2023-09-29T05:40:23,346 Created temporary directory: /tmp/pip-build-tracker-kts4npgx
2023-09-29T05:40:23,347 Initialized build tracking at /tmp/pip-build-tracker-kts4npgx
2023-09-29T05:40:23,347 Created build tracker: /tmp/pip-build-tracker-kts4npgx
2023-09-29T05:40:23,348 Entered build tracker: /tmp/pip-build-tracker-kts4npgx
2023-09-29T05:40:23,349 Created temporary directory: /tmp/pip-wheel-oo8fb4a8
2023-09-29T05:40:23,352 Created temporary directory: /tmp/pip-ephem-wheel-cache-0kmj3boy
2023-09-29T05:40:23,374 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-29T05:40:23,378 2 location(s) to search for versions of satmut-utils:
2023-09-29T05:40:23,378 * https://pypi.org/simple/satmut-utils/
2023-09-29T05:40:23,378 * https://www.piwheels.org/simple/satmut-utils/
2023-09-29T05:40:23,378 Fetching project page and analyzing links: https://pypi.org/simple/satmut-utils/
2023-09-29T05:40:23,379 Getting page https://pypi.org/simple/satmut-utils/
2023-09-29T05:40:23,381 Found index url https://pypi.org/simple/
2023-09-29T05:40:23,518 Fetched page https://pypi.org/simple/satmut-utils/ as application/vnd.pypi.simple.v1+json
2023-09-29T05:40:23,522   Skipping link: No binaries permitted for satmut-utils: https://files.pythonhosted.org/packages/9d/7d/aa6a904965242a0c56c1ecc510cf3f4840936f6087b6f0203a9a718743c1/satmut_utils-1.0.0-py3-none-any.whl (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,523   Found link https://files.pythonhosted.org/packages/a8/1b/4fc621a1dc7184b5ebb199d33f4792ce7755b61281fdf2313793423adfb9/satmut_utils-1.0.0.tar.gz (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7), version: 1.0.0
2023-09-29T05:40:23,524   Skipping link: No binaries permitted for satmut-utils: https://files.pythonhosted.org/packages/c1/c3/5c2d910cb9364b7f3a8ef7bea6aef6914c374cc1cfe7b7a217f4329fb167/satmut_utils-1.0.1-py3-none-any.whl (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,525   Found link https://files.pythonhosted.org/packages/3c/cb/1f7123f703b841687553195526b0253c632b3b13f17dbeefd1f24bfa7e9e/satmut_utils-1.0.1.tar.gz (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7), version: 1.0.1
2023-09-29T05:40:23,526   Skipping link: No binaries permitted for satmut-utils: https://files.pythonhosted.org/packages/66/c0/576dbee34d884808eac267f6726c217d0bb366d6aa0d0d24fea1f1103def/satmut_utils-1.0.2-py3-none-any.whl (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,527   Found link https://files.pythonhosted.org/packages/4b/1b/2697ef2eb5e7fc90aaeb8fbe64d2c24069dbd0871f1fb6b23e5c7f66273f/satmut_utils-1.0.2.tar.gz (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7), version: 1.0.2
2023-09-29T05:40:23,527   Skipping link: No binaries permitted for satmut-utils: https://files.pythonhosted.org/packages/85/2f/44449e247d8203168cd338bef490d92314d66b2dc0ea15ef3d03c6d7a9d1/satmut_utils-1.0.3-py3-none-any.whl (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,528   Found link https://files.pythonhosted.org/packages/33/f7/68da077554cf885a0fed028748c6e419bb97f64faa0a253ff4993fd08524/satmut_utils-1.0.3.tar.gz (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7), version: 1.0.3
2023-09-29T05:40:23,529   Skipping link: No binaries permitted for satmut-utils: https://files.pythonhosted.org/packages/6b/66/2954cd80d73c55edbb61264e43335a0366eed686d458e0dec85191729f59/satmut_utils-1.0.4-py3-none-any.whl (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,530   Found link https://files.pythonhosted.org/packages/af/18/b40883e3aafdf867c3bc41141a21857eb93526b46a6fd0d64321a66f1cf1/satmut_utils-1.0.4.tar.gz (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7), version: 1.0.4
2023-09-29T05:40:23,531   Skipping link: No binaries permitted for satmut-utils: https://files.pythonhosted.org/packages/35/c8/5c54c3de3fc74482be64cea35d3786a6bc1388d1f0cfce81a8480f1e8ec9/satmut_utils-1.1.0-py3-none-any.whl (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,532   Found link https://files.pythonhosted.org/packages/05/0b/7376e3610e664b48ee4c5d3a97924bae56338bb1a4c507e01b650e01b079/satmut_utils-1.1.0.tar.gz (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7), version: 1.1.0
2023-09-29T05:40:23,533   Skipping link: No binaries permitted for satmut-utils: https://files.pythonhosted.org/packages/6e/7c/ee78402b228696789f5664dd0af60d1a055332a6ded0fc4c764d99f58e74/satmut_utils-1.1.1-py3-none-any.whl (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,533   Found link https://files.pythonhosted.org/packages/e5/cf/de6d723ed9f741f52bfbf83e1e3fa516383d8e46a5190bfe10eda8afdfdb/satmut_utils-1.1.1.tar.gz (from https://pypi.org/simple/satmut-utils/) (requires-python:>=3.7), version: 1.1.1
2023-09-29T05:40:23,534 Fetching project page and analyzing links: https://www.piwheels.org/simple/satmut-utils/
2023-09-29T05:40:23,535 Getting page https://www.piwheels.org/simple/satmut-utils/
2023-09-29T05:40:23,536 Found index url https://www.piwheels.org/simple/
2023-09-29T05:40:23,701 Fetched page https://www.piwheels.org/simple/satmut-utils/ as text/html
2023-09-29T05:40:23,704   Skipping link: No binaries permitted for satmut-utils: https://www.piwheels.org/simple/satmut-utils/satmut_utils-1.1.0-py3-none-any.whl#sha256=5ddfee477c12473a423eb5f0bada11ea2267b234ff7c6f1bdcc8d2736ddb2498 (from https://www.piwheels.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,705   Skipping link: No binaries permitted for satmut-utils: https://www.piwheels.org/simple/satmut-utils/satmut_utils-1.0.4-py3-none-any.whl#sha256=323a13eb1dd75261586bd6c887dd223a40587742ca7aed6cdd40cbae05856a6f (from https://www.piwheels.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,705   Skipping link: No binaries permitted for satmut-utils: https://www.piwheels.org/simple/satmut-utils/satmut_utils-1.0.3-py3-none-any.whl#sha256=59c120e0a32ed07a847cb94d055d007d238e8c9aa7ec6bbe5c792542ffeab2ca (from https://www.piwheels.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,706   Skipping link: No binaries permitted for satmut-utils: https://www.piwheels.org/simple/satmut-utils/satmut_utils-1.0.2-py3-none-any.whl#sha256=b3eaebca5f040ebf0c60f26e3b9ccef1935ce70852728f24b3a1623f4c791c20 (from https://www.piwheels.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,707   Skipping link: No binaries permitted for satmut-utils: https://www.piwheels.org/simple/satmut-utils/satmut_utils-1.0.1-py3-none-any.whl#sha256=3f7c43b678b5e344409e2cb0718742684066d907768826a7d19b85b4c43adae6 (from https://www.piwheels.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,707   Skipping link: No binaries permitted for satmut-utils: https://www.piwheels.org/simple/satmut-utils/satmut_utils-1.0.0-py3-none-any.whl#sha256=851816d46080d9e7a7ac2f235ea191e2a32f936dbd625d4caff953f6b4c1495c (from https://www.piwheels.org/simple/satmut-utils/) (requires-python:>=3.7)
2023-09-29T05:40:23,708 Skipping link: not a file: https://www.piwheels.org/simple/satmut-utils/
2023-09-29T05:40:23,709 Skipping link: not a file: https://pypi.org/simple/satmut-utils/
2023-09-29T05:40:23,728 Given no hashes to check 1 links for project 'satmut-utils': discarding no candidates
2023-09-29T05:40:23,746 Collecting satmut-utils==1.1.1
2023-09-29T05:40:23,749   Created temporary directory: /tmp/pip-unpack-7s1g6ulz
2023-09-29T05:40:24,613   Downloading satmut_utils-1.1.1.tar.gz (12.0 MB)
2023-09-29T05:40:27,228   Added satmut-utils==1.1.1 from https://files.pythonhosted.org/packages/e5/cf/de6d723ed9f741f52bfbf83e1e3fa516383d8e46a5190bfe10eda8afdfdb/satmut_utils-1.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-kts4npgx'
2023-09-29T05:40:27,234   Created temporary directory: /tmp/pip-build-env-wfilc3ql
2023-09-29T05:40:27,249   Installing build dependencies: started
2023-09-29T05:40:27,252   Running command pip subprocess to install build dependencies
2023-09-29T05:40:28,426   Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11)
2023-09-29T05:40:28,966   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-09-29T05:40:30,509   Collecting setuptools>=59
2023-09-29T05:40:30,570     Using cached https://www.piwheels.org/simple/setuptools/setuptools-68.2.2-py3-none-any.whl (807 kB)
2023-09-29T05:40:30,814   Collecting wheel
2023-09-29T05:40:30,829     Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB)
2023-09-29T05:40:33,423   Installing collected packages: wheel, setuptools
2023-09-29T05:40:33,645     Creating /tmp/pip-build-env-wfilc3ql/overlay/local/bin
2023-09-29T05:40:33,647     changing mode of /tmp/pip-build-env-wfilc3ql/overlay/local/bin/wheel to 755
2023-09-29T05:40:36,546   Successfully installed setuptools-68.2.2 wheel-0.41.2
2023-09-29T05:40:37,078   Installing build dependencies: finished with status 'done'
2023-09-29T05:40:37,082   Getting requirements to build wheel: started
2023-09-29T05:40:37,083   Running command Getting requirements to build wheel
2023-09-29T05:40:37,743   running egg_info
2023-09-29T05:40:37,749   writing src/satmut_utils.egg-info/PKG-INFO
2023-09-29T05:40:37,753   writing dependency_links to src/satmut_utils.egg-info/dependency_links.txt
2023-09-29T05:40:37,755   writing entry points to src/satmut_utils.egg-info/entry_points.txt
2023-09-29T05:40:37,757   writing top-level names to src/satmut_utils.egg-info/top_level.txt
2023-09-29T05:40:37,781   reading manifest file 'src/satmut_utils.egg-info/SOURCES.txt'
2023-09-29T05:40:37,785   reading manifest template 'MANIFEST.in'
2023-09-29T05:40:37,788   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2023-09-29T05:40:37,789   adding license file 'LICENSE.txt'
2023-09-29T05:40:37,793   writing manifest file 'src/satmut_utils.egg-info/SOURCES.txt'
2023-09-29T05:40:37,869   Getting requirements to build wheel: finished with status 'done'
2023-09-29T05:40:37,882   Created temporary directory: /tmp/pip-modern-metadata-ruquj4dv
2023-09-29T05:40:37,885   Preparing metadata (pyproject.toml): started
2023-09-29T05:40:37,886   Running command Preparing metadata (pyproject.toml)
2023-09-29T05:40:38,466   running dist_info
2023-09-29T05:40:38,487   creating /tmp/pip-modern-metadata-ruquj4dv/satmut_utils.egg-info
2023-09-29T05:40:38,491   writing /tmp/pip-modern-metadata-ruquj4dv/satmut_utils.egg-info/PKG-INFO
2023-09-29T05:40:38,495   writing dependency_links to /tmp/pip-modern-metadata-ruquj4dv/satmut_utils.egg-info/dependency_links.txt
2023-09-29T05:40:38,497   writing entry points to /tmp/pip-modern-metadata-ruquj4dv/satmut_utils.egg-info/entry_points.txt
2023-09-29T05:40:38,499   writing top-level names to /tmp/pip-modern-metadata-ruquj4dv/satmut_utils.egg-info/top_level.txt
2023-09-29T05:40:38,501   writing manifest file '/tmp/pip-modern-metadata-ruquj4dv/satmut_utils.egg-info/SOURCES.txt'
2023-09-29T05:40:38,520   reading manifest file '/tmp/pip-modern-metadata-ruquj4dv/satmut_utils.egg-info/SOURCES.txt'
2023-09-29T05:40:38,522   reading manifest template 'MANIFEST.in'
2023-09-29T05:40:38,525   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2023-09-29T05:40:38,526   adding license file 'LICENSE.txt'
2023-09-29T05:40:38,529   writing manifest file '/tmp/pip-modern-metadata-ruquj4dv/satmut_utils.egg-info/SOURCES.txt'
2023-09-29T05:40:38,530   creating '/tmp/pip-modern-metadata-ruquj4dv/satmut_utils-1.1.1.dist-info'
2023-09-29T05:40:38,720   Preparing metadata (pyproject.toml): finished with status 'done'
2023-09-29T05:40:38,726   Source in /tmp/pip-wheel-oo8fb4a8/satmut-utils_751ebe96f06649918661012249983415 has version 1.1.1, which satisfies requirement satmut-utils==1.1.1 from https://files.pythonhosted.org/packages/e5/cf/de6d723ed9f741f52bfbf83e1e3fa516383d8e46a5190bfe10eda8afdfdb/satmut_utils-1.1.1.tar.gz
2023-09-29T05:40:38,727   Removed satmut-utils==1.1.1 from https://files.pythonhosted.org/packages/e5/cf/de6d723ed9f741f52bfbf83e1e3fa516383d8e46a5190bfe10eda8afdfdb/satmut_utils-1.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-kts4npgx'
2023-09-29T05:40:38,733 Created temporary directory: /tmp/pip-unpack-tfcn1nmo
2023-09-29T05:40:38,736 Created temporary directory: /tmp/pip-unpack-rnymcfmy
2023-09-29T05:40:38,740 Building wheels for collected packages: satmut-utils
2023-09-29T05:40:38,750   Created temporary directory: /tmp/pip-wheel-kzfjtukz
2023-09-29T05:40:38,751   Destination directory: /tmp/pip-wheel-kzfjtukz
2023-09-29T05:40:38,754   Building wheel for satmut-utils (pyproject.toml): started
2023-09-29T05:40:38,755   Running command Building wheel for satmut-utils (pyproject.toml)
2023-09-29T05:40:39,360   running bdist_wheel
2023-09-29T05:40:39,406   running build
2023-09-29T05:40:39,407   running build_py
2023-09-29T05:40:39,415   creating build
2023-09-29T05:40:39,416   creating build/lib
2023-09-29T05:40:39,417   creating build/lib/tests
2023-09-29T05:40:39,419   copying src/tests/__init__.py -> build/lib/tests
2023-09-29T05:40:39,423   creating build/lib/analysis
2023-09-29T05:40:39,425   copying src/analysis/variant_caller.py -> build/lib/analysis
2023-09-29T05:40:39,429   copying src/analysis/aligners.py -> build/lib/analysis
2023-09-29T05:40:39,431   copying src/analysis/references.py -> build/lib/analysis
2023-09-29T05:40:39,433   copying src/analysis/read_preprocessor.py -> build/lib/analysis
2023-09-29T05:40:39,437   copying src/analysis/read_editor.py -> build/lib/analysis
2023-09-29T05:40:39,441   copying src/analysis/coordinate_mapper.py -> build/lib/analysis
2023-09-29T05:40:39,444   copying src/analysis/__init__.py -> build/lib/analysis
2023-09-29T05:40:39,446   copying src/analysis/seq_utils.py -> build/lib/analysis
2023-09-29T05:40:39,450   creating build/lib/core_utils
2023-09-29T05:40:39,452   copying src/core_utils/feature_file_utils.py -> build/lib/core_utils
2023-09-29T05:40:39,455   copying src/core_utils/file_utils.py -> build/lib/core_utils
2023-09-29T05:40:39,457   copying src/core_utils/vcf_utils.py -> build/lib/core_utils
2023-09-29T05:40:39,460   copying src/core_utils/__init__.py -> build/lib/core_utils
2023-09-29T05:40:39,462   copying src/core_utils/string_utils.py -> build/lib/core_utils
2023-09-29T05:40:39,465   creating build/lib/satmut_utils
2023-09-29T05:40:39,465   copying src/satmut_utils/satmut_utils.py -> build/lib/satmut_utils
2023-09-29T05:40:39,468   copying src/satmut_utils/__init__.py -> build/lib/satmut_utils
2023-09-29T05:40:39,470   copying src/satmut_utils/definitions.py -> build/lib/satmut_utils
2023-09-29T05:40:39,472   creating build/lib/scripts
2023-09-29T05:40:39,473   copying src/scripts/run_fastq_preprocessor.py -> build/lib/scripts
2023-09-29T05:40:39,475   copying src/scripts/run_bowtie2_aligner.py -> build/lib/scripts
2023-09-29T05:40:39,477   copying src/scripts/__init__.py -> build/lib/scripts
2023-09-29T05:40:39,479   creating build/lib/tests/analysis
2023-09-29T05:40:39,480   copying src/tests/analysis/test_read_editor.py -> build/lib/tests/analysis
2023-09-29T05:40:39,484   copying src/tests/analysis/test_aligners.py -> build/lib/tests/analysis
2023-09-29T05:40:39,486   copying src/tests/analysis/test_seq_utils.py -> build/lib/tests/analysis
2023-09-29T05:40:39,490   copying src/tests/analysis/test_coordinate_mapper.py -> build/lib/tests/analysis
2023-09-29T05:40:39,494   copying src/tests/analysis/__init__.py -> build/lib/tests/analysis
2023-09-29T05:40:39,495   copying src/tests/analysis/test_variant_caller.py -> build/lib/tests/analysis
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2023-09-29T05:40:39,508   copying src/tests/analysis/test_references.py -> build/lib/tests/analysis
2023-09-29T05:40:39,512   creating build/lib/tests/core_utils
2023-09-29T05:40:39,513   copying src/tests/core_utils/test_file_utils.py -> build/lib/tests/core_utils
2023-09-29T05:40:39,516   copying src/tests/core_utils/test_string_utils.py -> build/lib/tests/core_utils
2023-09-29T05:40:39,519   copying src/tests/core_utils/__init__.py -> build/lib/tests/core_utils
2023-09-29T05:40:39,520   copying src/tests/core_utils/test_feature_file_utils.py -> build/lib/tests/core_utils
2023-09-29T05:40:39,524   creating build/lib/tests/test_data
2023-09-29T05:40:39,525   copying src/tests/test_data/__init__.py -> build/lib/tests/test_data
2023-09-29T05:40:39,527   running egg_info
2023-09-29T05:40:39,532   writing src/satmut_utils.egg-info/PKG-INFO
2023-09-29T05:40:39,535   writing dependency_links to src/satmut_utils.egg-info/dependency_links.txt
2023-09-29T05:40:39,537   writing entry points to src/satmut_utils.egg-info/entry_points.txt
2023-09-29T05:40:39,538   writing top-level names to src/satmut_utils.egg-info/top_level.txt
2023-09-29T05:40:39,550   reading manifest file 'src/satmut_utils.egg-info/SOURCES.txt'
2023-09-29T05:40:39,553   reading manifest template 'MANIFEST.in'
2023-09-29T05:40:39,556   warning: no previously-included files matching '*.py[cod]' found anywhere in distribution
2023-09-29T05:40:39,557   adding license file 'LICENSE.txt'
2023-09-29T05:40:39,561   writing manifest file 'src/satmut_utils.egg-info/SOURCES.txt'
2023-09-29T05:40:39,565   copying src/tests/test_data/CBS.fa -> build/lib/tests/test_data
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2023-09-29T05:40:39,649   copying src/tests/test_data/CBS_pEZY3.fa.fai -> build/lib/tests/test_data
2023-09-29T05:40:39,652   copying src/tests/test_data/CBS_pEZY3.fa.rev.1.bt2 -> build/lib/tests/test_data
2023-09-29T05:40:39,730   copying src/tests/test_data/CBS_pEZY3.fa.rev.2.bt2 -> build/lib/tests/test_data
2023-09-29T05:40:39,733   copying src/tests/test_data/CBS_pEZY3.gff -> build/lib/tests/test_data
2023-09-29T05:40:39,737   copying src/tests/test_data/CBS_pEZY3_primers.bed -> build/lib/tests/test_data
2023-09-29T05:40:39,740   copying src/tests/test_data/CBS_pEZY3_targets.bed -> build/lib/tests/test_data
2023-09-29T05:40:39,743   copying src/tests/test_data/CBS_sim.R1.fq.gz -> build/lib/tests/test_data
2023-09-29T05:40:39,746   copying src/tests/test_data/CBS_sim.R2.fq.gz -> build/lib/tests/test_data
2023-09-29T05:40:39,749   copying src/tests/test_data/CBS_sim.bam -> build/lib/tests/test_data
2023-09-29T05:40:39,751   copying src/tests/test_data/CBS_sim.bam.bai -> build/lib/tests/test_data
2023-09-29T05:40:39,753   copying src/tests/test_data/CBS_sim.vcf -> build/lib/tests/test_data
2023-09-29T05:40:39,756   copying src/tests/test_data/CBS_sim_primers.bed -> build/lib/tests/test_data
2023-09-29T05:40:39,758   copying src/tests/test_data/GRCh38.chr21.fa.gz -> build/lib/tests/test_data
2023-09-29T05:40:39,938   copying src/tests/test_data/PKNOX1.fa -> build/lib/tests/test_data
2023-09-29T05:40:39,941   copying src/tests/test_data/appris_human_24_01_2019_selected.fa -> build/lib/tests/test_data
2023-09-29T05:40:39,944   copying src/tests/test_data/appris_human_24_01_2019_selected.fa.fai -> build/lib/tests/test_data
2023-09-29T05:40:39,947   copying src/tests/test_data/appris_human_v1_actual_regions_contigs.txt -> build/lib/tests/test_data
2023-09-29T05:40:39,949   copying src/tests/test_data/appris_human_v1_actual_regions_gene_ids.txt -> build/lib/tests/test_data
2023-09-29T05:40:39,951   copying src/tests/test_data/appris_human_v1_actual_regions_trx_ids.txt -> build/lib/tests/test_data
2023-09-29T05:40:39,953   copying src/tests/test_data/gencode.v29.annotation.gtf -> build/lib/tests/test_data
2023-09-29T05:40:39,956   copying src/tests/test_data/test_preprocess.bam -> build/lib/tests/test_data
2023-09-29T05:40:39,959   copying src/tests/test_data/test_preprocess.bam.bai -> build/lib/tests/test_data
2023-09-29T05:40:39,961   copying src/tests/test_data/test_preprocess.sam -> build/lib/tests/test_data
2023-09-29T05:40:39,964   copying src/tests/test_data/test_preprocess.sort.bam -> build/lib/tests/test_data
2023-09-29T05:40:39,966   copying src/tests/test_data/test_preprocess.sort.bam.bai -> build/lib/tests/test_data
2023-09-29T05:40:39,982   installing to build/bdist.linux-armv7l/wheel
2023-09-29T05:40:39,982   running install
2023-09-29T05:40:40,007   running install_lib
2023-09-29T05:40:40,014   creating build/bdist.linux-armv7l
2023-09-29T05:40:40,015   creating build/bdist.linux-armv7l/wheel
2023-09-29T05:40:40,017   creating build/bdist.linux-armv7l/wheel/tests
2023-09-29T05:40:40,018   creating build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,020   copying build/lib/tests/analysis/test_read_editor.py -> build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,023   copying build/lib/tests/analysis/test_aligners.py -> build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,025   copying build/lib/tests/analysis/test_seq_utils.py -> build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,028   copying build/lib/tests/analysis/test_coordinate_mapper.py -> build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,031   copying build/lib/tests/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,033   copying build/lib/tests/analysis/test_variant_caller.py -> build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,038   copying build/lib/tests/analysis/test_read_preprocessor.py -> build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,043   copying build/lib/tests/analysis/test_references.py -> build/bdist.linux-armv7l/wheel/tests/analysis
2023-09-29T05:40:40,047   creating build/bdist.linux-armv7l/wheel/tests/core_utils
2023-09-29T05:40:40,048   copying build/lib/tests/core_utils/test_file_utils.py -> build/bdist.linux-armv7l/wheel/tests/core_utils
2023-09-29T05:40:40,051   copying build/lib/tests/core_utils/test_string_utils.py -> build/bdist.linux-armv7l/wheel/tests/core_utils
2023-09-29T05:40:40,057   copying build/lib/tests/core_utils/__init__.py -> build/bdist.linux-armv7l/wheel/tests/core_utils
2023-09-29T05:40:40,059   copying build/lib/tests/core_utils/test_feature_file_utils.py -> build/bdist.linux-armv7l/wheel/tests/core_utils
2023-09-29T05:40:40,065   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests
2023-09-29T05:40:40,072   creating build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,073   copying build/lib/tests/test_data/CBS_sim.R2.fq.gz -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,079   copying build/lib/tests/test_data/test_preprocess.sort.bam -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,087   copying build/lib/tests/test_data/CBS_pEZY3.fa.fai -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,097   copying build/lib/tests/test_data/CBS_pEZY3.fa.rev.1.bt2 -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,170   copying build/lib/tests/test_data/CBS_pEZY3.fa.2.bt2 -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,172   copying build/lib/tests/test_data/test_preprocess.sort.bam.bai -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,174   copying build/lib/tests/test_data/CBS_sim.bam -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,177   copying build/lib/tests/test_data/CBS_pEZY3.fa.1.bt2 -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,239   copying build/lib/tests/test_data/CBS.fa -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,242   copying build/lib/tests/test_data/GRCh38.chr21.fa.gz -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,446   copying build/lib/tests/test_data/test_preprocess.bam.bai -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,448   copying build/lib/tests/test_data/CBS_sim.bam.bai -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,451   copying build/lib/tests/test_data/gencode.v29.annotation.gtf -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,454   copying build/lib/tests/test_data/appris_human_v1_actual_regions_contigs.txt -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,457   copying build/lib/tests/test_data/CBS_pEZY3.fa -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,460   copying build/lib/tests/test_data/appris_human_24_01_2019_selected.fa -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,463   copying build/lib/tests/test_data/PKNOX1.fa -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,465   copying build/lib/tests/test_data/appris_human_v1_actual_regions_trx_ids.txt -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,468   copying build/lib/tests/test_data/appris_human_24_01_2019_selected.fa.fai -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,470   copying build/lib/tests/test_data/CBS_pEZY3_primers.bed -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,473   copying build/lib/tests/test_data/CBS_sim.vcf -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,475   copying build/lib/tests/test_data/__init__.py -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,478   copying build/lib/tests/test_data/CBS_pEZY3.fa.rev.2.bt2 -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,480   copying build/lib/tests/test_data/CBS_sim_primers.bed -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,483   copying build/lib/tests/test_data/CBS_pEZY3_targets.bed -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,485   copying build/lib/tests/test_data/appris_human_v1_actual_regions_gene_ids.txt -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,487   copying build/lib/tests/test_data/CBS_pEZY3.fa.4.bt2 -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,490   copying build/lib/tests/test_data/CBS_pEZY3.gff -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,493   copying build/lib/tests/test_data/CBS_sim.R1.fq.gz -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,495   copying build/lib/tests/test_data/test_preprocess.bam -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,497   copying build/lib/tests/test_data/test_preprocess.sam -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,500   copying build/lib/tests/test_data/CBS_pEZY3.fa.3.bt2 -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,502   copying build/lib/tests/test_data/CBS.gff -> build/bdist.linux-armv7l/wheel/tests/test_data
2023-09-29T05:40:40,505   creating build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,507   copying build/lib/analysis/variant_caller.py -> build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,510   copying build/lib/analysis/aligners.py -> build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,514   copying build/lib/analysis/references.py -> build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,517   copying build/lib/analysis/read_preprocessor.py -> build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,522   copying build/lib/analysis/read_editor.py -> build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,526   copying build/lib/analysis/coordinate_mapper.py -> build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,532   copying build/lib/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,535   copying build/lib/analysis/seq_utils.py -> build/bdist.linux-armv7l/wheel/analysis
2023-09-29T05:40:40,540   creating build/bdist.linux-armv7l/wheel/core_utils
2023-09-29T05:40:40,541   copying build/lib/core_utils/feature_file_utils.py -> build/bdist.linux-armv7l/wheel/core_utils
2023-09-29T05:40:40,545   copying build/lib/core_utils/file_utils.py -> build/bdist.linux-armv7l/wheel/core_utils
2023-09-29T05:40:40,547   copying build/lib/core_utils/vcf_utils.py -> build/bdist.linux-armv7l/wheel/core_utils
2023-09-29T05:40:40,550   copying build/lib/core_utils/__init__.py -> build/bdist.linux-armv7l/wheel/core_utils
2023-09-29T05:40:40,552   copying build/lib/core_utils/string_utils.py -> build/bdist.linux-armv7l/wheel/core_utils
2023-09-29T05:40:40,555   creating build/bdist.linux-armv7l/wheel/satmut_utils
2023-09-29T05:40:40,556   copying build/lib/satmut_utils/satmut_utils.py -> build/bdist.linux-armv7l/wheel/satmut_utils
2023-09-29T05:40:40,559   copying build/lib/satmut_utils/__init__.py -> build/bdist.linux-armv7l/wheel/satmut_utils
2023-09-29T05:40:40,561   copying build/lib/satmut_utils/definitions.py -> build/bdist.linux-armv7l/wheel/satmut_utils
2023-09-29T05:40:40,563   creating build/bdist.linux-armv7l/wheel/scripts
2023-09-29T05:40:40,564   copying build/lib/scripts/run_fastq_preprocessor.py -> build/bdist.linux-armv7l/wheel/scripts
2023-09-29T05:40:40,567   copying build/lib/scripts/run_bowtie2_aligner.py -> build/bdist.linux-armv7l/wheel/scripts
2023-09-29T05:40:40,569   copying build/lib/scripts/__init__.py -> build/bdist.linux-armv7l/wheel/scripts
2023-09-29T05:40:40,571   running install_egg_info
2023-09-29T05:40:40,582   Copying src/satmut_utils.egg-info to build/bdist.linux-armv7l/wheel/satmut_utils-1.1.1-py3.11.egg-info
2023-09-29T05:40:40,593   running install_scripts
2023-09-29T05:40:40,608   creating build/bdist.linux-armv7l/wheel/satmut_utils-1.1.1.dist-info/WHEEL
2023-09-29T05:40:40,610   creating '/tmp/pip-wheel-kzfjtukz/.tmp-_42l3oh0/satmut_utils-1.1.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-09-29T05:40:40,612   adding 'analysis/__init__.py'
2023-09-29T05:40:40,614   adding 'analysis/aligners.py'
2023-09-29T05:40:40,622   adding 'analysis/coordinate_mapper.py'
2023-09-29T05:40:40,627   adding 'analysis/read_editor.py'
2023-09-29T05:40:40,636   adding 'analysis/read_preprocessor.py'
2023-09-29T05:40:40,638   adding 'analysis/references.py'
2023-09-29T05:40:40,641   adding 'analysis/seq_utils.py'
2023-09-29T05:40:40,649   adding 'analysis/variant_caller.py'
2023-09-29T05:40:40,651   adding 'core_utils/__init__.py'
2023-09-29T05:40:40,653   adding 'core_utils/feature_file_utils.py'
2023-09-29T05:40:40,655   adding 'core_utils/file_utils.py'
2023-09-29T05:40:40,656   adding 'core_utils/string_utils.py'
2023-09-29T05:40:40,660   adding 'core_utils/vcf_utils.py'
2023-09-29T05:40:40,662   adding 'satmut_utils/__init__.py'
2023-09-29T05:40:40,663   adding 'satmut_utils/definitions.py'
2023-09-29T05:40:40,667   adding 'satmut_utils/satmut_utils.py'
2023-09-29T05:40:40,670   adding 'scripts/__init__.py'
2023-09-29T05:40:40,672   adding 'scripts/run_bowtie2_aligner.py'
2023-09-29T05:40:40,673   adding 'scripts/run_fastq_preprocessor.py'
2023-09-29T05:40:40,675   adding 'tests/__init__.py'
2023-09-29T05:40:40,677   adding 'tests/analysis/__init__.py'
2023-09-29T05:40:40,678   adding 'tests/analysis/test_aligners.py'
2023-09-29T05:40:40,681   adding 'tests/analysis/test_coordinate_mapper.py'
2023-09-29T05:40:40,685   adding 'tests/analysis/test_read_editor.py'
2023-09-29T05:40:40,691   adding 'tests/analysis/test_read_preprocessor.py'
2023-09-29T05:40:40,694   adding 'tests/analysis/test_references.py'
2023-09-29T05:40:40,697   adding 'tests/analysis/test_seq_utils.py'
2023-09-29T05:40:40,702   adding 'tests/analysis/test_variant_caller.py'
2023-09-29T05:40:40,704   adding 'tests/core_utils/__init__.py'
2023-09-29T05:40:40,706   adding 'tests/core_utils/test_feature_file_utils.py'
2023-09-29T05:40:40,708   adding 'tests/core_utils/test_file_utils.py'
2023-09-29T05:40:40,710   adding 'tests/core_utils/test_string_utils.py'
2023-09-29T05:40:40,713   adding 'tests/test_data/CBS.fa'
2023-09-29T05:40:40,714   adding 'tests/test_data/CBS.gff'
2023-09-29T05:40:40,718   adding 'tests/test_data/CBS_pEZY3.fa'
2023-09-29T05:40:40,811   adding 'tests/test_data/CBS_pEZY3.fa.1.bt2'
2023-09-29T05:40:40,846   adding 'tests/test_data/CBS_pEZY3.fa.2.bt2'
2023-09-29T05:40:40,848   adding 'tests/test_data/CBS_pEZY3.fa.3.bt2'
2023-09-29T05:40:40,850   adding 'tests/test_data/CBS_pEZY3.fa.4.bt2'
2023-09-29T05:40:40,851   adding 'tests/test_data/CBS_pEZY3.fa.fai'
2023-09-29T05:40:40,944   adding 'tests/test_data/CBS_pEZY3.fa.rev.1.bt2'
2023-09-29T05:40:40,980   adding 'tests/test_data/CBS_pEZY3.fa.rev.2.bt2'
2023-09-29T05:40:40,981   adding 'tests/test_data/CBS_pEZY3.gff'
2023-09-29T05:40:40,983   adding 'tests/test_data/CBS_pEZY3_primers.bed'
2023-09-29T05:40:40,984   adding 'tests/test_data/CBS_pEZY3_targets.bed'
2023-09-29T05:40:40,986   adding 'tests/test_data/CBS_sim.R1.fq.gz'
2023-09-29T05:40:40,988   adding 'tests/test_data/CBS_sim.R2.fq.gz'
2023-09-29T05:40:40,990   adding 'tests/test_data/CBS_sim.bam'
2023-09-29T05:40:40,991   adding 'tests/test_data/CBS_sim.bam.bai'
2023-09-29T05:40:40,992   adding 'tests/test_data/CBS_sim.vcf'
2023-09-29T05:40:40,994   adding 'tests/test_data/CBS_sim_primers.bed'
2023-09-29T05:40:42,292   adding 'tests/test_data/GRCh38.chr21.fa.gz'
2023-09-29T05:40:42,388   adding 'tests/test_data/PKNOX1.fa'
2023-09-29T05:40:42,389   adding 'tests/test_data/__init__.py'
2023-09-29T05:40:42,393   adding 'tests/test_data/appris_human_24_01_2019_selected.fa'
2023-09-29T05:40:42,394   adding 'tests/test_data/appris_human_24_01_2019_selected.fa.fai'
2023-09-29T05:40:42,395   adding 'tests/test_data/appris_human_v1_actual_regions_contigs.txt'
2023-09-29T05:40:42,396   adding 'tests/test_data/appris_human_v1_actual_regions_gene_ids.txt'
2023-09-29T05:40:42,397   adding 'tests/test_data/appris_human_v1_actual_regions_trx_ids.txt'
2023-09-29T05:40:42,399   adding 'tests/test_data/gencode.v29.annotation.gtf'
2023-09-29T05:40:42,401   adding 'tests/test_data/test_preprocess.bam'
2023-09-29T05:40:42,402   adding 'tests/test_data/test_preprocess.bam.bai'
2023-09-29T05:40:42,404   adding 'tests/test_data/test_preprocess.sam'
2023-09-29T05:40:42,406   adding 'tests/test_data/test_preprocess.sort.bam'
2023-09-29T05:40:42,407   adding 'tests/test_data/test_preprocess.sort.bam.bai'
2023-09-29T05:40:42,413   adding 'satmut_utils-1.1.1.dist-info/LICENSE.txt'
2023-09-29T05:40:42,415   adding 'satmut_utils-1.1.1.dist-info/METADATA'
2023-09-29T05:40:42,416   adding 'satmut_utils-1.1.1.dist-info/WHEEL'
2023-09-29T05:40:42,417   adding 'satmut_utils-1.1.1.dist-info/entry_points.txt'
2023-09-29T05:40:42,418   adding 'satmut_utils-1.1.1.dist-info/top_level.txt'
2023-09-29T05:40:42,420   adding 'satmut_utils-1.1.1.dist-info/RECORD'
2023-09-29T05:40:42,545   removing build/bdist.linux-armv7l/wheel
2023-09-29T05:40:42,670   Building wheel for satmut-utils (pyproject.toml): finished with status 'done'
2023-09-29T05:40:42,959   Created wheel for satmut-utils: filename=satmut_utils-1.1.1-py3-none-any.whl size=12001910 sha256=ab9ac8084249c0619e3f56e5c88b1ea01cfaa4e07cd498a5f1567391540a231b
2023-09-29T05:40:42,960   Stored in directory: /tmp/pip-ephem-wheel-cache-0kmj3boy/wheels/0d/b9/12/f936e709f2f1426cf2f9d7448849a52599d48d6643c87d49ab
2023-09-29T05:40:42,979 Successfully built satmut-utils
2023-09-29T05:40:43,380 Removed build tracker: '/tmp/pip-build-tracker-kts4npgx'