools 2026-01-13T11:53:09,959 copying tools/gatk.py -> build/lib/tools 2026-01-13T11:53:09,961 creating build/lib/cli 2026-01-13T11:53:09,962 copying cli/__init__.py -> build/lib/cli 2026-01-13T11:53:09,964 copying cli/cli.py -> build/lib/cli 2026-01-13T11:53:09,966 creating build/lib/gui 2026-01-13T11:53:09,967 copying gui/__init__.py -> build/lib/gui 2026-01-13T11:53:09,970 copying gui/main.py -> build/lib/gui 2026-01-13T11:53:09,972 creating build/lib/web 2026-01-13T11:53:09,973 copying web/__init__.py -> build/lib/web 2026-01-13T11:53:09,975 copying web/api.py -> build/lib/web 2026-01-13T11:53:09,976 running egg_info 2026-01-13T11:53:09,988 writing biobuntu.egg-info/PKG-INFO 2026-01-13T11:53:09,991 writing dependency_links to biobuntu.egg-info/dependency_links.txt 2026-01-13T11:53:09,993 writing entry points to biobuntu.egg-info/entry_points.txt 2026-01-13T11:53:09,994 writing requirements to biobuntu.egg-info/requires.txt 2026-01-13T11:53:09,995 writing top-level names to biobuntu.egg-info/top_level.txt 2026-01-13T11:53:10,008 reading manifest file 'biobuntu.egg-info/SOURCES.txt' 2026-01-13T11:53:10,011 adding license file 'LICENSE' 2026-01-13T11:53:10,014 writing manifest file 'biobuntu.egg-info/SOURCES.txt' 2026-01-13T11:53:10,030 installing to build/bdist.linux-armv7l/wheel 2026-01-13T11:53:10,030 running install 2026-01-13T11:53:10,054 running install_lib 2026-01-13T11:53:10,060 creating build/bdist.linux-armv7l/wheel 2026-01-13T11:53:10,062 creating build/bdist.linux-armv7l/wheel/core 2026-01-13T11:53:10,063 copying build/lib/core/project_manager.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T11:53:10,065 copying build/lib/core/__init__.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T11:53:10,067 copying build/lib/core/config.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T11:53:10,069 copying build/lib/core/utils.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T11:53:10,071 copying build/lib/core/file_manager.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T11:53:10,072 copying build/lib/core/engine.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T11:53:10,074 copying build/lib/core/logger.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T11:53:10,076 copying build/lib/core/runner.py -> build/bdist.linux-armv7l/wheel/./core 2026-01-13T11:53:10,078 creating build/bdist.linux-armv7l/wheel/tools 2026-01-13T11:53:10,079 copying build/lib/tools/samtools.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T11:53:10,081 copying build/lib/tools/bwa.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T11:53:10,083 copying build/lib/tools/fastqc.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T11:53:10,084 copying build/lib/tools/hisat2.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T11:53:10,086 copying build/lib/tools/gatk.py -> build/bdist.linux-armv7l/wheel/./tools 2026-01-13T11:53:10,088 creating build/bdist.linux-armv7l/wheel/cli 2026-01-13T11:53:10,089 copying build/lib/cli/__init__.py -> build/bdist.linux-armv7l/wheel/./cli 2026-01-13T11:53:10,091 copying build/lib/cli/cli.py -> build/bdist.linux-armv7l/wheel/./cli 2026-01-13T11:53:10,093 creating build/bdist.linux-armv7l/wheel/gui 2026-01-13T11:53:10,094 copying build/lib/gui/__init__.py -> build/bdist.linux-armv7l/wheel/./gui 2026-01-13T11:53:10,096 copying build/lib/gui/main.py -> build/bdist.linux-armv7l/wheel/./gui 2026-01-13T11:53:10,098 creating build/bdist.linux-armv7l/wheel/web 2026-01-13T11:53:10,099 copying build/lib/web/__init__.py -> build/bdist.linux-armv7l/wheel/./web 2026-01-13T11:53:10,101 copying build/lib/web/api.py -> build/bdist.linux-armv7l/wheel/./web 2026-01-13T11:53:10,103 running install_egg_info 2026-01-13T11:53:10,108 Copying biobuntu.egg-info to build/bdist.linux-armv7l/wheel/./biobuntu-1.0.0-py3.11.egg-info 2026-01-13T11:53:10,119 running install_scripts 2026-01-13T11:53:10,130 creating build/bdist.linux-armv7l/wheel/biobuntu-1.0.0.dist-info/WHEEL 2026-01-13T11:53:10,133 creating '/tmp/pip-wheel-3131kw16/.tmp-rkj8ntqh/biobuntu-1.0.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-01-13T11:53:10,136 adding 'biobuntu-1.0.0.dist-info/licenses/LICENSE' 2026-01-13T11:53:10,138 adding 'cli/__init__.py' 2026-01-13T11:53:10,139 adding 'cli/cli.py' 2026-01-13T11:53:10,141 adding 'core/__init__.py' 2026-01-13T11:53:10,142 adding 'core/config.py' 2026-01-13T11:53:10,143 adding 'core/engine.py' 2026-01-13T11:53:10,144 adding 'core/file_manager.py' 2026-01-13T11:53:10,146 adding 'core/logger.py' 2026-01-13T11:53:10,147 adding 'core/project_manager.py' 2026-01-13T11:53:10,148 adding 'core/runner.py' 2026-01-13T11:53:10,149 adding 'core/utils.py' 2026-01-13T11:53:10,151 adding 'gui/__init__.py' 2026-01-13T11:53:10,152 adding 'gui/main.py' 2026-01-13T11:53:10,154 adding 'tools/bwa.py' 2026-01-13T11:53:10,155 adding 'tools/fastqc.py' 2026-01-13T11:53:10,156 adding 'tools/gatk.py' 2026-01-13T11:53:10,157 adding 'tools/hisat2.py' 2026-01-13T11:53:10,159 adding 'tools/samtools.py' 2026-01-13T11:53:10,160 adding 'web/__init__.py' 2026-01-13T11:53:10,162 adding 'web/api.py' 2026-01-13T11:53:10,163 adding 'biobuntu-1.0.0.dist-info/METADATA' 2026-01-13T11:53:10,164 adding 'biobuntu-1.0.0.dist-info/WHEEL' 2026-01-13T11:53:10,165 adding 'biobuntu-1.0.0.dist-info/entry_points.txt' 2026-01-13T11:53:10,166 adding 'biobuntu-1.0.0.dist-info/top_level.txt' 2026-01-13T11:53:10,167 adding 'biobuntu-1.0.0.dist-info/RECORD' 2026-01-13T11:53:10,168 removing build/bdist.linux-armv7l/wheel 2026-01-13T11:53:10,275 Building wheel for biobuntu (pyproject.toml): finished with status 'done' 2026-01-13T11:53:10,279 Created wheel for biobuntu: filename=biobuntu-1.0.0-py3-none-any.whl size=14293 sha256=0bae1f2ded17d096ad7b72099eab157e4606d8c6ecbc16b94bc8a81f30e238a0 2026-01-13T11:53:10,280 Stored in directory: /tmp/pip-ephem-wheel-cache-r6ohpaph/wheels/a2/01/85/f4a1e5f24b72ccd0772299ee1d5677a62be9c7da0e4da30f4f 2026-01-13T11:53:10,292 Successfully built biobuntu 2026-01-13T11:53:10,295 Removed build tracker: '/tmp/pip-build-tracker-to6vrf0a'