2026-04-25T09:49:25,887 Created temporary directory: /tmp/pip-ephem-wheel-cache-ptz17de4 2026-04-25T09:49:25,889 Created temporary directory: /tmp/pip-build-tracker-a7_lqjk5 2026-04-25T09:49:25,889 Initialized build tracking at /tmp/pip-build-tracker-a7_lqjk5 2026-04-25T09:49:25,890 Created build tracker: /tmp/pip-build-tracker-a7_lqjk5 2026-04-25T09:49:25,890 Entered build tracker: /tmp/pip-build-tracker-a7_lqjk5 2026-04-25T09:49:25,891 Created temporary directory: /tmp/pip-wheel-5v0czzwb 2026-04-25T09:49:25,894 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 2026-04-25T09:49:25,896 Created temporary directory: /tmp/pip-ephem-wheel-cache-5pk5nqtj 2026-04-25T09:49:25,918 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-25T09:49:25,921 2 location(s) to search for versions of somaticseq: 2026-04-25T09:49:25,921 * https://pypi.org/simple/somaticseq/ 2026-04-25T09:49:25,921 * https://www.piwheels.org/simple/somaticseq/ 2026-04-25T09:49:25,922 Fetching project page and analyzing links: https://pypi.org/simple/somaticseq/ 2026-04-25T09:49:25,923 Getting page https://pypi.org/simple/somaticseq/ 2026-04-25T09:49:25,924 Found index url https://pypi.org/simple 2026-04-25T09:49:26,161 Fetched page https://pypi.org/simple/somaticseq/ as application/vnd.pypi.simple.v1+json 2026-04-25T09:49:26,164 Found link https://files.pythonhosted.org/packages/66/a1/52de812952b5ebc3df0b945d88d8c72a15fde3a6d44c7761042a4704cdc3/somaticseq-3.7.3.tar.gz (from https://pypi.org/simple/somaticseq/), version: 3.7.3 2026-04-25T09:49:26,165 Found link https://files.pythonhosted.org/packages/17/b0/17d3cb01fae1f469ac27f88b2094e0918704cc402b4d0194ea6f1e32b800/somaticseq-3.7.4.tar.gz (from https://pypi.org/simple/somaticseq/), version: 3.7.4 2026-04-25T09:49:26,166 Found link https://files.pythonhosted.org/packages/53/d3/ae6ee18a759498f405592c94c0499842faa0603b6c23b607e3e66c22d7a4/somaticseq-3.8.0.tar.gz (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.10.0), version: 3.8.0 2026-04-25T09:49:26,167 Skipping link: No binaries permitted for somaticseq: https://files.pythonhosted.org/packages/46/a7/ecb99f60e6813358d7dc47f5fa579e2b240225f33d51163e05a4905089a3/somaticseq-3.9.0-py3-none-any.whl (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,168 Found link https://files.pythonhosted.org/packages/41/53/d7c3eac00caba5144f1f89dcf4efff45d3ac62bb3c1d91fc9dd4340b6b64/somaticseq-3.9.0.tar.gz (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0), version: 3.9.0 2026-04-25T09:49:26,169 Skipping link: No binaries permitted for somaticseq: https://files.pythonhosted.org/packages/69/a7/985e96ada63b3999a038381c7eda5210d34b4a72e2464ef95051089852f3/somaticseq-3.9.1-py3-none-any.whl (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,170 Found link https://files.pythonhosted.org/packages/10/2b/71131ea2a9b22c0610b94400dc67fd85ea179ce74be47a0324a0d7be272c/somaticseq-3.9.1.tar.gz (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0), version: 3.9.1 2026-04-25T09:49:26,170 Skipping link: No binaries permitted for somaticseq: https://files.pythonhosted.org/packages/bf/ed/f459e33d8c4980c219f277c0d20bc81efcd18aef702257f6484125ebdb54/somaticseq-3.10.0-py3-none-any.whl (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,171 Found link https://files.pythonhosted.org/packages/d6/c3/c3f8aa5b485d62ca47e8dba85eb757360f5aad0af7511b25d47662134428/somaticseq-3.10.0.tar.gz (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0), version: 3.10.0 2026-04-25T09:49:26,172 Skipping link: No binaries permitted for somaticseq: https://files.pythonhosted.org/packages/79/71/3d7299b6fa1fc138aa288943ca568c53ee0da2490e5bb719f12bcf5b2e4b/somaticseq-3.11.0-py3-none-any.whl (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,173 Found link https://files.pythonhosted.org/packages/9f/b6/44c6f8d53f0b702e00f9ed02296180448da85ebf34c3f7b9a8fe1f36809d/somaticseq-3.11.0.tar.gz (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0), version: 3.11.0 2026-04-25T09:49:26,174 Skipping link: No binaries permitted for somaticseq: https://files.pythonhosted.org/packages/44/35/57d65ac22fc8336df58627b6b730bdca98ee30952aac394ebdc51fed6e85/somaticseq-3.11.1-py3-none-any.whl (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,175 Found link https://files.pythonhosted.org/packages/0c/31/ebe6bdb4c5fd3bfc4ce780623c62ab6c706aac99de5beafb8b11a675c293/somaticseq-3.11.1.tar.gz (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0), version: 3.11.1 2026-04-25T09:49:26,175 Skipping link: No binaries permitted for somaticseq: https://files.pythonhosted.org/packages/d5/f3/cc5072d61301e34ccda1ab401acc2c1a030174d2d2eb2d374626a25de47d/somaticseq-3.12.0-py3-none-any.whl (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,176 Found link https://files.pythonhosted.org/packages/d5/db/348764331e92d1595557b05813e3f443b88fc73bc5380f004fc1bfc87512/somaticseq-3.12.0.tar.gz (from https://pypi.org/simple/somaticseq/) (requires-python:>=3.11.0), version: 3.12.0 2026-04-25T09:49:26,177 Fetching project page and analyzing links: https://www.piwheels.org/simple/somaticseq/ 2026-04-25T09:49:26,178 Getting page https://www.piwheels.org/simple/somaticseq/ 2026-04-25T09:49:26,179 Found index url https://www.piwheels.org/simple 2026-04-25T09:49:26,354 Fetched page https://www.piwheels.org/simple/somaticseq/ as text/html 2026-04-25T09:49:26,357 Skipping link: No binaries permitted for somaticseq: https://archive1.piwheels.org/simple/somaticseq/somaticseq-3.11.1-py3-none-any.whl#sha256=635ee9314f85fb4a1fdfd95fccf0d2ca7d741dbdea0c9aa05bff0ccf0979fb3a (from https://www.piwheels.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,358 Skipping link: No binaries permitted for somaticseq: https://archive1.piwheels.org/simple/somaticseq/somaticseq-3.11.0-py3-none-any.whl#sha256=735fbdef18191c68a2cd57bd2e657820279b7a46fa8a15eb589aa6563455542b (from https://www.piwheels.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,358 Skipping link: No binaries permitted for somaticseq: https://archive1.piwheels.org/simple/somaticseq/somaticseq-3.10.0-py3-none-any.whl#sha256=034da23ea25ca84b3a6ac60febc822a56d0aeb035dcbce10bbd9d6f46bb25a4c (from https://www.piwheels.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,359 Skipping link: No binaries permitted for somaticseq: https://archive1.piwheels.org/simple/somaticseq/somaticseq-3.9.1-py3-none-any.whl#sha256=758bb9baa0540f093b37001f5ddbc2212f3b2f50ce5a2996cb76b73dce602066 (from https://www.piwheels.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,360 Skipping link: No binaries permitted for somaticseq: https://archive1.piwheels.org/simple/somaticseq/somaticseq-3.9.0-py3-none-any.whl#sha256=31f5ece20a162d4e98406c9c5f588f6ebb28624f20e4177aad41fd7681bfa11b (from https://www.piwheels.org/simple/somaticseq/) (requires-python:>=3.11.0) 2026-04-25T09:49:26,360 Skipping link: No binaries permitted for somaticseq: https://archive1.piwheels.org/simple/somaticseq/somaticseq-3.8.0-py3-none-any.whl#sha256=02cf9678ebe683363a38a2bb89a4645fdc408e8c2f079693a2682e067e85523f (from https://www.piwheels.org/simple/somaticseq/) (requires-python:>=3.10.0) 2026-04-25T09:49:26,361 Skipping link: No binaries permitted for somaticseq: https://archive1.piwheels.org/simple/somaticseq/somaticseq-3.7.4-py3-none-any.whl#sha256=2ab6487255fe614e97cf1e771576df0f07771a923286483c3f16a551897d9294 (from https://www.piwheels.org/simple/somaticseq/) 2026-04-25T09:49:26,361 Skipping link: No binaries permitted for somaticseq: https://archive1.piwheels.org/simple/somaticseq/somaticseq-3.7.3-py3-none-any.whl#sha256=ffd2a113ca4746e6d200ae746559246271776a2dd38b2af16327199d91bf9ea1 (from https://www.piwheels.org/simple/somaticseq/) 2026-04-25T09:49:26,362 Skipping link: not a file: https://www.piwheels.org/simple/somaticseq/ 2026-04-25T09:49:26,363 Skipping link: not a file: https://pypi.org/simple/somaticseq/ 2026-04-25T09:49:26,384 Given no hashes to check 1 links for project 'somaticseq': discarding no candidates 2026-04-25T09:49:26,403 Collecting somaticseq==3.12.0 2026-04-25T09:49:26,405 Created temporary directory: /tmp/pip-unpack-pyyhnra0 2026-04-25T09:49:26,557 Downloading somaticseq-3.12.0.tar.gz (143 kB) 2026-04-25T09:49:26,855 Added somaticseq==3.12.0 from https://files.pythonhosted.org/packages/d5/db/348764331e92d1595557b05813e3f443b88fc73bc5380f004fc1bfc87512/somaticseq-3.12.0.tar.gz to build tracker '/tmp/pip-build-tracker-a7_lqjk5' 2026-04-25T09:49:26,862 Created temporary directory: /tmp/pip-build-env-7f_cvt2z 2026-04-25T09:49:26,867 Installing build dependencies: started 2026-04-25T09:49:26,868 Running command pip subprocess to install build dependencies 2026-04-25T09:49:28,019 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-04-25T09:49:28,443 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 2026-04-25T09:49:28,467 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-04-25T09:49:30,234 Collecting setuptools>=61 2026-04-25T09:49:30,316 Using cached https://www.piwheels.org/simple/setuptools/setuptools-82.0.1-py3-none-any.whl (1.0 MB) 2026-04-25T09:49:30,590 Collecting wheel 2026-04-25T09:49:30,607 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-04-25T09:49:30,787 Collecting packaging>=24.0 2026-04-25T09:49:30,806 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-04-25T09:49:33,753 Installing collected packages: setuptools, packaging, wheel 2026-04-25T09:49:37,257 Creating /tmp/pip-build-env-7f_cvt2z/overlay/local/bin 2026-04-25T09:49:37,259 changing mode of /tmp/pip-build-env-7f_cvt2z/overlay/local/bin/wheel to 755 2026-04-25T09:49:37,674 Successfully installed packaging-26.2 setuptools-82.0.1 wheel-0.47.0 2026-04-25T09:49:37,976 Installing build dependencies: finished with status 'done' 2026-04-25T09:49:37,983 Getting requirements to build wheel: started 2026-04-25T09:49:37,984 Running command Getting requirements to build wheel 2026-04-25T09:49:38,631 /tmp/pip-build-env-7f_cvt2z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-04-25T09:49:38,632 !! 2026-04-25T09:49:38,633 ******************************************************************************** 2026-04-25T09:49:38,633 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-04-25T09:49:38,635 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-04-25T09:49:38,635 or your builds will no longer be supported. 2026-04-25T09:49:38,637 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-25T09:49:38,637 ******************************************************************************** 2026-04-25T09:49:38,638 !! 2026-04-25T09:49:38,639 corresp(dist, value, root_dir) 2026-04-25T09:49:38,713 running egg_info 2026-04-25T09:49:38,719 writing somaticseq.egg-info/PKG-INFO 2026-04-25T09:49:38,724 writing dependency_links to somaticseq.egg-info/dependency_links.txt 2026-04-25T09:49:38,727 writing entry points to somaticseq.egg-info/entry_points.txt 2026-04-25T09:49:38,729 writing requirements to somaticseq.egg-info/requires.txt 2026-04-25T09:49:38,730 writing top-level names to somaticseq.egg-info/top_level.txt 2026-04-25T09:49:38,767 reading manifest file 'somaticseq.egg-info/SOURCES.txt' 2026-04-25T09:49:38,774 adding license file 'LICENSE.txt' 2026-04-25T09:49:38,781 writing manifest file 'somaticseq.egg-info/SOURCES.txt' 2026-04-25T09:49:38,878 Getting requirements to build wheel: finished with status 'done' 2026-04-25T09:49:38,882 Created temporary directory: /tmp/pip-modern-metadata-ot88lqdl 2026-04-25T09:49:38,884 Preparing metadata (pyproject.toml): started 2026-04-25T09:49:38,885 Running command Preparing metadata (pyproject.toml) 2026-04-25T09:49:39,492 /tmp/pip-build-env-7f_cvt2z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-04-25T09:49:39,493 !! 2026-04-25T09:49:39,494 ******************************************************************************** 2026-04-25T09:49:39,494 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-04-25T09:49:39,495 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-04-25T09:49:39,496 or your builds will no longer be supported. 2026-04-25T09:49:39,497 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-25T09:49:39,497 ******************************************************************************** 2026-04-25T09:49:39,498 !! 2026-04-25T09:49:39,499 corresp(dist, value, root_dir) 2026-04-25T09:49:39,574 running dist_info 2026-04-25T09:49:39,584 creating /tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info 2026-04-25T09:49:39,585 writing /tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info/PKG-INFO 2026-04-25T09:49:39,590 writing dependency_links to /tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info/dependency_links.txt 2026-04-25T09:49:39,593 writing entry points to /tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info/entry_points.txt 2026-04-25T09:49:39,595 writing requirements to /tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info/requires.txt 2026-04-25T09:49:39,596 writing top-level names to /tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info/top_level.txt 2026-04-25T09:49:39,598 writing manifest file '/tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info/SOURCES.txt' 2026-04-25T09:49:39,631 reading manifest file '/tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info/SOURCES.txt' 2026-04-25T09:49:39,634 adding license file 'LICENSE.txt' 2026-04-25T09:49:39,639 writing manifest file '/tmp/pip-modern-metadata-ot88lqdl/somaticseq.egg-info/SOURCES.txt' 2026-04-25T09:49:39,641 creating '/tmp/pip-modern-metadata-ot88lqdl/somaticseq-3.12.0.dist-info' 2026-04-25T09:49:39,768 Preparing metadata (pyproject.toml): finished with status 'done' 2026-04-25T09:49:39,773 Source in /tmp/pip-wheel-5v0czzwb/somaticseq_f526034c32d8495ebb901a0b6cd63034 has version 3.12.0, which satisfies requirement somaticseq==3.12.0 from https://files.pythonhosted.org/packages/d5/db/348764331e92d1595557b05813e3f443b88fc73bc5380f004fc1bfc87512/somaticseq-3.12.0.tar.gz 2026-04-25T09:49:39,775 Removed somaticseq==3.12.0 from https://files.pythonhosted.org/packages/d5/db/348764331e92d1595557b05813e3f443b88fc73bc5380f004fc1bfc87512/somaticseq-3.12.0.tar.gz from build tracker '/tmp/pip-build-tracker-a7_lqjk5' 2026-04-25T09:49:39,781 Created temporary directory: /tmp/pip-unpack-uldpklsg 2026-04-25T09:49:39,782 Building wheels for collected packages: somaticseq 2026-04-25T09:49:39,787 Created temporary directory: /tmp/pip-wheel-e1lv609z 2026-04-25T09:49:39,787 Destination directory: /tmp/pip-wheel-e1lv609z 2026-04-25T09:49:39,790 Building wheel for somaticseq (pyproject.toml): started 2026-04-25T09:49:39,791 Running command Building wheel for somaticseq (pyproject.toml) 2026-04-25T09:49:40,345 /tmp/pip-build-env-7f_cvt2z/overlay/local/lib/python3.11/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated 2026-04-25T09:49:40,345 !! 2026-04-25T09:49:40,346 ******************************************************************************** 2026-04-25T09:49:40,347 Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0). 2026-04-25T09:49:40,348 By 2027-Feb-18, you need to update your project and remove deprecated calls 2026-04-25T09:49:40,348 or your builds will no longer be supported. 2026-04-25T09:49:40,349 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2026-04-25T09:49:40,350 ******************************************************************************** 2026-04-25T09:49:40,350 !! 2026-04-25T09:49:40,351 corresp(dist, value, root_dir) 2026-04-25T09:49:40,415 running bdist_wheel 2026-04-25T09:49:40,432 running build 2026-04-25T09:49:40,433 running build_py 2026-04-25T09:49:40,439 creating build/lib/somaticseq 2026-04-25T09:49:40,441 copying somaticseq/single_sample_vcf2tsv.py -> build/lib/somaticseq 2026-04-25T09:49:40,443 copying somaticseq/__init__.py -> build/lib/somaticseq 2026-04-25T09:49:40,445 copying somaticseq/somatic_tsv2vcf.py -> build/lib/somaticseq 2026-04-25T09:49:40,448 copying somaticseq/somatic_vcf2tsv.py -> build/lib/somaticseq 2026-04-25T09:49:40,451 copying somaticseq/_version.py -> build/lib/somaticseq 2026-04-25T09:49:40,453 copying somaticseq/somatic_xgboost.py -> build/lib/somaticseq 2026-04-25T09:49:40,455 copying somaticseq/ntchange_type.py -> build/lib/somaticseq 2026-04-25T09:49:40,457 copying somaticseq/defaults.py -> build/lib/somaticseq 2026-04-25T09:49:40,459 copying somaticseq/tsv2vcf.py -> build/lib/somaticseq 2026-04-25T09:49:40,462 copying somaticseq/sequencing_features.py -> build/lib/somaticseq 2026-04-25T09:49:40,464 copying somaticseq/combine_callers.py -> build/lib/somaticseq 2026-04-25T09:49:40,467 copying somaticseq/bam_features.py -> build/lib/somaticseq 2026-04-25T09:49:40,469 copying somaticseq/annotate_caller.py -> build/lib/somaticseq 2026-04-25T09:49:40,472 copying somaticseq/somaticseq_parallel.py -> build/lib/somaticseq 2026-04-25T09:49:40,474 copying somaticseq/run_somaticseq.py -> build/lib/somaticseq 2026-04-25T09:49:40,478 creating build/lib/r_scripts 2026-04-25T09:49:40,479 copying r_scripts/__init__.py -> build/lib/r_scripts 2026-04-25T09:49:40,481 creating build/lib/somaticseq/utilities 2026-04-25T09:49:40,482 copying somaticseq/utilities/bedFileHandler.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,484 copying somaticseq/utilities/lociCounterWithLabels.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,486 copying somaticseq/utilities/linguistic_sequence_complexity.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,488 copying somaticseq/utilities/bamQC.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,490 copying somaticseq/utilities/__init__.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,492 copying somaticseq/utilities/paired_end_bam2fastq.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,494 copying somaticseq/utilities/BAM_filter.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,496 copying somaticseq/utilities/variant_annotation.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,498 copying somaticseq/utilities/plot_TPvsFP.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,500 copying somaticseq/utilities/filter_SomaticSeq_VCF.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,503 copying somaticseq/utilities/split_mergedBed.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,505 copying somaticseq/utilities/multi-nucleotide_phaser.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,507 copying somaticseq/utilities/split_bed_into_equal_regions.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,509 copying somaticseq/utilities/tally_MyVCF_vs_Truth.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,511 copying somaticseq/utilities/attach_pileupVAF.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,513 copying somaticseq/utilities/reformat_VCF2SEQC2.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,515 copying somaticseq/utilities/combo_callers_evaluator.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,517 copying somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,520 copying somaticseq/utilities/trimSoftClippedReads.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,522 copying somaticseq/utilities/lociCounters.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,524 copying somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/lib/somaticseq/utilities 2026-04-25T09:49:40,527 creating build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,529 copying somaticseq/vcf_modifier/copy_TextFile.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,531 copying somaticseq/vcf_modifier/modify_ssMuTect2.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,533 copying somaticseq/vcf_modifier/__init__.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,535 copying somaticseq/vcf_modifier/split_vcf.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,537 copying somaticseq/vcf_modifier/modify_SomaticSniper.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,539 copying somaticseq/vcf_modifier/getUniqueVcfPositions.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,541 copying somaticseq/vcf_modifier/modify_VarDict.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,544 copying somaticseq/vcf_modifier/modify_MuTect2.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,546 copying somaticseq/vcf_modifier/modify_ssStrelka.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,548 copying somaticseq/vcf_modifier/complex2indel.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,551 copying somaticseq/vcf_modifier/modify_MuTect.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,553 copying somaticseq/vcf_modifier/modify_VarScan2.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,555 copying somaticseq/vcf_modifier/modify_JointSNVMix2.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,557 copying somaticseq/vcf_modifier/leftAlign.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,559 copying somaticseq/vcf_modifier/bed_util.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,561 copying somaticseq/vcf_modifier/modify_Strelka.py -> build/lib/somaticseq/vcf_modifier 2026-04-25T09:49:40,563 creating build/lib/somaticseq/genomic_file_parsers 2026-04-25T09:49:40,564 copying somaticseq/genomic_file_parsers/__init__.py -> build/lib/somaticseq/genomic_file_parsers 2026-04-25T09:49:40,566 copying somaticseq/genomic_file_parsers/genomic_file_handlers.py -> build/lib/somaticseq/genomic_file_parsers 2026-04-25T09:49:40,568 copying somaticseq/genomic_file_parsers/pileup_reader.py -> build/lib/somaticseq/genomic_file_parsers 2026-04-25T09:49:40,571 copying somaticseq/genomic_file_parsers/concat.py -> build/lib/somaticseq/genomic_file_parsers 2026-04-25T09:49:40,573 copying somaticseq/genomic_file_parsers/read_info_extractor.py -> build/lib/somaticseq/genomic_file_parsers 2026-04-25T09:49:40,576 creating build/lib/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,577 copying somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/lib/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,579 copying somaticseq/utilities/dockered_pipelines/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,581 copying somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/lib/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,583 copying somaticseq/utilities/dockered_pipelines/container_option.py -> build/lib/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,585 copying somaticseq/utilities/dockered_pipelines/tumor_normal_run.py -> build/lib/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,588 copying somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/lib/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,590 copying somaticseq/utilities/dockered_pipelines/tumor_only_run.py -> build/lib/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,593 creating build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,594 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,596 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,598 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,600 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,602 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,605 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,607 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,609 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,611 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,613 copying somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py -> build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,616 creating build/lib/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,617 copying somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,619 copying somaticseq/utilities/dockered_pipelines/alignments/__init__.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,621 copying somaticseq/utilities/dockered_pipelines/alignments/markdup.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,623 copying somaticseq/utilities/dockered_pipelines/alignments/align.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,625 copying somaticseq/utilities/dockered_pipelines/alignments/trim.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,628 copying somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,630 copying somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py -> build/lib/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,640 copying r_scripts/ada_model_builder_ntChange.R -> build/lib/r_scripts 2026-04-25T09:49:40,642 copying r_scripts/ada_model_predictor.R -> build/lib/r_scripts 2026-04-25T09:49:40,644 copying r_scripts/ada_cross_validation.R -> build/lib/r_scripts 2026-04-25T09:49:40,646 copying r_scripts/ada_model_builder.R -> build/lib/r_scripts 2026-04-25T09:49:40,653 running build_scripts 2026-04-25T09:49:40,654 creating build/scripts-3.11 2026-04-25T09:49:40,655 copying and adjusting somaticseq/somaticseq_parallel.py -> build/scripts-3.11 2026-04-25T09:49:40,658 copying and adjusting somaticseq/run_somaticseq.py -> build/scripts-3.11 2026-04-25T09:49:40,662 copying and adjusting somaticseq/single_sample_vcf2tsv.py -> build/scripts-3.11 2026-04-25T09:49:40,666 copying and adjusting somaticseq/somatic_vcf2tsv.py -> build/scripts-3.11 2026-04-25T09:49:40,669 copying and adjusting somaticseq/somatic_xgboost.py -> build/scripts-3.11 2026-04-25T09:49:40,671 copying and adjusting somaticseq/somatic_tsv2vcf.py -> build/scripts-3.11 2026-04-25T09:49:40,674 copying and adjusting somaticseq/genomic_file_parsers/concat.py -> build/scripts-3.11 2026-04-25T09:49:40,676 copying and adjusting somaticseq/utilities/linguistic_sequence_complexity.py -> build/scripts-3.11 2026-04-25T09:49:40,677 copying and adjusting somaticseq/utilities/lociCounterWithLabels.py -> build/scripts-3.11 2026-04-25T09:49:40,680 copying and adjusting somaticseq/utilities/paired_end_bam2fastq.py -> build/scripts-3.11 2026-04-25T09:49:40,681 copying and adjusting somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/scripts-3.11 2026-04-25T09:49:40,683 copying and adjusting somaticseq/utilities/split_bed_into_equal_regions.py -> build/scripts-3.11 2026-04-25T09:49:40,685 copying and adjusting somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/scripts-3.11 2026-04-25T09:49:40,687 copying and adjusting somaticseq/utilities/variant_annotation.py -> build/scripts-3.11 2026-04-25T09:49:40,689 copying somaticseq/utilities/vcfsorter.pl -> build/scripts-3.11 2026-04-25T09:49:40,691 copying and adjusting somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/scripts-3.11 2026-04-25T09:49:40,693 copying and adjusting somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/scripts-3.11 2026-04-25T09:49:40,696 copying and adjusting somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/scripts-3.11 2026-04-25T09:49:40,698 copying and adjusting somaticseq/vcf_modifier/split_vcf.py -> build/scripts-3.11 2026-04-25T09:49:40,700 copying r_scripts/ada_model_builder_ntChange.R -> build/scripts-3.11 2026-04-25T09:49:40,702 copying r_scripts/ada_model_predictor.R -> build/scripts-3.11 2026-04-25T09:49:40,704 changing mode of build/scripts-3.11/somaticseq_parallel.py from 644 to 755 2026-04-25T09:49:40,704 changing mode of build/scripts-3.11/run_somaticseq.py from 644 to 755 2026-04-25T09:49:40,705 changing mode of build/scripts-3.11/single_sample_vcf2tsv.py from 644 to 755 2026-04-25T09:49:40,705 changing mode of build/scripts-3.11/somatic_vcf2tsv.py from 644 to 755 2026-04-25T09:49:40,706 changing mode of build/scripts-3.11/somatic_xgboost.py from 644 to 755 2026-04-25T09:49:40,706 changing mode of build/scripts-3.11/somatic_tsv2vcf.py from 644 to 755 2026-04-25T09:49:40,707 changing mode of build/scripts-3.11/concat.py from 644 to 755 2026-04-25T09:49:40,707 changing mode of build/scripts-3.11/linguistic_sequence_complexity.py from 644 to 755 2026-04-25T09:49:40,708 changing mode of build/scripts-3.11/lociCounterWithLabels.py from 644 to 755 2026-04-25T09:49:40,708 changing mode of build/scripts-3.11/paired_end_bam2fastq.py from 644 to 755 2026-04-25T09:49:40,709 changing mode of build/scripts-3.11/remove_callers_from_somaticseq_tsv.py from 644 to 755 2026-04-25T09:49:40,709 changing mode of build/scripts-3.11/split_bed_into_equal_regions.py from 644 to 755 2026-04-25T09:49:40,710 changing mode of build/scripts-3.11/tally_variants_from_multiple_vcfs.py from 644 to 755 2026-04-25T09:49:40,710 changing mode of build/scripts-3.11/variant_annotation.py from 644 to 755 2026-04-25T09:49:40,711 changing mode of build/scripts-3.11/makeAlignmentScripts.py from 644 to 755 2026-04-25T09:49:40,711 changing mode of build/scripts-3.11/makeSomaticScripts.py from 644 to 755 2026-04-25T09:49:40,712 changing mode of build/scripts-3.11/run_workflows.py from 644 to 755 2026-04-25T09:49:40,712 changing mode of build/scripts-3.11/split_vcf.py from 644 to 755 2026-04-25T09:49:40,719 installing to build/bdist.linux-armv7l/wheel 2026-04-25T09:49:40,720 running install 2026-04-25T09:49:40,743 running install_lib 2026-04-25T09:49:40,749 creating build/bdist.linux-armv7l/wheel 2026-04-25T09:49:40,751 creating build/bdist.linux-armv7l/wheel/somaticseq 2026-04-25T09:49:40,752 copying build/lib/somaticseq/single_sample_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,754 copying build/lib/somaticseq/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,756 copying build/lib/somaticseq/somatic_tsv2vcf.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,758 copying build/lib/somaticseq/somatic_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,761 copying build/lib/somaticseq/_version.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,763 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities 2026-04-25T09:49:40,764 copying build/lib/somaticseq/utilities/bedFileHandler.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,767 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,767 copying build/lib/somaticseq/utilities/dockered_pipelines/run_workflows.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,770 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,771 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,773 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,775 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,777 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,780 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,782 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,784 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,786 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,789 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,791 copying build/lib/somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/somatic_mutations 2026-04-25T09:49:40,793 copying build/lib/somaticseq/utilities/dockered_pipelines/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,794 copying build/lib/somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,797 copying build/lib/somaticseq/utilities/dockered_pipelines/container_option.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,799 copying build/lib/somaticseq/utilities/dockered_pipelines/tumor_normal_run.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,801 copying build/lib/somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,804 copying build/lib/somaticseq/utilities/dockered_pipelines/tumor_only_run.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines 2026-04-25T09:49:40,807 creating build/bdist.linux-armv7l/wheel/somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,808 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,810 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,811 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/markdup.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,814 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/align.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,816 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/trim.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,818 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,820 copying build/lib/somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities/dockered_pipelines/alignments 2026-04-25T09:49:40,822 copying build/lib/somaticseq/utilities/lociCounterWithLabels.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,825 copying build/lib/somaticseq/utilities/linguistic_sequence_complexity.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,827 copying build/lib/somaticseq/utilities/bamQC.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,829 copying build/lib/somaticseq/utilities/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,830 copying build/lib/somaticseq/utilities/paired_end_bam2fastq.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,832 copying build/lib/somaticseq/utilities/BAM_filter.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,834 copying build/lib/somaticseq/utilities/variant_annotation.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,836 copying build/lib/somaticseq/utilities/plot_TPvsFP.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,839 copying build/lib/somaticseq/utilities/filter_SomaticSeq_VCF.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,841 copying build/lib/somaticseq/utilities/split_mergedBed.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,843 copying build/lib/somaticseq/utilities/multi-nucleotide_phaser.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,845 copying build/lib/somaticseq/utilities/split_bed_into_equal_regions.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,848 copying build/lib/somaticseq/utilities/tally_MyVCF_vs_Truth.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,850 copying build/lib/somaticseq/utilities/attach_pileupVAF.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,852 copying build/lib/somaticseq/utilities/reformat_VCF2SEQC2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,854 copying build/lib/somaticseq/utilities/combo_callers_evaluator.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,856 copying build/lib/somaticseq/utilities/tally_variants_from_multiple_vcfs.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,859 copying build/lib/somaticseq/utilities/trimSoftClippedReads.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,861 copying build/lib/somaticseq/utilities/lociCounters.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,863 copying build/lib/somaticseq/utilities/remove_callers_from_somaticseq_tsv.py -> build/bdist.linux-armv7l/wheel/./somaticseq/utilities 2026-04-25T09:49:40,865 copying build/lib/somaticseq/somatic_xgboost.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,867 copying build/lib/somaticseq/ntchange_type.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,870 creating build/bdist.linux-armv7l/wheel/somaticseq/vcf_modifier 2026-04-25T09:49:40,871 copying build/lib/somaticseq/vcf_modifier/copy_TextFile.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,873 copying build/lib/somaticseq/vcf_modifier/modify_ssMuTect2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,875 copying build/lib/somaticseq/vcf_modifier/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,877 copying build/lib/somaticseq/vcf_modifier/split_vcf.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,879 copying build/lib/somaticseq/vcf_modifier/modify_SomaticSniper.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,881 copying build/lib/somaticseq/vcf_modifier/getUniqueVcfPositions.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,883 copying build/lib/somaticseq/vcf_modifier/modify_VarDict.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,886 copying build/lib/somaticseq/vcf_modifier/modify_MuTect2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,888 copying build/lib/somaticseq/vcf_modifier/modify_ssStrelka.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,890 copying build/lib/somaticseq/vcf_modifier/complex2indel.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,892 copying build/lib/somaticseq/vcf_modifier/modify_MuTect.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,894 copying build/lib/somaticseq/vcf_modifier/modify_VarScan2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,896 copying build/lib/somaticseq/vcf_modifier/modify_JointSNVMix2.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,898 copying build/lib/somaticseq/vcf_modifier/leftAlign.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,900 copying build/lib/somaticseq/vcf_modifier/bed_util.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,902 copying build/lib/somaticseq/vcf_modifier/modify_Strelka.py -> build/bdist.linux-armv7l/wheel/./somaticseq/vcf_modifier 2026-04-25T09:49:40,904 copying build/lib/somaticseq/defaults.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,906 copying build/lib/somaticseq/tsv2vcf.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,909 creating build/bdist.linux-armv7l/wheel/somaticseq/genomic_file_parsers 2026-04-25T09:49:40,910 copying build/lib/somaticseq/genomic_file_parsers/__init__.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2026-04-25T09:49:40,912 copying build/lib/somaticseq/genomic_file_parsers/genomic_file_handlers.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2026-04-25T09:49:40,914 copying build/lib/somaticseq/genomic_file_parsers/pileup_reader.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2026-04-25T09:49:40,916 copying build/lib/somaticseq/genomic_file_parsers/concat.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2026-04-25T09:49:40,919 copying build/lib/somaticseq/genomic_file_parsers/read_info_extractor.py -> build/bdist.linux-armv7l/wheel/./somaticseq/genomic_file_parsers 2026-04-25T09:49:40,921 copying build/lib/somaticseq/sequencing_features.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,923 copying build/lib/somaticseq/combine_callers.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,926 copying build/lib/somaticseq/bam_features.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,928 copying build/lib/somaticseq/annotate_caller.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,930 copying build/lib/somaticseq/somaticseq_parallel.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,933 copying build/lib/somaticseq/run_somaticseq.py -> build/bdist.linux-armv7l/wheel/./somaticseq 2026-04-25T09:49:40,936 creating build/bdist.linux-armv7l/wheel/r_scripts 2026-04-25T09:49:40,937 copying build/lib/r_scripts/ada_model_builder_ntChange.R -> build/bdist.linux-armv7l/wheel/./r_scripts 2026-04-25T09:49:40,939 copying build/lib/r_scripts/__init__.py -> build/bdist.linux-armv7l/wheel/./r_scripts 2026-04-25T09:49:40,941 copying build/lib/r_scripts/ada_model_predictor.R -> build/bdist.linux-armv7l/wheel/./r_scripts 2026-04-25T09:49:40,943 copying build/lib/r_scripts/ada_cross_validation.R -> build/bdist.linux-armv7l/wheel/./r_scripts 2026-04-25T09:49:40,945 copying build/lib/r_scripts/ada_model_builder.R -> build/bdist.linux-armv7l/wheel/./r_scripts 2026-04-25T09:49:40,946 running install_egg_info 2026-04-25T09:49:40,955 running egg_info 2026-04-25T09:49:40,960 writing somaticseq.egg-info/PKG-INFO 2026-04-25T09:49:40,965 writing dependency_links to somaticseq.egg-info/dependency_links.txt 2026-04-25T09:49:40,967 writing entry points to somaticseq.egg-info/entry_points.txt 2026-04-25T09:49:40,969 writing requirements to somaticseq.egg-info/requires.txt 2026-04-25T09:49:40,970 writing top-level names to somaticseq.egg-info/top_level.txt 2026-04-25T09:49:40,989 reading manifest file 'somaticseq.egg-info/SOURCES.txt' 2026-04-25T09:49:40,996 adding license file 'LICENSE.txt' 2026-04-25T09:49:41,003 writing manifest file 'somaticseq.egg-info/SOURCES.txt' 2026-04-25T09:49:41,005 Copying somaticseq.egg-info to build/bdist.linux-armv7l/wheel/./somaticseq-3.12.0-py3.11.egg-info 2026-04-25T09:49:41,017 running install_scripts 2026-04-25T09:49:41,018 creating build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,020 copying build/scripts-3.11/run_workflows.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,022 copying build/scripts-3.11/single_sample_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,026 copying build/scripts-3.11/lociCounterWithLabels.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,028 copying build/scripts-3.11/linguistic_sequence_complexity.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,030 copying build/scripts-3.11/ada_model_builder_ntChange.R -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,033 copying build/scripts-3.11/paired_end_bam2fastq.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,035 copying build/scripts-3.11/ada_model_predictor.R -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,037 copying build/scripts-3.11/somatic_tsv2vcf.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,040 copying build/scripts-3.11/split_vcf.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,043 copying build/scripts-3.11/somatic_vcf2tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,046 copying build/scripts-3.11/variant_annotation.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,048 copying build/scripts-3.11/somatic_xgboost.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,051 copying build/scripts-3.11/makeSomaticScripts.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,054 copying build/scripts-3.11/split_bed_into_equal_regions.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,056 copying build/scripts-3.11/vcfsorter.pl -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,058 copying build/scripts-3.11/concat.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,061 copying build/scripts-3.11/makeAlignmentScripts.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,064 copying build/scripts-3.11/tally_variants_from_multiple_vcfs.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,066 copying build/scripts-3.11/somaticseq_parallel.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,069 copying build/scripts-3.11/run_somaticseq.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,072 copying build/scripts-3.11/remove_callers_from_somaticseq_tsv.py -> build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts 2026-04-25T09:49:41,074 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/run_workflows.py to 755 2026-04-25T09:49:41,075 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/single_sample_vcf2tsv.py to 755 2026-04-25T09:49:41,076 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/lociCounterWithLabels.py to 755 2026-04-25T09:49:41,077 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/linguistic_sequence_complexity.py to 755 2026-04-25T09:49:41,077 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/ada_model_builder_ntChange.R to 755 2026-04-25T09:49:41,078 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/paired_end_bam2fastq.py to 755 2026-04-25T09:49:41,079 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/ada_model_predictor.R to 755 2026-04-25T09:49:41,079 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/somatic_tsv2vcf.py to 755 2026-04-25T09:49:41,080 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/split_vcf.py to 755 2026-04-25T09:49:41,081 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/somatic_vcf2tsv.py to 755 2026-04-25T09:49:41,081 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/variant_annotation.py to 755 2026-04-25T09:49:41,082 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/somatic_xgboost.py to 755 2026-04-25T09:49:41,083 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/makeSomaticScripts.py to 755 2026-04-25T09:49:41,083 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/split_bed_into_equal_regions.py to 755 2026-04-25T09:49:41,084 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/vcfsorter.pl to 755 2026-04-25T09:49:41,085 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/concat.py to 755 2026-04-25T09:49:41,085 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/makeAlignmentScripts.py to 755 2026-04-25T09:49:41,086 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/tally_variants_from_multiple_vcfs.py to 755 2026-04-25T09:49:41,086 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/somaticseq_parallel.py to 755 2026-04-25T09:49:41,087 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/run_somaticseq.py to 755 2026-04-25T09:49:41,088 changing mode of build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.data/scripts/remove_callers_from_somaticseq_tsv.py to 755 2026-04-25T09:49:41,099 creating build/bdist.linux-armv7l/wheel/somaticseq-3.12.0.dist-info/WHEEL 2026-04-25T09:49:41,102 creating '/tmp/pip-wheel-e1lv609z/.tmp-vur2dicg/somaticseq-3.12.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-04-25T09:49:41,105 adding 'r_scripts/__init__.py' 2026-04-25T09:49:41,107 adding 'r_scripts/ada_cross_validation.R' 2026-04-25T09:49:41,108 adding 'r_scripts/ada_model_builder.R' 2026-04-25T09:49:41,110 adding 'r_scripts/ada_model_builder_ntChange.R' 2026-04-25T09:49:41,112 adding 'r_scripts/ada_model_predictor.R' 2026-04-25T09:49:41,114 adding 'somaticseq/__init__.py' 2026-04-25T09:49:41,116 adding 'somaticseq/_version.py' 2026-04-25T09:49:41,118 adding 'somaticseq/annotate_caller.py' 2026-04-25T09:49:41,121 adding 'somaticseq/bam_features.py' 2026-04-25T09:49:41,124 adding 'somaticseq/combine_callers.py' 2026-04-25T09:49:41,126 adding 'somaticseq/defaults.py' 2026-04-25T09:49:41,128 adding 'somaticseq/ntchange_type.py' 2026-04-25T09:49:41,131 adding 'somaticseq/run_somaticseq.py' 2026-04-25T09:49:41,134 adding 'somaticseq/sequencing_features.py' 2026-04-25T09:49:41,138 adding 'somaticseq/single_sample_vcf2tsv.py' 2026-04-25T09:49:41,141 adding 'somaticseq/somatic_tsv2vcf.py' 2026-04-25T09:49:41,146 adding 'somaticseq/somatic_vcf2tsv.py' 2026-04-25T09:49:41,149 adding 'somaticseq/somatic_xgboost.py' 2026-04-25T09:49:41,151 adding 'somaticseq/somaticseq_parallel.py' 2026-04-25T09:49:41,155 adding 'somaticseq/tsv2vcf.py' 2026-04-25T09:49:41,157 adding 'somaticseq/genomic_file_parsers/__init__.py' 2026-04-25T09:49:41,159 adding 'somaticseq/genomic_file_parsers/concat.py' 2026-04-25T09:49:41,162 adding 'somaticseq/genomic_file_parsers/genomic_file_handlers.py' 2026-04-25T09:49:41,164 adding 'somaticseq/genomic_file_parsers/pileup_reader.py' 2026-04-25T09:49:41,168 adding 'somaticseq/genomic_file_parsers/read_info_extractor.py' 2026-04-25T09:49:41,170 adding 'somaticseq/utilities/BAM_filter.py' 2026-04-25T09:49:41,172 adding 'somaticseq/utilities/__init__.py' 2026-04-25T09:49:41,174 adding 'somaticseq/utilities/attach_pileupVAF.py' 2026-04-25T09:49:41,176 adding 'somaticseq/utilities/bamQC.py' 2026-04-25T09:49:41,178 adding 'somaticseq/utilities/bedFileHandler.py' 2026-04-25T09:49:41,179 adding 'somaticseq/utilities/combo_callers_evaluator.py' 2026-04-25T09:49:41,181 adding 'somaticseq/utilities/filter_SomaticSeq_VCF.py' 2026-04-25T09:49:41,183 adding 'somaticseq/utilities/linguistic_sequence_complexity.py' 2026-04-25T09:49:41,186 adding 'somaticseq/utilities/lociCounterWithLabels.py' 2026-04-25T09:49:41,187 adding 'somaticseq/utilities/lociCounters.py' 2026-04-25T09:49:41,190 adding 'somaticseq/utilities/multi-nucleotide_phaser.py' 2026-04-25T09:49:41,192 adding 'somaticseq/utilities/paired_end_bam2fastq.py' 2026-04-25T09:49:41,194 adding 'somaticseq/utilities/plot_TPvsFP.py' 2026-04-25T09:49:41,196 adding 'somaticseq/utilities/reformat_VCF2SEQC2.py' 2026-04-25T09:49:41,198 adding 'somaticseq/utilities/remove_callers_from_somaticseq_tsv.py' 2026-04-25T09:49:41,200 adding 'somaticseq/utilities/split_bed_into_equal_regions.py' 2026-04-25T09:49:41,202 adding 'somaticseq/utilities/split_mergedBed.py' 2026-04-25T09:49:41,204 adding 'somaticseq/utilities/tally_MyVCF_vs_Truth.py' 2026-04-25T09:49:41,206 adding 'somaticseq/utilities/tally_variants_from_multiple_vcfs.py' 2026-04-25T09:49:41,208 adding 'somaticseq/utilities/trimSoftClippedReads.py' 2026-04-25T09:49:41,210 adding 'somaticseq/utilities/variant_annotation.py' 2026-04-25T09:49:41,212 adding 'somaticseq/utilities/dockered_pipelines/__init__.py' 2026-04-25T09:49:41,214 adding 'somaticseq/utilities/dockered_pipelines/container_option.py' 2026-04-25T09:49:41,216 adding 'somaticseq/utilities/dockered_pipelines/makeAlignmentScripts.py' 2026-04-25T09:49:41,219 adding 'somaticseq/utilities/dockered_pipelines/makeSomaticScripts.py' 2026-04-25T09:49:41,222 adding 'somaticseq/utilities/dockered_pipelines/run_workflows.py' 2026-04-25T09:49:41,225 adding 'somaticseq/utilities/dockered_pipelines/tumor_normal_run.py' 2026-04-25T09:49:41,227 adding 'somaticseq/utilities/dockered_pipelines/tumor_only_run.py' 2026-04-25T09:49:41,230 adding 'somaticseq/utilities/dockered_pipelines/alignments/__init__.py' 2026-04-25T09:49:41,232 adding 'somaticseq/utilities/dockered_pipelines/alignments/align.py' 2026-04-25T09:49:41,234 adding 'somaticseq/utilities/dockered_pipelines/alignments/markdup.py' 2026-04-25T09:49:41,236 adding 'somaticseq/utilities/dockered_pipelines/alignments/mergeBams.py' 2026-04-25T09:49:41,238 adding 'somaticseq/utilities/dockered_pipelines/alignments/mergeFastqs.py' 2026-04-25T09:49:41,240 adding 'somaticseq/utilities/dockered_pipelines/alignments/spreadFastq.py' 2026-04-25T09:49:41,242 adding 'somaticseq/utilities/dockered_pipelines/alignments/trim.py' 2026-04-25T09:49:41,244 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/JointSNVMix2.py' 2026-04-25T09:49:41,246 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/LoFreq.py' 2026-04-25T09:49:41,248 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/MuSE.py' 2026-04-25T09:49:41,250 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/MuTect2.py' 2026-04-25T09:49:41,252 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/Scalpel.py' 2026-04-25T09:49:41,254 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/SomaticSniper.py' 2026-04-25T09:49:41,256 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/Strelka2.py' 2026-04-25T09:49:41,259 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/VarDict.py' 2026-04-25T09:49:41,261 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/VarScan2.py' 2026-04-25T09:49:41,262 adding 'somaticseq/utilities/dockered_pipelines/somatic_mutations/__init__.py' 2026-04-25T09:49:41,265 adding 'somaticseq/vcf_modifier/__init__.py' 2026-04-25T09:49:41,266 adding 'somaticseq/vcf_modifier/bed_util.py' 2026-04-25T09:49:41,268 adding 'somaticseq/vcf_modifier/complex2indel.py' 2026-04-25T09:49:41,270 adding 'somaticseq/vcf_modifier/copy_TextFile.py' 2026-04-25T09:49:41,271 adding 'somaticseq/vcf_modifier/getUniqueVcfPositions.py' 2026-04-25T09:49:41,273 adding 'somaticseq/vcf_modifier/leftAlign.py' 2026-04-25T09:49:41,275 adding 'somaticseq/vcf_modifier/modify_JointSNVMix2.py' 2026-04-25T09:49:41,277 adding 'somaticseq/vcf_modifier/modify_MuTect.py' 2026-04-25T09:49:41,279 adding 'somaticseq/vcf_modifier/modify_MuTect2.py' 2026-04-25T09:49:41,281 adding 'somaticseq/vcf_modifier/modify_SomaticSniper.py' 2026-04-25T09:49:41,283 adding 'somaticseq/vcf_modifier/modify_Strelka.py' 2026-04-25T09:49:41,285 adding 'somaticseq/vcf_modifier/modify_VarDict.py' 2026-04-25T09:49:41,287 adding 'somaticseq/vcf_modifier/modify_VarScan2.py' 2026-04-25T09:49:41,289 adding 'somaticseq/vcf_modifier/modify_ssMuTect2.py' 2026-04-25T09:49:41,290 adding 'somaticseq/vcf_modifier/modify_ssStrelka.py' 2026-04-25T09:49:41,293 adding 'somaticseq/vcf_modifier/split_vcf.py' 2026-04-25T09:49:41,295 adding 'somaticseq-3.12.0.data/scripts/ada_model_builder_ntChange.R' 2026-04-25T09:49:41,297 adding 'somaticseq-3.12.0.data/scripts/ada_model_predictor.R' 2026-04-25T09:49:41,299 adding 'somaticseq-3.12.0.data/scripts/concat.py' 2026-04-25T09:49:41,300 adding 'somaticseq-3.12.0.data/scripts/linguistic_sequence_complexity.py' 2026-04-25T09:49:41,303 adding 'somaticseq-3.12.0.data/scripts/lociCounterWithLabels.py' 2026-04-25T09:49:41,305 adding 'somaticseq-3.12.0.data/scripts/makeAlignmentScripts.py' 2026-04-25T09:49:41,308 adding 'somaticseq-3.12.0.data/scripts/makeSomaticScripts.py' 2026-04-25T09:49:41,310 adding 'somaticseq-3.12.0.data/scripts/paired_end_bam2fastq.py' 2026-04-25T09:49:41,311 adding 'somaticseq-3.12.0.data/scripts/remove_callers_from_somaticseq_tsv.py' 2026-04-25T09:49:41,315 adding 'somaticseq-3.12.0.data/scripts/run_somaticseq.py' 2026-04-25T09:49:41,317 adding 'somaticseq-3.12.0.data/scripts/run_workflows.py' 2026-04-25T09:49:41,321 adding 'somaticseq-3.12.0.data/scripts/single_sample_vcf2tsv.py' 2026-04-25T09:49:41,325 adding 'somaticseq-3.12.0.data/scripts/somatic_tsv2vcf.py' 2026-04-25T09:49:41,329 adding 'somaticseq-3.12.0.data/scripts/somatic_vcf2tsv.py' 2026-04-25T09:49:41,332 adding 'somaticseq-3.12.0.data/scripts/somatic_xgboost.py' 2026-04-25T09:49:41,334 adding 'somaticseq-3.12.0.data/scripts/somaticseq_parallel.py' 2026-04-25T09:49:41,336 adding 'somaticseq-3.12.0.data/scripts/split_bed_into_equal_regions.py' 2026-04-25T09:49:41,338 adding 'somaticseq-3.12.0.data/scripts/split_vcf.py' 2026-04-25T09:49:41,341 adding 'somaticseq-3.12.0.data/scripts/tally_variants_from_multiple_vcfs.py' 2026-04-25T09:49:41,342 adding 'somaticseq-3.12.0.data/scripts/variant_annotation.py' 2026-04-25T09:49:41,344 adding 'somaticseq-3.12.0.data/scripts/vcfsorter.pl' 2026-04-25T09:49:41,347 adding 'somaticseq-3.12.0.dist-info/licenses/LICENSE.txt' 2026-04-25T09:49:41,350 adding 'somaticseq-3.12.0.dist-info/METADATA' 2026-04-25T09:49:41,351 adding 'somaticseq-3.12.0.dist-info/WHEEL' 2026-04-25T09:49:41,352 adding 'somaticseq-3.12.0.dist-info/entry_points.txt' 2026-04-25T09:49:41,354 adding 'somaticseq-3.12.0.dist-info/top_level.txt' 2026-04-25T09:49:41,357 adding 'somaticseq-3.12.0.dist-info/RECORD' 2026-04-25T09:49:41,361 removing build/bdist.linux-armv7l/wheel 2026-04-25T09:49:41,483 Building wheel for somaticseq (pyproject.toml): finished with status 'done' 2026-04-25T09:49:41,493 Created wheel for somaticseq: filename=somaticseq-3.12.0-py3-none-any.whl size=252575 sha256=245b14c0b05305e5ef975474342b51a6d16ba7212a949cccb6c13c5cfb901d91 2026-04-25T09:49:41,494 Stored in directory: /tmp/pip-ephem-wheel-cache-5pk5nqtj/wheels/7d/90/6e/47bc480f775adac5560fb5118adee126f7288e2c9728e1e352 2026-04-25T09:49:41,510 Successfully built somaticseq 2026-04-25T09:49:41,519 Removed build tracker: '/tmp/pip-build-tracker-a7_lqjk5'