2023-05-14T01:00:51,601 Created temporary directory: /tmp/pip-build-tracker-3j1bmsro
2023-05-14T01:00:51,604 Initialized build tracking at /tmp/pip-build-tracker-3j1bmsro
2023-05-14T01:00:51,604 Created build tracker: /tmp/pip-build-tracker-3j1bmsro
2023-05-14T01:00:51,605 Entered build tracker: /tmp/pip-build-tracker-3j1bmsro
2023-05-14T01:00:51,606 Created temporary directory: /tmp/pip-wheel-vm7355dx
2023-05-14T01:00:51,614 Created temporary directory: /tmp/pip-ephem-wheel-cache-g53fzt9j
2023-05-14T01:00:51,670 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-05-14T01:00:51,678 2 location(s) to search for versions of phasefilter:
2023-05-14T01:00:51,678 * https://pypi.org/simple/phasefilter/
2023-05-14T01:00:51,678 * https://www.piwheels.org/simple/phasefilter/
2023-05-14T01:00:51,679 Fetching project page and analyzing links: https://pypi.org/simple/phasefilter/
2023-05-14T01:00:51,680 Getting page https://pypi.org/simple/phasefilter/
2023-05-14T01:00:51,684 Found index url https://pypi.org/simple/
2023-05-14T01:00:52,056 Fetched page https://pypi.org/simple/phasefilter/ as application/vnd.pypi.simple.v1+json
2023-05-14T01:00:52,065   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/70/5b/a12acb782bfb5510c9281ffac13440c2089c4de283d92773f87408ebe857/PHASEfilter-0.0.1a1-py3-none-any.whl (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,067   Found link https://files.pythonhosted.org/packages/59/cb/fd5b96878a1f815759667d3556a4c72151d4f2bed79879dd817a0602c62f/PHASEfilter-0.0.1a1.tar.gz (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.0.1a1
2023-05-14T01:00:52,067   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/50/c6/3d3933d1c8f89a5ee4ec5e9a954a42ddd2f616015b4e9de18132bccfc321/PHASEfilter-0.3.2-py3-none-any.whl (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,069   Found link https://files.pythonhosted.org/packages/41/62/26390ce2c8f9d3fe2739a79da1f0705fd646df1b32200df2697bba0852f2/PHASEfilter-0.3.2.tar.gz (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.2
2023-05-14T01:00:52,070   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/4b/df/18736673d0a18ec858646025792d9808b1a6fedde5cbdf9609187e4f7d6f/PHASEfilter-0.3.3-py3-none-any.whl (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,071   Found link https://files.pythonhosted.org/packages/06/1b/6b3db72941b86ea609af642664e09e6fb15afbaa742c367815e5b30e9f43/PHASEfilter-0.3.3.tar.gz (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.3
2023-05-14T01:00:52,071   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/2f/ec/44fde574b28162fe0a07742b785fe0a1bb8218719858f62e0117ee7f6e78/PHASEfilter-0.3.4-py3-none-any.whl (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,073   Found link https://files.pythonhosted.org/packages/d5/4b/6b7afc0d15ec9e7763d7cb1c1d1969f717c7a181d6db6e6fa4e3c16786bf/PHASEfilter-0.3.4.tar.gz (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.4
2023-05-14T01:00:52,073   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/7c/69/702e45c82eb74d8b26493ad9f88fd152c36aab9580f88da7006a6024bd18/PHASEfilter-0.3.5-py3-none-any.whl (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,075   Found link https://files.pythonhosted.org/packages/80/3e/40e84d7d008a4866be91ad4e64b7c659ce0bfc80fec720119a0f380d55a5/PHASEfilter-0.3.5.tar.gz (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.5
2023-05-14T01:00:52,076   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/81/c8/4aadad0ed90553c940306b7f001b34bb4d5e9cd2a1cebece86d73ab6ef0f/PHASEfilter-0.3.6-py3-none-any.whl (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,077   Found link https://files.pythonhosted.org/packages/7f/5b/e32eac2e68f14e5e748667c531bba0160af86aa2ec5e30f748678d8722df/PHASEfilter-0.3.6.tar.gz (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.6
2023-05-14T01:00:52,078   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/94/b2/5a52d68dc9ee186e1db119b670fa69bdca363e9ae03124c5bcdedffcfcc4/PHASEfilter-0.3.7-py3-none-any.whl (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,079   Found link https://files.pythonhosted.org/packages/ad/f5/5acada4467d63421ae3438a9bab4c1e76219c41fb79df7af04d60e5b93d6/PHASEfilter-0.3.7.tar.gz (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.7
2023-05-14T01:00:52,080   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/e8/0c/b1ba707d308767faf0768f96d331da1e112b9a337f43b56ee9f8d6d8aff6/PHASEfilter-1.1.0-py3-none-any.whl (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,081   Found link https://files.pythonhosted.org/packages/45/4f/4afad6213ebd3b21f8a36cbcd8b17c3c6264054507b9790378441c6fd589/PHASEfilter-1.1.0.tar.gz (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 1.1.0
2023-05-14T01:00:52,082 Fetching project page and analyzing links: https://www.piwheels.org/simple/phasefilter/
2023-05-14T01:00:52,083 Getting page https://www.piwheels.org/simple/phasefilter/
2023-05-14T01:00:52,085 Found index url https://www.piwheels.org/simple/
2023-05-14T01:00:52,537 Fetched page https://www.piwheels.org/simple/phasefilter/ as text/html
2023-05-14T01:00:52,545   Skipping link: No binaries permitted for phasefilter: https://www.piwheels.org/simple/phasefilter/PHASEfilter-1.1.0-py3-none-any.whl#sha256=576445faaf8bdd2b9ac9c3355ed11dd37864d0e3372db05bc251e1834b391934 (from https://www.piwheels.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,546   Skipping link: No binaries permitted for phasefilter: https://www.piwheels.org/simple/phasefilter/PHASEfilter-0.3.7-py3-none-any.whl#sha256=9933589a83da01436d58f7088da67077b37d8cfcfed654f0863bd663badc07f4 (from https://www.piwheels.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,546   Skipping link: No binaries permitted for phasefilter: https://www.piwheels.org/simple/phasefilter/PHASEfilter-0.3.6-py3-none-any.whl#sha256=a7afd823c160a6c47d0e5a3e2cf8223835de50f0f8285d4d631768efbdff1dbe (from https://www.piwheels.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,547   Skipping link: No binaries permitted for phasefilter: https://www.piwheels.org/simple/phasefilter/PHASEfilter-0.3.5-py3-none-any.whl#sha256=50bd2b14fbcf7b4cb03a16b7f74d54beaefebe9c588361186ad7d712b61982da (from https://www.piwheels.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,547   Skipping link: No binaries permitted for phasefilter: https://www.piwheels.org/simple/phasefilter/PHASEfilter-0.3.4-py3-none-any.whl#sha256=56a9dea2ecab01677b300d8e01d3f79c867521c0cf4e0d11bb3571ebd49ca11c (from https://www.piwheels.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,548   Skipping link: No binaries permitted for phasefilter: https://www.piwheels.org/simple/phasefilter/PHASEfilter-0.3.3-py3-none-any.whl#sha256=f201c1bb78408dc19e9a8864e46fcf91bf051ecacc8672f1878dab375ca1b676 (from https://www.piwheels.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,548   Skipping link: No binaries permitted for phasefilter: https://www.piwheels.org/simple/phasefilter/PHASEfilter-0.3.2-py3-none-any.whl#sha256=faf7a59bd43b3d436e6eeb9d9e1205e95908bb5ca75eac67452cddcc557915b4 (from https://www.piwheels.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,549   Skipping link: No binaries permitted for phasefilter: https://www.piwheels.org/simple/phasefilter/PHASEfilter-0.0.1a1-py3-none-any.whl#sha256=f5d05fcef0bebaebddc8b37dd6c1a85ce75fac6cee2a44c1cff7c46aca20d121 (from https://www.piwheels.org/simple/phasefilter/) (requires-python:>=3.5)
2023-05-14T01:00:52,549 Skipping link: not a file: https://www.piwheels.org/simple/phasefilter/
2023-05-14T01:00:52,550 Skipping link: not a file: https://pypi.org/simple/phasefilter/
2023-05-14T01:00:52,585 Given no hashes to check 1 links for project 'phasefilter': discarding no candidates
2023-05-14T01:00:52,615 Collecting phasefilter==1.1.0
2023-05-14T01:00:52,619   Created temporary directory: /tmp/pip-unpack-0a8bxnuy
2023-05-14T01:00:52,974   Downloading PHASEfilter-1.1.0.tar.gz (61 kB)
2023-05-14T01:00:53,237   Added phasefilter==1.1.0 from https://files.pythonhosted.org/packages/45/4f/4afad6213ebd3b21f8a36cbcd8b17c3c6264054507b9790378441c6fd589/PHASEfilter-1.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-3j1bmsro'
2023-05-14T01:00:53,241   Running setup.py (path:/tmp/pip-wheel-vm7355dx/phasefilter_013c729238ae4c4eb4fb0603e6fc712b/setup.py) egg_info for package phasefilter
2023-05-14T01:00:53,242   Created temporary directory: /tmp/pip-pip-egg-info-km74n6n3
2023-05-14T01:00:53,243   Preparing metadata (setup.py): started
2023-05-14T01:00:53,245   Running command python setup.py egg_info
2023-05-14T01:00:55,242   running egg_info
2023-05-14T01:00:55,245   creating /tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info
2023-05-14T01:00:55,302   writing /tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info/PKG-INFO
2023-05-14T01:00:55,307   writing dependency_links to /tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info/dependency_links.txt
2023-05-14T01:00:55,311   writing entry points to /tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info/entry_points.txt
2023-05-14T01:00:55,314   writing requirements to /tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info/requires.txt
2023-05-14T01:00:55,316   writing top-level names to /tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info/top_level.txt
2023-05-14T01:00:55,318   writing manifest file '/tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info/SOURCES.txt'
2023-05-14T01:00:55,580   reading manifest file '/tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info/SOURCES.txt'
2023-05-14T01:00:55,590   writing manifest file '/tmp/pip-pip-egg-info-km74n6n3/PHASEfilter.egg-info/SOURCES.txt'
2023-05-14T01:00:55,593   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
2023-05-14T01:00:55,593   !!

2023-05-14T01:00:55,594           ********************************************************************************
2023-05-14T01:00:55,594           Usage of dash-separated 'dist-dir' will not be supported in future
2023-05-14T01:00:55,595           versions. Please use the underscore name 'dist_dir' instead.

2023-05-14T01:00:55,596           By 2023-Sep-26, you need to update your project and remove deprecated calls
2023-05-14T01:00:55,596           or your builds will no longer be supported.

2023-05-14T01:00:55,597           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2023-05-14T01:00:55,598           ********************************************************************************

2023-05-14T01:00:55,599   !!
2023-05-14T01:00:55,599     opt = self.warn_dash_deprecation(opt, section)
2023-05-14T01:00:55,733   Preparing metadata (setup.py): finished with status 'done'
2023-05-14T01:00:55,747   Source in /tmp/pip-wheel-vm7355dx/phasefilter_013c729238ae4c4eb4fb0603e6fc712b has version 1.1.0, which satisfies requirement phasefilter==1.1.0 from https://files.pythonhosted.org/packages/45/4f/4afad6213ebd3b21f8a36cbcd8b17c3c6264054507b9790378441c6fd589/PHASEfilter-1.1.0.tar.gz
2023-05-14T01:00:55,749   Removed phasefilter==1.1.0 from https://files.pythonhosted.org/packages/45/4f/4afad6213ebd3b21f8a36cbcd8b17c3c6264054507b9790378441c6fd589/PHASEfilter-1.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-3j1bmsro'
2023-05-14T01:00:55,766 Created temporary directory: /tmp/pip-unpack-0prb0m7o
2023-05-14T01:00:55,768 Building wheels for collected packages: phasefilter
2023-05-14T01:00:55,776   Created temporary directory: /tmp/pip-wheel-n4s4nff4
2023-05-14T01:00:55,777   Building wheel for phasefilter (setup.py): started
2023-05-14T01:00:55,779   Destination directory: /tmp/pip-wheel-n4s4nff4
2023-05-14T01:00:55,779   Running command python setup.py bdist_wheel
2023-05-14T01:00:57,547   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:755: SetuptoolsDeprecationWarning: Invalid dash-separated options
2023-05-14T01:00:57,548   !!

2023-05-14T01:00:57,549           ********************************************************************************
2023-05-14T01:00:57,549           Usage of dash-separated 'dist-dir' will not be supported in future
2023-05-14T01:00:57,550           versions. Please use the underscore name 'dist_dir' instead.

2023-05-14T01:00:57,550           By 2023-Sep-26, you need to update your project and remove deprecated calls
2023-05-14T01:00:57,551           or your builds will no longer be supported.

2023-05-14T01:00:57,551           See https://setuptools.pypa.io/en/latest/userguide/declarative_config.html for details.
2023-05-14T01:00:57,552           ********************************************************************************

2023-05-14T01:00:57,552   !!
2023-05-14T01:00:57,552     opt = self.warn_dash_deprecation(opt, section)
2023-05-14T01:00:57,853   running bdist_wheel
2023-05-14T01:00:58,048   running build
2023-05-14T01:00:58,048   running build_py
2023-05-14T01:00:58,112   creating build
2023-05-14T01:00:58,113   creating build/lib
2023-05-14T01:00:58,115   creating build/lib/PHASEfilter
2023-05-14T01:00:58,117   copying PHASEfilter/__init__.py -> build/lib/PHASEfilter
2023-05-14T01:00:58,122   creating build/lib/PHASEfilter/lib
2023-05-14T01:00:58,123   copying PHASEfilter/lib/__init__.py -> build/lib/PHASEfilter/lib
2023-05-14T01:00:58,129   creating build/lib/PHASEfilter/bin
2023-05-14T01:00:58,130   copying PHASEfilter/bin/phasefilter_single.py -> build/lib/PHASEfilter/bin
2023-05-14T01:00:58,135   copying PHASEfilter/bin/synchronize_genomes.py -> build/lib/PHASEfilter/bin
2023-05-14T01:00:58,140   copying PHASEfilter/bin/reference_statistics.py -> build/lib/PHASEfilter/bin
2023-05-14T01:00:58,145   copying PHASEfilter/bin/copy_raw_data_example_phasefilter.py -> build/lib/PHASEfilter/bin
2023-05-14T01:00:58,149   copying PHASEfilter/bin/make_alignment.py -> build/lib/PHASEfilter/bin
2023-05-14T01:00:58,153   copying PHASEfilter/bin/__init__.py -> build/lib/PHASEfilter/bin
2023-05-14T01:00:58,156   copying PHASEfilter/bin/phasefilter.py -> build/lib/PHASEfilter/bin
2023-05-14T01:00:58,163   creating build/lib/PHASEfilter/tests
2023-05-14T01:00:58,165   copying PHASEfilter/tests/test_process_genomes.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,171   copying PHASEfilter/tests/test_run_extra_software.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,175   copying PHASEfilter/tests/test_chain.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,180   copying PHASEfilter/tests/test_utils.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,185   copying PHASEfilter/tests/test_synchronization.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,190   copying PHASEfilter/tests/test_reference.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,195   copying PHASEfilter/tests/test_lift_over.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,201   copying PHASEfilter/tests/test_vcf.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,206   copying PHASEfilter/tests/__init__.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,210   copying PHASEfilter/tests/test_software.py -> build/lib/PHASEfilter/tests
2023-05-14T01:00:58,218   creating build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,220   copying PHASEfilter/lib/utils/read_gff.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,224   copying PHASEfilter/lib/utils/util.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,229   copying PHASEfilter/lib/utils/vcf_process.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,236   copying PHASEfilter/lib/utils/reference.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,241   copying PHASEfilter/lib/utils/software.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,245   copying PHASEfilter/lib/utils/chain.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,250   copying PHASEfilter/lib/utils/testing_software.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,253   copying PHASEfilter/lib/utils/run_extra_software.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,257   copying PHASEfilter/lib/utils/lift_over_simple.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,264   copying PHASEfilter/lib/utils/blast_two_sequences.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,270   copying PHASEfilter/lib/utils/lastz_two_sequences.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,273   copying PHASEfilter/lib/utils/__init__.py -> build/lib/PHASEfilter/lib/utils
2023-05-14T01:00:58,278   creating build/lib/PHASEfilter/lib/constants
2023-05-14T01:00:58,280   copying PHASEfilter/lib/constants/version.py -> build/lib/PHASEfilter/lib/constants
2023-05-14T01:00:58,284   copying PHASEfilter/lib/constants/constants.py -> build/lib/PHASEfilter/lib/constants
2023-05-14T01:00:58,287   copying PHASEfilter/lib/constants/__init__.py -> build/lib/PHASEfilter/lib/constants
2023-05-14T01:00:58,292   creating build/lib/PHASEfilter/lib/process
2023-05-14T01:00:58,293   copying PHASEfilter/lib/process/process_references.py -> build/lib/PHASEfilter/lib/process
2023-05-14T01:00:58,298   copying PHASEfilter/lib/process/process_genomes.py -> build/lib/PHASEfilter/lib/process
2023-05-14T01:00:58,302   copying PHASEfilter/lib/process/__init__.py -> build/lib/PHASEfilter/lib/process
2023-05-14T01:00:58,305   running egg_info
2023-05-14T01:00:58,440   writing PHASEfilter.egg-info/PKG-INFO
2023-05-14T01:00:58,444   writing dependency_links to PHASEfilter.egg-info/dependency_links.txt
2023-05-14T01:00:58,449   writing entry points to PHASEfilter.egg-info/entry_points.txt
2023-05-14T01:00:58,451   writing requirements to PHASEfilter.egg-info/requires.txt
2023-05-14T01:00:58,453   writing top-level names to PHASEfilter.egg-info/top_level.txt
2023-05-14T01:00:58,528   reading manifest file 'PHASEfilter.egg-info/SOURCES.txt'
2023-05-14T01:00:58,544   writing manifest file 'PHASEfilter.egg-info/SOURCES.txt'
2023-05-14T01:00:58,552   copying PHASEfilter/bin/install_phasefilter_dependencies.sh -> build/lib/PHASEfilter/bin
2023-05-14T01:00:58,565   running build_scripts
2023-05-14T01:00:58,566   creating build/scripts-3.7
2023-05-14T01:00:58,570   copying and adjusting PHASEfilter/bin/phasefilter.py -> build/scripts-3.7
2023-05-14T01:00:58,575   copying and adjusting PHASEfilter/bin/phasefilter_single.py -> build/scripts-3.7
2023-05-14T01:00:58,580   copying and adjusting PHASEfilter/bin/make_alignment.py -> build/scripts-3.7
2023-05-14T01:00:58,585   copying and adjusting PHASEfilter/bin/reference_statistics.py -> build/scripts-3.7
2023-05-14T01:00:58,589   copying and adjusting PHASEfilter/bin/synchronize_genomes.py -> build/scripts-3.7
2023-05-14T01:00:58,593   copying and adjusting PHASEfilter/bin/copy_raw_data_example_phasefilter.py -> build/scripts-3.7
2023-05-14T01:00:58,597   copying PHASEfilter/bin/install_phasefilter_dependencies.sh -> build/scripts-3.7
2023-05-14T01:00:58,601   changing mode of build/scripts-3.7/phasefilter.py from 644 to 755
2023-05-14T01:00:58,601   changing mode of build/scripts-3.7/phasefilter_single.py from 644 to 755
2023-05-14T01:00:58,602   changing mode of build/scripts-3.7/make_alignment.py from 644 to 755
2023-05-14T01:00:58,603   changing mode of build/scripts-3.7/reference_statistics.py from 644 to 755
2023-05-14T01:00:58,604   changing mode of build/scripts-3.7/synchronize_genomes.py from 644 to 755
2023-05-14T01:00:58,605   changing mode of build/scripts-3.7/copy_raw_data_example_phasefilter.py from 644 to 755
2023-05-14T01:00:58,672   /usr/local/lib/python3.7/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2023-05-14T01:00:58,673   !!

2023-05-14T01:00:58,674           ********************************************************************************
2023-05-14T01:00:58,674           Please avoid running ``setup.py`` directly.
2023-05-14T01:00:58,674           Instead, use pypa/build, pypa/installer, pypa/build or
2023-05-14T01:00:58,675           other standards-based tools.

2023-05-14T01:00:58,675           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2023-05-14T01:00:58,676           ********************************************************************************

2023-05-14T01:00:58,676   !!
2023-05-14T01:00:58,677     self.initialize_options()
2023-05-14T01:00:58,735   installing to build/bdist.linux-armv7l/wheel
2023-05-14T01:00:58,736   running install
2023-05-14T01:00:58,796   running install_lib
2023-05-14T01:00:58,858   creating build/bdist.linux-armv7l
2023-05-14T01:00:58,859   creating build/bdist.linux-armv7l/wheel
2023-05-14T01:00:58,863   creating build/bdist.linux-armv7l/wheel/PHASEfilter
2023-05-14T01:00:58,866   creating build/bdist.linux-armv7l/wheel/PHASEfilter/lib
2023-05-14T01:00:58,871   creating build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,873   copying build/lib/PHASEfilter/lib/utils/read_gff.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,877   copying build/lib/PHASEfilter/lib/utils/util.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,883   copying build/lib/PHASEfilter/lib/utils/vcf_process.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,888   copying build/lib/PHASEfilter/lib/utils/reference.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,893   copying build/lib/PHASEfilter/lib/utils/software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,898   copying build/lib/PHASEfilter/lib/utils/chain.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,902   copying build/lib/PHASEfilter/lib/utils/testing_software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,906   copying build/lib/PHASEfilter/lib/utils/run_extra_software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,911   copying build/lib/PHASEfilter/lib/utils/lift_over_simple.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,919   copying build/lib/PHASEfilter/lib/utils/blast_two_sequences.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,925   copying build/lib/PHASEfilter/lib/utils/lastz_two_sequences.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,930   copying build/lib/PHASEfilter/lib/utils/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2023-05-14T01:00:58,934   creating build/bdist.linux-armv7l/wheel/PHASEfilter/lib/constants
2023-05-14T01:00:58,936   copying build/lib/PHASEfilter/lib/constants/version.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/constants
2023-05-14T01:00:58,941   copying build/lib/PHASEfilter/lib/constants/constants.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/constants
2023-05-14T01:00:58,945   copying build/lib/PHASEfilter/lib/constants/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/constants
2023-05-14T01:00:58,949   copying build/lib/PHASEfilter/lib/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib
2023-05-14T01:00:58,953   creating build/bdist.linux-armv7l/wheel/PHASEfilter/lib/process
2023-05-14T01:00:58,955   copying build/lib/PHASEfilter/lib/process/process_references.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/process
2023-05-14T01:00:58,959   copying build/lib/PHASEfilter/lib/process/process_genomes.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/process
2023-05-14T01:00:58,964   copying build/lib/PHASEfilter/lib/process/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/process
2023-05-14T01:00:58,967   copying build/lib/PHASEfilter/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter
2023-05-14T01:00:58,971   creating build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:58,973   copying build/lib/PHASEfilter/bin/phasefilter_single.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:58,978   copying build/lib/PHASEfilter/bin/synchronize_genomes.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:58,982   copying build/lib/PHASEfilter/bin/reference_statistics.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:58,985   copying build/lib/PHASEfilter/bin/copy_raw_data_example_phasefilter.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:58,989   copying build/lib/PHASEfilter/bin/install_phasefilter_dependencies.sh -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:58,993   copying build/lib/PHASEfilter/bin/make_alignment.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:58,997   copying build/lib/PHASEfilter/bin/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:59,000   copying build/lib/PHASEfilter/bin/phasefilter.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2023-05-14T01:00:59,005   creating build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,007   copying build/lib/PHASEfilter/tests/test_process_genomes.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,011   copying build/lib/PHASEfilter/tests/test_run_extra_software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,015   copying build/lib/PHASEfilter/tests/test_chain.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,020   copying build/lib/PHASEfilter/tests/test_utils.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,024   copying build/lib/PHASEfilter/tests/test_synchronization.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,028   copying build/lib/PHASEfilter/tests/test_reference.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,032   copying build/lib/PHASEfilter/tests/test_lift_over.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,037   copying build/lib/PHASEfilter/tests/test_vcf.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,042   copying build/lib/PHASEfilter/tests/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,045   copying build/lib/PHASEfilter/tests/test_software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2023-05-14T01:00:59,049   running install_egg_info
2023-05-14T01:00:59,119   Copying PHASEfilter.egg-info to build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0-py3.7.egg-info
2023-05-14T01:00:59,145   running install_scripts
2023-05-14T01:00:59,148   creating build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data
2023-05-14T01:00:59,149   creating build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts
2023-05-14T01:00:59,151   copying build/scripts-3.7/phasefilter_single.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts
2023-05-14T01:00:59,157   copying build/scripts-3.7/synchronize_genomes.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts
2023-05-14T01:00:59,161   copying build/scripts-3.7/reference_statistics.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts
2023-05-14T01:00:59,165   copying build/scripts-3.7/copy_raw_data_example_phasefilter.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts
2023-05-14T01:00:59,170   copying build/scripts-3.7/install_phasefilter_dependencies.sh -> build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts
2023-05-14T01:00:59,174   copying build/scripts-3.7/make_alignment.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts
2023-05-14T01:00:59,179   copying build/scripts-3.7/phasefilter.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts
2023-05-14T01:00:59,183   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts/phasefilter_single.py to 755
2023-05-14T01:00:59,183   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts/synchronize_genomes.py to 755
2023-05-14T01:00:59,184   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts/reference_statistics.py to 755
2023-05-14T01:00:59,185   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts/copy_raw_data_example_phasefilter.py to 755
2023-05-14T01:00:59,186   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts/install_phasefilter_dependencies.sh to 755
2023-05-14T01:00:59,187   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts/make_alignment.py to 755
2023-05-14T01:00:59,188   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.data/scripts/phasefilter.py to 755
2023-05-14T01:00:59,248   creating build/bdist.linux-armv7l/wheel/PHASEfilter-1.1.0.dist-info/WHEEL
2023-05-14T01:00:59,253   creating '/tmp/pip-wheel-n4s4nff4/PHASEfilter-1.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2023-05-14T01:00:59,258   adding 'PHASEfilter/__init__.py'
2023-05-14T01:00:59,262   adding 'PHASEfilter/bin/__init__.py'
2023-05-14T01:00:59,265   adding 'PHASEfilter/bin/copy_raw_data_example_phasefilter.py'
2023-05-14T01:00:59,268   adding 'PHASEfilter/bin/install_phasefilter_dependencies.sh'
2023-05-14T01:00:59,271   adding 'PHASEfilter/bin/make_alignment.py'
2023-05-14T01:00:59,275   adding 'PHASEfilter/bin/phasefilter.py'
2023-05-14T01:00:59,280   adding 'PHASEfilter/bin/phasefilter_single.py'
2023-05-14T01:00:59,283   adding 'PHASEfilter/bin/reference_statistics.py'
2023-05-14T01:00:59,286   adding 'PHASEfilter/bin/synchronize_genomes.py'
2023-05-14T01:00:59,290   adding 'PHASEfilter/lib/__init__.py'
2023-05-14T01:00:59,293   adding 'PHASEfilter/lib/constants/__init__.py'
2023-05-14T01:00:59,295   adding 'PHASEfilter/lib/constants/constants.py'
2023-05-14T01:00:59,298   adding 'PHASEfilter/lib/constants/version.py'
2023-05-14T01:00:59,301   adding 'PHASEfilter/lib/process/__init__.py'
2023-05-14T01:00:59,305   adding 'PHASEfilter/lib/process/process_genomes.py'
2023-05-14T01:00:59,309   adding 'PHASEfilter/lib/process/process_references.py'
2023-05-14T01:00:59,313   adding 'PHASEfilter/lib/utils/__init__.py'
2023-05-14T01:00:59,321   adding 'PHASEfilter/lib/utils/blast_two_sequences.py'
2023-05-14T01:00:59,324   adding 'PHASEfilter/lib/utils/chain.py'
2023-05-14T01:00:59,328   adding 'PHASEfilter/lib/utils/lastz_two_sequences.py'
2023-05-14T01:00:59,340   adding 'PHASEfilter/lib/utils/lift_over_simple.py'
2023-05-14T01:00:59,344   adding 'PHASEfilter/lib/utils/read_gff.py'
2023-05-14T01:00:59,348   adding 'PHASEfilter/lib/utils/reference.py'
2023-05-14T01:00:59,351   adding 'PHASEfilter/lib/utils/run_extra_software.py'
2023-05-14T01:00:59,355   adding 'PHASEfilter/lib/utils/software.py'
2023-05-14T01:00:59,358   adding 'PHASEfilter/lib/utils/testing_software.py'
2023-05-14T01:00:59,364   adding 'PHASEfilter/lib/utils/util.py'
2023-05-14T01:00:59,372   adding 'PHASEfilter/lib/utils/vcf_process.py'
2023-05-14T01:00:59,376   adding 'PHASEfilter/tests/__init__.py'
2023-05-14T01:00:59,380   adding 'PHASEfilter/tests/test_chain.py'
2023-05-14T01:00:59,385   adding 'PHASEfilter/tests/test_lift_over.py'
2023-05-14T01:00:59,388   adding 'PHASEfilter/tests/test_process_genomes.py'
2023-05-14T01:00:59,391   adding 'PHASEfilter/tests/test_reference.py'
2023-05-14T01:00:59,394   adding 'PHASEfilter/tests/test_run_extra_software.py'
2023-05-14T01:00:59,397   adding 'PHASEfilter/tests/test_software.py'
2023-05-14T01:00:59,400   adding 'PHASEfilter/tests/test_synchronization.py'
2023-05-14T01:00:59,404   adding 'PHASEfilter/tests/test_utils.py'
2023-05-14T01:00:59,408   adding 'PHASEfilter/tests/test_vcf.py'
2023-05-14T01:00:59,414   adding 'PHASEfilter-1.1.0.data/scripts/copy_raw_data_example_phasefilter.py'
2023-05-14T01:00:59,416   adding 'PHASEfilter-1.1.0.data/scripts/install_phasefilter_dependencies.sh'
2023-05-14T01:00:59,420   adding 'PHASEfilter-1.1.0.data/scripts/make_alignment.py'
2023-05-14T01:00:59,424   adding 'PHASEfilter-1.1.0.data/scripts/phasefilter.py'
2023-05-14T01:00:59,428   adding 'PHASEfilter-1.1.0.data/scripts/phasefilter_single.py'
2023-05-14T01:00:59,431   adding 'PHASEfilter-1.1.0.data/scripts/reference_statistics.py'
2023-05-14T01:00:59,435   adding 'PHASEfilter-1.1.0.data/scripts/synchronize_genomes.py'
2023-05-14T01:00:59,441   adding 'PHASEfilter-1.1.0.dist-info/METADATA'
2023-05-14T01:00:59,444   adding 'PHASEfilter-1.1.0.dist-info/WHEEL'
2023-05-14T01:00:59,446   adding 'PHASEfilter-1.1.0.dist-info/entry_points.txt'
2023-05-14T01:00:59,448   adding 'PHASEfilter-1.1.0.dist-info/top_level.txt'
2023-05-14T01:00:59,450   adding 'PHASEfilter-1.1.0.dist-info/RECORD'
2023-05-14T01:00:59,456   removing build/bdist.linux-armv7l/wheel
2023-05-14T01:00:59,680   Building wheel for phasefilter (setup.py): finished with status 'done'
2023-05-14T01:00:59,784   Created wheel for phasefilter: filename=PHASEfilter-1.1.0-py3-none-any.whl size=96305 sha256=6dabeab1d636557f1f4576e8da88025f7e57ec7f0efa8b09cc133a876ad4841f
2023-05-14T01:00:59,786   Stored in directory: /tmp/pip-ephem-wheel-cache-g53fzt9j/wheels/7a/f9/31/a1e858be35f9c872364b24d033d215635ade8e18b3c5218dc4
2023-05-14T01:00:59,817 Successfully built phasefilter
2023-05-14T01:00:59,833 Removed build tracker: '/tmp/pip-build-tracker-3j1bmsro'