2022-01-07T16:34:26,351 Created temporary directory: /tmp/pip-ephem-wheel-cache-f6r25rsv
2022-01-07T16:34:26,357 Created temporary directory: /tmp/pip-req-tracker-xl50j0oe
2022-01-07T16:34:26,358 Initialized build tracking at /tmp/pip-req-tracker-xl50j0oe
2022-01-07T16:34:26,358 Created build tracker: /tmp/pip-req-tracker-xl50j0oe
2022-01-07T16:34:26,358 Entered build tracker: /tmp/pip-req-tracker-xl50j0oe
2022-01-07T16:34:26,360 Created temporary directory: /tmp/pip-wheel-0w_y72yj
2022-01-07T16:34:26,424 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-01-07T16:34:26,429 2 location(s) to search for versions of phasefilter:
2022-01-07T16:34:26,429 * https://pypi.org/simple/phasefilter/
2022-01-07T16:34:26,429 * https://www.piwheels.org/simple/phasefilter/
2022-01-07T16:34:26,430 Fetching project page and analyzing links: https://pypi.org/simple/phasefilter/
2022-01-07T16:34:26,432 Getting page https://pypi.org/simple/phasefilter/
2022-01-07T16:34:26,435 Found index url https://pypi.org/simple
2022-01-07T16:34:26,648   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/70/5b/a12acb782bfb5510c9281ffac13440c2089c4de283d92773f87408ebe857/PHASEfilter-0.0.1a1-py3-none-any.whl#sha256=f5d05fcef0bebaebddc8b37dd6c1a85ce75fac6cee2a44c1cff7c46aca20d121 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2022-01-07T16:34:26,650   Found link https://files.pythonhosted.org/packages/59/cb/fd5b96878a1f815759667d3556a4c72151d4f2bed79879dd817a0602c62f/PHASEfilter-0.0.1a1.tar.gz#sha256=ef3277b4002541318cf08e41a549bb5dd56a69418953dcb6f3f2276b14156735 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.0.1a1
2022-01-07T16:34:26,651   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/50/c6/3d3933d1c8f89a5ee4ec5e9a954a42ddd2f616015b4e9de18132bccfc321/PHASEfilter-0.3.2-py3-none-any.whl#sha256=9d5cc14813af003c8660f3cb5874b081b94bdbbf09d1464c5dd12b6c9526d3c6 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2022-01-07T16:34:26,652   Found link https://files.pythonhosted.org/packages/41/62/26390ce2c8f9d3fe2739a79da1f0705fd646df1b32200df2697bba0852f2/PHASEfilter-0.3.2.tar.gz#sha256=95374b7d27212f89165da946b659325b446db282fe1e4244915394a9f676f2d6 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.2
2022-01-07T16:34:26,653   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/4b/df/18736673d0a18ec858646025792d9808b1a6fedde5cbdf9609187e4f7d6f/PHASEfilter-0.3.3-py3-none-any.whl#sha256=f5b3cf53debb91e2600106a4b3a64e6dc242ef94d10d40db417e90a7a16d75d0 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2022-01-07T16:34:26,654   Found link https://files.pythonhosted.org/packages/06/1b/6b3db72941b86ea609af642664e09e6fb15afbaa742c367815e5b30e9f43/PHASEfilter-0.3.3.tar.gz#sha256=0e075565814be73bd03e6b799fba3352d21b62b358c2eb3f9a1c6e694782aa5f (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.3
2022-01-07T16:34:26,655   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/2f/ec/44fde574b28162fe0a07742b785fe0a1bb8218719858f62e0117ee7f6e78/PHASEfilter-0.3.4-py3-none-any.whl#sha256=298e024c74e35d6226e256a1249aa243c74291d38a08087e63342059d058c768 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2022-01-07T16:34:26,656   Found link https://files.pythonhosted.org/packages/d5/4b/6b7afc0d15ec9e7763d7cb1c1d1969f717c7a181d6db6e6fa4e3c16786bf/PHASEfilter-0.3.4.tar.gz#sha256=d4801e6c7671b772453d0f3c2593140b86c610643f759a6f3449e4b933103961 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.4
2022-01-07T16:34:26,657   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/7c/69/702e45c82eb74d8b26493ad9f88fd152c36aab9580f88da7006a6024bd18/PHASEfilter-0.3.5-py3-none-any.whl#sha256=bfbd69f07cc71d24533d499ac617424e1ae06c047550793e20ec5e84cf5825e8 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2022-01-07T16:34:26,658   Found link https://files.pythonhosted.org/packages/80/3e/40e84d7d008a4866be91ad4e64b7c659ce0bfc80fec720119a0f380d55a5/PHASEfilter-0.3.5.tar.gz#sha256=0476ef19e9e932b0741d97560245b02e591eb9fb59ebccdcc02e9847535d98de (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.5
2022-01-07T16:34:26,659   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/81/c8/4aadad0ed90553c940306b7f001b34bb4d5e9cd2a1cebece86d73ab6ef0f/PHASEfilter-0.3.6-py3-none-any.whl#sha256=0fef7e8e2a0ad69f3a96aa4c4b1685cd397fae2b5a4808a1f71b0e29cc29956d (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2022-01-07T16:34:26,660   Found link https://files.pythonhosted.org/packages/7f/5b/e32eac2e68f14e5e748667c531bba0160af86aa2ec5e30f748678d8722df/PHASEfilter-0.3.6.tar.gz#sha256=c6c14c7b8e5483a7401dc5433601c83750dfcc4e3452eec937cb342a880dfa66 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.6
2022-01-07T16:34:26,660   Skipping link: No binaries permitted for phasefilter: https://files.pythonhosted.org/packages/94/b2/5a52d68dc9ee186e1db119b670fa69bdca363e9ae03124c5bcdedffcfcc4/PHASEfilter-0.3.7-py3-none-any.whl#sha256=7b5368594df3a10147445aae58207752524bf8a6af75c5fd71525cf62008bbc7 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5)
2022-01-07T16:34:26,662   Found link https://files.pythonhosted.org/packages/ad/f5/5acada4467d63421ae3438a9bab4c1e76219c41fb79df7af04d60e5b93d6/PHASEfilter-0.3.7.tar.gz#sha256=cc7795406a8b399c37ffa262861020560341e673098968b921b188e01ef46238 (from https://pypi.org/simple/phasefilter/) (requires-python:>=3.5), version: 0.3.7
2022-01-07T16:34:26,663 Fetching project page and analyzing links: https://www.piwheels.org/simple/phasefilter/
2022-01-07T16:34:26,663 Getting page https://www.piwheels.org/simple/phasefilter/
2022-01-07T16:34:26,665 Found index url https://www.piwheels.org/simple
2022-01-07T16:34:26,882   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)
2022-01-07T16:34:26,883   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)
2022-01-07T16:34:26,883   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)
2022-01-07T16:34:26,884   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)
2022-01-07T16:34:26,884   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)
2022-01-07T16:34:26,885   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)
2022-01-07T16:34:26,885 Skipping link: not a file: https://www.piwheels.org/simple/phasefilter/
2022-01-07T16:34:26,886 Skipping link: not a file: https://pypi.org/simple/phasefilter/
2022-01-07T16:34:26,920 Given no hashes to check 1 links for project 'phasefilter': discarding no candidates
2022-01-07T16:34:26,950 Collecting phasefilter==0.3.7
2022-01-07T16:34:26,953   Created temporary directory: /tmp/pip-unpack-n_g87wbx
2022-01-07T16:34:27,049   Downloading PHASEfilter-0.3.7.tar.gz (56 kB)
2022-01-07T16:34:27,270   Added phasefilter==0.3.7 from https://files.pythonhosted.org/packages/ad/f5/5acada4467d63421ae3438a9bab4c1e76219c41fb79df7af04d60e5b93d6/PHASEfilter-0.3.7.tar.gz#sha256=cc7795406a8b399c37ffa262861020560341e673098968b921b188e01ef46238 to build tracker '/tmp/pip-req-tracker-xl50j0oe'
2022-01-07T16:34:27,272   Running setup.py (path:/tmp/pip-wheel-0w_y72yj/phasefilter_0f50eb42f38d487a9fdcbe35e0e2d41b/setup.py) egg_info for package phasefilter
2022-01-07T16:34:27,273   Created temporary directory: /tmp/pip-pip-egg-info-qaj3gq9j
2022-01-07T16:34:27,274   Preparing metadata (setup.py): started
2022-01-07T16:34:27,274   Running command python setup.py egg_info
2022-01-07T16:34:29,168   running egg_info
2022-01-07T16:34:29,172   creating /tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info
2022-01-07T16:34:29,174   writing /tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info/PKG-INFO
2022-01-07T16:34:29,179   writing dependency_links to /tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info/dependency_links.txt
2022-01-07T16:34:29,182   writing entry points to /tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info/entry_points.txt
2022-01-07T16:34:29,184   writing requirements to /tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info/requires.txt
2022-01-07T16:34:29,186   writing top-level names to /tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info/top_level.txt
2022-01-07T16:34:29,189   writing manifest file '/tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info/SOURCES.txt'
2022-01-07T16:34:29,225   reading manifest file '/tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info/SOURCES.txt'
2022-01-07T16:34:29,235   writing manifest file '/tmp/pip-pip-egg-info-qaj3gq9j/PHASEfilter.egg-info/SOURCES.txt'
2022-01-07T16:34:29,237   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:726: UserWarning: Usage of dash-separated 'dist-dir' will not be supported in future versions. Please use the underscore name 'dist_dir' instead
2022-01-07T16:34:29,237     % (opt, underscore_opt)
2022-01-07T16:34:29,340   Preparing metadata (setup.py): finished with status 'done'
2022-01-07T16:34:29,350   Source in /tmp/pip-wheel-0w_y72yj/phasefilter_0f50eb42f38d487a9fdcbe35e0e2d41b has version 0.3.7, which satisfies requirement phasefilter==0.3.7 from https://files.pythonhosted.org/packages/ad/f5/5acada4467d63421ae3438a9bab4c1e76219c41fb79df7af04d60e5b93d6/PHASEfilter-0.3.7.tar.gz#sha256=cc7795406a8b399c37ffa262861020560341e673098968b921b188e01ef46238
2022-01-07T16:34:29,352   Removed phasefilter==0.3.7 from https://files.pythonhosted.org/packages/ad/f5/5acada4467d63421ae3438a9bab4c1e76219c41fb79df7af04d60e5b93d6/PHASEfilter-0.3.7.tar.gz#sha256=cc7795406a8b399c37ffa262861020560341e673098968b921b188e01ef46238 from build tracker '/tmp/pip-req-tracker-xl50j0oe'
2022-01-07T16:34:29,367 Created temporary directory: /tmp/pip-unpack-9knqm157
2022-01-07T16:34:29,368 Building wheels for collected packages: phasefilter
2022-01-07T16:34:29,376   Created temporary directory: /tmp/pip-wheel-ohr2yccx
2022-01-07T16:34:29,377   Building wheel for phasefilter (setup.py): started
2022-01-07T16:34:29,377   Destination directory: /tmp/pip-wheel-ohr2yccx
2022-01-07T16:34:29,378   Running command /usr/bin/python3 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-0w_y72yj/phasefilter_0f50eb42f38d487a9fdcbe35e0e2d41b/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-0w_y72yj/phasefilter_0f50eb42f38d487a9fdcbe35e0e2d41b/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ohr2yccx
2022-01-07T16:34:30,967   /usr/local/lib/python3.7/dist-packages/setuptools/dist.py:726: UserWarning: Usage of dash-separated 'dist-dir' will not be supported in future versions. Please use the underscore name 'dist_dir' instead
2022-01-07T16:34:30,969     % (opt, underscore_opt)
2022-01-07T16:34:31,253   running bdist_wheel
2022-01-07T16:34:31,262   running build
2022-01-07T16:34:31,262   running build_py
2022-01-07T16:34:31,271   creating build
2022-01-07T16:34:31,272   creating build/lib
2022-01-07T16:34:31,273   creating build/lib/PHASEfilter
2022-01-07T16:34:31,275   copying PHASEfilter/__init__.py -> build/lib/PHASEfilter
2022-01-07T16:34:31,279   creating build/lib/PHASEfilter/bin
2022-01-07T16:34:31,280   copying PHASEfilter/bin/__init__.py -> build/lib/PHASEfilter/bin
2022-01-07T16:34:31,283   copying PHASEfilter/bin/copy_raw_data_example_phasefilter.py -> build/lib/PHASEfilter/bin
2022-01-07T16:34:31,286   copying PHASEfilter/bin/synchronize_genomes.py -> build/lib/PHASEfilter/bin
2022-01-07T16:34:31,290   copying PHASEfilter/bin/reference_statistics.py -> build/lib/PHASEfilter/bin
2022-01-07T16:34:31,293   copying PHASEfilter/bin/phasefilter_single.py -> build/lib/PHASEfilter/bin
2022-01-07T16:34:31,297   copying PHASEfilter/bin/make_alignment.py -> build/lib/PHASEfilter/bin
2022-01-07T16:34:31,301   copying PHASEfilter/bin/phasefilter.py -> build/lib/PHASEfilter/bin
2022-01-07T16:34:31,307   creating build/lib/PHASEfilter/tests
2022-01-07T16:34:31,308   copying PHASEfilter/tests/test_vcf.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,314   copying PHASEfilter/tests/__init__.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,317   copying PHASEfilter/tests/test_software.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,321   copying PHASEfilter/tests/test_lift_over.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,326   copying PHASEfilter/tests/test_synchronization.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,330   copying PHASEfilter/tests/test_process_genomes.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,334   copying PHASEfilter/tests/test_run_extra_software.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,337   copying PHASEfilter/tests/test_utils.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,341   copying PHASEfilter/tests/test_reference.py -> build/lib/PHASEfilter/tests
2022-01-07T16:34:31,345   creating build/lib/PHASEfilter/lib
2022-01-07T16:34:31,347   copying PHASEfilter/lib/__init__.py -> build/lib/PHASEfilter/lib
2022-01-07T16:34:31,350   creating build/lib/PHASEfilter/lib/process
2022-01-07T16:34:31,351   copying PHASEfilter/lib/process/process_genomes.py -> build/lib/PHASEfilter/lib/process
2022-01-07T16:34:31,356   copying PHASEfilter/lib/process/__init__.py -> build/lib/PHASEfilter/lib/process
2022-01-07T16:34:31,358   copying PHASEfilter/lib/process/process_references.py -> build/lib/PHASEfilter/lib/process
2022-01-07T16:34:31,363   creating build/lib/PHASEfilter/lib/constants
2022-01-07T16:34:31,365   copying PHASEfilter/lib/constants/__init__.py -> build/lib/PHASEfilter/lib/constants
2022-01-07T16:34:31,368   copying PHASEfilter/lib/constants/version.py -> build/lib/PHASEfilter/lib/constants
2022-01-07T16:34:31,371   copying PHASEfilter/lib/constants/constants.py -> build/lib/PHASEfilter/lib/constants
2022-01-07T16:34:31,375   creating build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,377   copying PHASEfilter/lib/utils/lastz_two_sequences.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,380   copying PHASEfilter/lib/utils/lift_over_simple.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,386   copying PHASEfilter/lib/utils/__init__.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,389   copying PHASEfilter/lib/utils/software.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,393   copying PHASEfilter/lib/utils/util.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,397   copying PHASEfilter/lib/utils/reference.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,400   copying PHASEfilter/lib/utils/run_extra_software.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,404   copying PHASEfilter/lib/utils/testing_software.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,407   copying PHASEfilter/lib/utils/vcf_process.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,411   copying PHASEfilter/lib/utils/blast_two_sequences.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,417   copying PHASEfilter/lib/utils/read_gff.py -> build/lib/PHASEfilter/lib/utils
2022-01-07T16:34:31,420   running egg_info
2022-01-07T16:34:31,445   writing PHASEfilter.egg-info/PKG-INFO
2022-01-07T16:34:31,450   writing dependency_links to PHASEfilter.egg-info/dependency_links.txt
2022-01-07T16:34:31,454   writing entry points to PHASEfilter.egg-info/entry_points.txt
2022-01-07T16:34:31,457   writing requirements to PHASEfilter.egg-info/requires.txt
2022-01-07T16:34:31,459   writing top-level names to PHASEfilter.egg-info/top_level.txt
2022-01-07T16:34:31,478   reading manifest file 'PHASEfilter.egg-info/SOURCES.txt'
2022-01-07T16:34:31,493   writing manifest file 'PHASEfilter.egg-info/SOURCES.txt'
2022-01-07T16:34:31,500   copying PHASEfilter/bin/install_phasefilter_dependencies.sh -> build/lib/PHASEfilter/bin
2022-01-07T16:34:31,513   running build_scripts
2022-01-07T16:34:31,514   creating build/scripts-3.7
2022-01-07T16:34:31,516   copying and adjusting PHASEfilter/bin/phasefilter.py -> build/scripts-3.7
2022-01-07T16:34:31,521   copying and adjusting PHASEfilter/bin/phasefilter_single.py -> build/scripts-3.7
2022-01-07T16:34:31,525   copying and adjusting PHASEfilter/bin/make_alignment.py -> build/scripts-3.7
2022-01-07T16:34:31,530   copying and adjusting PHASEfilter/bin/reference_statistics.py -> build/scripts-3.7
2022-01-07T16:34:31,533   copying and adjusting PHASEfilter/bin/synchronize_genomes.py -> build/scripts-3.7
2022-01-07T16:34:31,537   copying and adjusting PHASEfilter/bin/copy_raw_data_example_phasefilter.py -> build/scripts-3.7
2022-01-07T16:34:31,541   copying PHASEfilter/bin/install_phasefilter_dependencies.sh -> build/scripts-3.7
2022-01-07T16:34:31,544   changing mode of build/scripts-3.7/phasefilter.py from 644 to 755
2022-01-07T16:34:31,545   changing mode of build/scripts-3.7/phasefilter_single.py from 644 to 755
2022-01-07T16:34:31,546   changing mode of build/scripts-3.7/make_alignment.py from 644 to 755
2022-01-07T16:34:31,547   changing mode of build/scripts-3.7/reference_statistics.py from 644 to 755
2022-01-07T16:34:31,548   changing mode of build/scripts-3.7/synchronize_genomes.py from 644 to 755
2022-01-07T16:34:31,549   changing mode of build/scripts-3.7/copy_raw_data_example_phasefilter.py from 644 to 755
2022-01-07T16:34:31,555   /usr/local/lib/python3.7/dist-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
2022-01-07T16:34:31,556     setuptools.SetuptoolsDeprecationWarning,
2022-01-07T16:34:31,561   installing to build/bdist.linux-armv7l/wheel
2022-01-07T16:34:31,561   running install
2022-01-07T16:34:31,564   running install_lib
2022-01-07T16:34:31,571   creating build/bdist.linux-armv7l
2022-01-07T16:34:31,572   creating build/bdist.linux-armv7l/wheel
2022-01-07T16:34:31,576   creating build/bdist.linux-armv7l/wheel/PHASEfilter
2022-01-07T16:34:31,579   creating build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,581   copying build/lib/PHASEfilter/bin/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,585   copying build/lib/PHASEfilter/bin/copy_raw_data_example_phasefilter.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,589   copying build/lib/PHASEfilter/bin/install_phasefilter_dependencies.sh -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,593   copying build/lib/PHASEfilter/bin/synchronize_genomes.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,597   copying build/lib/PHASEfilter/bin/reference_statistics.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,601   copying build/lib/PHASEfilter/bin/phasefilter_single.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,606   copying build/lib/PHASEfilter/bin/make_alignment.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,611   copying build/lib/PHASEfilter/bin/phasefilter.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/bin
2022-01-07T16:34:31,616   copying build/lib/PHASEfilter/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter
2022-01-07T16:34:31,620   creating build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,622   copying build/lib/PHASEfilter/tests/test_vcf.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,628   copying build/lib/PHASEfilter/tests/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,632   copying build/lib/PHASEfilter/tests/test_software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,637   copying build/lib/PHASEfilter/tests/test_lift_over.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,642   copying build/lib/PHASEfilter/tests/test_synchronization.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,646   copying build/lib/PHASEfilter/tests/test_process_genomes.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,650   copying build/lib/PHASEfilter/tests/test_run_extra_software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,653   copying build/lib/PHASEfilter/tests/test_utils.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,657   copying build/lib/PHASEfilter/tests/test_reference.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/tests
2022-01-07T16:34:31,662   creating build/bdist.linux-armv7l/wheel/PHASEfilter/lib
2022-01-07T16:34:31,665   creating build/bdist.linux-armv7l/wheel/PHASEfilter/lib/process
2022-01-07T16:34:31,666   copying build/lib/PHASEfilter/lib/process/process_genomes.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/process
2022-01-07T16:34:31,671   copying build/lib/PHASEfilter/lib/process/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/process
2022-01-07T16:34:31,674   copying build/lib/PHASEfilter/lib/process/process_references.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/process
2022-01-07T16:34:31,678   copying build/lib/PHASEfilter/lib/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib
2022-01-07T16:34:31,682   creating build/bdist.linux-armv7l/wheel/PHASEfilter/lib/constants
2022-01-07T16:34:31,683   copying build/lib/PHASEfilter/lib/constants/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/constants
2022-01-07T16:34:31,687   copying build/lib/PHASEfilter/lib/constants/version.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/constants
2022-01-07T16:34:31,690   copying build/lib/PHASEfilter/lib/constants/constants.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/constants
2022-01-07T16:34:31,695   creating build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,696   copying build/lib/PHASEfilter/lib/utils/lastz_two_sequences.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,700   copying build/lib/PHASEfilter/lib/utils/lift_over_simple.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,706   copying build/lib/PHASEfilter/lib/utils/__init__.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,709   copying build/lib/PHASEfilter/lib/utils/software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,713   copying build/lib/PHASEfilter/lib/utils/util.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,718   copying build/lib/PHASEfilter/lib/utils/reference.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,722   copying build/lib/PHASEfilter/lib/utils/run_extra_software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,726   copying build/lib/PHASEfilter/lib/utils/testing_software.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,729   copying build/lib/PHASEfilter/lib/utils/vcf_process.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,734   copying build/lib/PHASEfilter/lib/utils/blast_two_sequences.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,740   copying build/lib/PHASEfilter/lib/utils/read_gff.py -> build/bdist.linux-armv7l/wheel/PHASEfilter/lib/utils
2022-01-07T16:34:31,742   running install_egg_info
2022-01-07T16:34:31,757   Copying PHASEfilter.egg-info to build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7-py3.7.egg-info
2022-01-07T16:34:31,779   running install_scripts
2022-01-07T16:34:31,897   creating build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data
2022-01-07T16:34:31,898   creating build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts
2022-01-07T16:34:31,900   copying build/scripts-3.7/copy_raw_data_example_phasefilter.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts
2022-01-07T16:34:31,904   copying build/scripts-3.7/install_phasefilter_dependencies.sh -> build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts
2022-01-07T16:34:31,907   copying build/scripts-3.7/synchronize_genomes.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts
2022-01-07T16:34:31,911   copying build/scripts-3.7/reference_statistics.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts
2022-01-07T16:34:31,914   copying build/scripts-3.7/phasefilter_single.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts
2022-01-07T16:34:31,919   copying build/scripts-3.7/make_alignment.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts
2022-01-07T16:34:31,923   copying build/scripts-3.7/phasefilter.py -> build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts
2022-01-07T16:34:31,926   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts/copy_raw_data_example_phasefilter.py to 755
2022-01-07T16:34:31,927   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts/install_phasefilter_dependencies.sh to 755
2022-01-07T16:34:31,927   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts/synchronize_genomes.py to 755
2022-01-07T16:34:31,928   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts/reference_statistics.py to 755
2022-01-07T16:34:31,928   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts/phasefilter_single.py to 755
2022-01-07T16:34:31,929   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts/make_alignment.py to 755
2022-01-07T16:34:31,929   changing mode of build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.data/scripts/phasefilter.py to 755
2022-01-07T16:34:31,986   creating build/bdist.linux-armv7l/wheel/PHASEfilter-0.3.7.dist-info/WHEEL
2022-01-07T16:34:31,991   creating '/tmp/pip-wheel-ohr2yccx/PHASEfilter-0.3.7-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2022-01-07T16:34:31,995   adding 'PHASEfilter/__init__.py'
2022-01-07T16:34:31,998   adding 'PHASEfilter/bin/__init__.py'
2022-01-07T16:34:32,001   adding 'PHASEfilter/bin/copy_raw_data_example_phasefilter.py'
2022-01-07T16:34:32,003   adding 'PHASEfilter/bin/install_phasefilter_dependencies.sh'
2022-01-07T16:34:32,006   adding 'PHASEfilter/bin/make_alignment.py'
2022-01-07T16:34:32,010   adding 'PHASEfilter/bin/phasefilter.py'
2022-01-07T16:34:32,014   adding 'PHASEfilter/bin/phasefilter_single.py'
2022-01-07T16:34:32,016   adding 'PHASEfilter/bin/reference_statistics.py'
2022-01-07T16:34:32,019   adding 'PHASEfilter/bin/synchronize_genomes.py'
2022-01-07T16:34:32,022   adding 'PHASEfilter/lib/__init__.py'
2022-01-07T16:34:32,026   adding 'PHASEfilter/lib/constants/__init__.py'
2022-01-07T16:34:32,028   adding 'PHASEfilter/lib/constants/constants.py'
2022-01-07T16:34:32,030   adding 'PHASEfilter/lib/constants/version.py'
2022-01-07T16:34:32,033   adding 'PHASEfilter/lib/process/__init__.py'
2022-01-07T16:34:32,036   adding 'PHASEfilter/lib/process/process_genomes.py'
2022-01-07T16:34:32,040   adding 'PHASEfilter/lib/process/process_references.py'
2022-01-07T16:34:32,044   adding 'PHASEfilter/lib/utils/__init__.py'
2022-01-07T16:34:32,051   adding 'PHASEfilter/lib/utils/blast_two_sequences.py'
2022-01-07T16:34:32,054   adding 'PHASEfilter/lib/utils/lastz_two_sequences.py'
2022-01-07T16:34:32,064   adding 'PHASEfilter/lib/utils/lift_over_simple.py'
2022-01-07T16:34:32,067   adding 'PHASEfilter/lib/utils/read_gff.py'
2022-01-07T16:34:32,071   adding 'PHASEfilter/lib/utils/reference.py'
2022-01-07T16:34:32,074   adding 'PHASEfilter/lib/utils/run_extra_software.py'
2022-01-07T16:34:32,077   adding 'PHASEfilter/lib/utils/software.py'
2022-01-07T16:34:32,080   adding 'PHASEfilter/lib/utils/testing_software.py'
2022-01-07T16:34:32,086   adding 'PHASEfilter/lib/utils/util.py'
2022-01-07T16:34:32,093   adding 'PHASEfilter/lib/utils/vcf_process.py'
2022-01-07T16:34:32,097   adding 'PHASEfilter/tests/__init__.py'
2022-01-07T16:34:32,101   adding 'PHASEfilter/tests/test_lift_over.py'
2022-01-07T16:34:32,104   adding 'PHASEfilter/tests/test_process_genomes.py'
2022-01-07T16:34:32,107   adding 'PHASEfilter/tests/test_reference.py'
2022-01-07T16:34:32,109   adding 'PHASEfilter/tests/test_run_extra_software.py'
2022-01-07T16:34:32,112   adding 'PHASEfilter/tests/test_software.py'
2022-01-07T16:34:32,115   adding 'PHASEfilter/tests/test_synchronization.py'
2022-01-07T16:34:32,118   adding 'PHASEfilter/tests/test_utils.py'
2022-01-07T16:34:32,122   adding 'PHASEfilter/tests/test_vcf.py'
2022-01-07T16:34:32,127   adding 'PHASEfilter-0.3.7.data/scripts/copy_raw_data_example_phasefilter.py'
2022-01-07T16:34:32,130   adding 'PHASEfilter-0.3.7.data/scripts/install_phasefilter_dependencies.sh'
2022-01-07T16:34:32,133   adding 'PHASEfilter-0.3.7.data/scripts/make_alignment.py'
2022-01-07T16:34:32,136   adding 'PHASEfilter-0.3.7.data/scripts/phasefilter.py'
2022-01-07T16:34:32,140   adding 'PHASEfilter-0.3.7.data/scripts/phasefilter_single.py'
2022-01-07T16:34:32,143   adding 'PHASEfilter-0.3.7.data/scripts/reference_statistics.py'
2022-01-07T16:34:32,146   adding 'PHASEfilter-0.3.7.data/scripts/synchronize_genomes.py'
2022-01-07T16:34:32,151   adding 'PHASEfilter-0.3.7.dist-info/METADATA'
2022-01-07T16:34:32,153   adding 'PHASEfilter-0.3.7.dist-info/WHEEL'
2022-01-07T16:34:32,154   adding 'PHASEfilter-0.3.7.dist-info/entry_points.txt'
2022-01-07T16:34:32,156   adding 'PHASEfilter-0.3.7.dist-info/top_level.txt'
2022-01-07T16:34:32,157   adding 'PHASEfilter-0.3.7.dist-info/RECORD'
2022-01-07T16:34:32,164   removing build/bdist.linux-armv7l/wheel
2022-01-07T16:34:32,313   Building wheel for phasefilter (setup.py): finished with status 'done'
2022-01-07T16:34:32,319   Created wheel for phasefilter: filename=PHASEfilter-0.3.7-py3-none-any.whl size=90146 sha256=9933589a83da01436d58f7088da67077b37d8cfcfed654f0863bd663badc07f4
2022-01-07T16:34:32,320   Stored in directory: /tmp/pip-ephem-wheel-cache-f6r25rsv/wheels/08/e0/a3/455a6dbce9ad127dd3ea827884bab7a10c6bb3c009130f5632
2022-01-07T16:34:32,346 Successfully built phasefilter
2022-01-07T16:34:32,359 Removed build tracker: '/tmp/pip-req-tracker-xl50j0oe'