2024-11-16T05:39:24,525 Created temporary directory: /tmp/pip-build-tracker-iy_y4fyl
2024-11-16T05:39:24,527 Initialized build tracking at /tmp/pip-build-tracker-iy_y4fyl
2024-11-16T05:39:24,528 Created build tracker: /tmp/pip-build-tracker-iy_y4fyl
2024-11-16T05:39:24,529 Entered build tracker: /tmp/pip-build-tracker-iy_y4fyl
2024-11-16T05:39:24,530 Created temporary directory: /tmp/pip-wheel-nqg7op_8
2024-11-16T05:39:24,533 Created temporary directory: /tmp/pip-ephem-wheel-cache-xpiwhmnt
2024-11-16T05:39:24,578 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2024-11-16T05:39:24,580 2 location(s) to search for versions of biobakery-workflows:
2024-11-16T05:39:24,580 * https://pypi.org/simple/biobakery-workflows/
2024-11-16T05:39:24,580 * https://www.piwheels.org/simple/biobakery-workflows/
2024-11-16T05:39:24,581 Fetching project page and analyzing links: https://pypi.org/simple/biobakery-workflows/
2024-11-16T05:39:24,582 Getting page https://pypi.org/simple/biobakery-workflows/
2024-11-16T05:39:24,583 Found index url https://pypi.org/simple/
2024-11-16T05:39:24,801 Fetched page https://pypi.org/simple/biobakery-workflows/ as application/vnd.pypi.simple.v1+json
2024-11-16T05:39:24,807   Found link https://files.pythonhosted.org/packages/1c/b8/2d49305112ddce416e9f37d6bbd9cdd50eeda669d91954e9b4188b00aa9c/biobakery_workflows-0.3.0.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.3.0
2024-11-16T05:39:24,807   Found link https://files.pythonhosted.org/packages/70/7c/64769accee73cfba802fd536ca6b19990bfd444dc429038a0b0e970d4707/biobakery_workflows-0.3.1.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.3.1
2024-11-16T05:39:24,808   Found link https://files.pythonhosted.org/packages/10/51/511c7456972a3e51fb98416e153eaaf2f2e091683763a9030bcfd9278dee/biobakery_workflows-0.9.0.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.9.0
2024-11-16T05:39:24,809   Found link https://files.pythonhosted.org/packages/26/56/14a401341149cc14532ab03e8e327c21518b3e03c07ab4f8b9469abc4d11/biobakery_workflows-0.12.1.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.12.1
2024-11-16T05:39:24,809   Found link https://files.pythonhosted.org/packages/10/5f/a627ee61e221c02dc272c5d77c2208be7f47e274f0241cc4a6052b5c17eb/biobakery_workflows-0.13.0.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.0
2024-11-16T05:39:24,810   Found link https://files.pythonhosted.org/packages/51/63/a9f0055e5c798017111b959383b92a79d77716a8aae668353f46985f48da/biobakery_workflows-0.13.1.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.1
2024-11-16T05:39:24,811   Found link https://files.pythonhosted.org/packages/4b/5f/e8a487a22758156034d8a9ecd9846f10383e610780cd8b5d90ecfb32faf9/biobakery_workflows-0.13.2.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.2
2024-11-16T05:39:24,811   Found link https://files.pythonhosted.org/packages/cc/87/d006df9363f78ade3e5c766c61113ad96d18036e2cca432c6f174fa87340/biobakery_workflows-0.13.3.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.3
2024-11-16T05:39:24,812   Found link https://files.pythonhosted.org/packages/cb/c6/ff6d693a51709e1a48870184ad3390ee690fd9f240a557e373755829cb4d/biobakery_workflows-0.13.4.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.4
2024-11-16T05:39:24,812   Found link https://files.pythonhosted.org/packages/a8/07/8fca14b4626560e71b8c43dc209c0f6c0b028d0be5633d681fa3176c1b8d/biobakery_workflows-0.13.5.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.5
2024-11-16T05:39:24,813   Found link https://files.pythonhosted.org/packages/e1/de/5b3da5aca1d31c8a68642e94663e3e23e037397ab6397af891ae388c95ca/biobakery_workflows-0.14.1.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.14.1
2024-11-16T05:39:24,814   Found link https://files.pythonhosted.org/packages/56/fd/8c492771a384b1ee53db56903eff6d850f5bbb3059784f5f205d5a8dc297/biobakery_workflows-0.14.2.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.14.2
2024-11-16T05:39:24,814   Found link https://files.pythonhosted.org/packages/97/44/dc0bdd6b40a5ea79a6b0fac53d119644ebeb61daefb3fe4756cd5eed2cea/biobakery_workflows-0.14.3.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.14.3
2024-11-16T05:39:24,815   Found link https://files.pythonhosted.org/packages/52/24/2fcc8032cb2f3ac6e62b9f7c0fc3e23ff2eb644a7962c9e1c4ac6a717f11/biobakery_workflows-0.15.0.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.15.0
2024-11-16T05:39:24,816   Found link https://files.pythonhosted.org/packages/2f/4e/992ed567f8094c64e39cb5728d2f899678415ac398cc8346e1b2750d14c9/biobakery_workflows-0.15.1.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 0.15.1
2024-11-16T05:39:24,816   Found link https://files.pythonhosted.org/packages/f5/4c/5e631276b617f23bd0fdd6569bd5a8223936c1f4230acd48fdb28d8772be/biobakery_workflows-3.0.0a0.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a0
2024-11-16T05:39:24,817   Found link https://files.pythonhosted.org/packages/19/55/22b8a4c499049c4e3abeda7dbe0998e9fb773b38943c862afb64786295e9/biobakery_workflows-3.0.0a1.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a1
2024-11-16T05:39:24,817   Found link https://files.pythonhosted.org/packages/6a/4d/2775b25e75bfe3c769b3ead36eff1ef3d7bb2aee8142a74492b1d3c63d70/biobakery_workflows-3.0.0a2.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a2
2024-11-16T05:39:24,818   Found link https://files.pythonhosted.org/packages/90/c2/6b34fa5d6bfad28790eae27778468c7092b0e29a501ba1eb6265b771cbf7/biobakery_workflows-3.0.0a3.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a3
2024-11-16T05:39:24,818   Found link https://files.pythonhosted.org/packages/e9/76/ba376c1958d671c238f1198a934b117c8d133ef9b1558f82fc7f494495ef/biobakery_workflows-3.0.0a4.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a4
2024-11-16T05:39:24,819   Found link https://files.pythonhosted.org/packages/f7/66/714144f76398d9055b80803d04c20a5dc5cc25059514786caaf7454389a0/biobakery_workflows-3.0.0a5.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a5
2024-11-16T05:39:24,820   Found link https://files.pythonhosted.org/packages/2d/94/a35b04d3a7202fea932bffdeca372c13fc45b6d463c62dcb8293e0893e95/biobakery_workflows-3.0.0-alpha.6.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0-alpha.6
2024-11-16T05:39:24,820   Found link https://files.pythonhosted.org/packages/c0/04/503cf382ef99894d05171a39ca39ee70866ce815cb369ca6b6215538df5e/biobakery_workflows-3.0.0a7.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a7
2024-11-16T05:39:24,821   Found link https://files.pythonhosted.org/packages/9e/7c/8b19b9e18cff1aebd3087871ce06563761d4946715f4fc28d99af7b99b07/biobakery_workflows-3.1.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 3.1
2024-11-16T05:39:24,822   Skipping link: No binaries permitted for biobakery-workflows: https://files.pythonhosted.org/packages/6d/4b/5e04f7dc36af3e57c685075f1b4c59cc68230483a0aa2f0c488b3ab275da/biobakery_workflows-4.0.0a1-py3-none-any.whl (from https://pypi.org/simple/biobakery-workflows/)
2024-11-16T05:39:24,822   Found link https://files.pythonhosted.org/packages/a2/f5/b37b8eac3a57544f5891fe1a34b54dabde3ea5f763603445627cfe17ec11/biobakery_workflows-4.0.0a1.tar.gz (from https://pypi.org/simple/biobakery-workflows/), version: 4.0.0a1
2024-11-16T05:39:24,823 Fetching project page and analyzing links: https://www.piwheels.org/simple/biobakery-workflows/
2024-11-16T05:39:24,824 Getting page https://www.piwheels.org/simple/biobakery-workflows/
2024-11-16T05:39:24,825 Found index url https://www.piwheels.org/simple/
2024-11-16T05:39:24,991 Fetched page https://www.piwheels.org/simple/biobakery-workflows/ as text/html
2024-11-16T05:39:24,996   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.1-py3-none-any.whl#sha256=cd6f19db7a54407ce0596dcf273e53cf5a3221255d6ac9092e646bbdf7a653ed (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:24,997   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.0.0a7-py3-none-any.whl#sha256=3dc1f34656c0d1c4390b9102b73ec613ae32bad3d1b399a6a572c9c21af41acc (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:24,998   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.0.0a6-py3-none-any.whl#sha256=5f6ddf07d2fac43e5e1a8d91605685b4d40f2db68249c5bde31d82624791224c (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:24,999   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.0.0a5-py3-none-any.whl#sha256=f0f19ebf792c6fbafa6ac65f1e16fb0429229b5e96a06cf2514076b48d2cc5bc (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:24,999   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.0.0a4-py3-none-any.whl#sha256=509d19450e3f6b166364946f806b53bd7de79de40d162b3d324d08593f5bd485 (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:24,999   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.0.0a3-py3-none-any.whl#sha256=ad9ffc894e7466552722b0710d1a9ff4b94c909223e15ed7cabf77585e7c98e8 (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,000   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.0.0a2-py3-none-any.whl#sha256=3ae10419c8da72a9032a4c12961ac09648af55ba3e53b661977cf63df554fc5d (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,000   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.0.0a1-py3-none-any.whl#sha256=6f4ad76cb90973255601b0093f97ec00f167a9defbec22f60264a81b9a253167 (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,001   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-3.0.0a0-py3-none-any.whl#sha256=1b314f9d4225c20c30273ae511ed759e5d1b3575b29ebd826adab7667c3fd643 (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,001   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-0.15.1-py3-none-any.whl#sha256=399aa551616482f671eacac02aeeb63dec4ac6f92d6c324467e9e246070f9cba (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,002   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-0.15.0-py3-none-any.whl#sha256=ac829f9fcaf1a375a9739e0a6b88ecc149c73082776812db23d8544251bab942 (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,003   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-0.14.3-py3-none-any.whl#sha256=3f74604a69b5c3f160a924bd498fc597eaaaf24a39018c6089780de28982e15c (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,003   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-0.14.2-py3-none-any.whl#sha256=46111f41748ec6a49bc8839ab8009eced384bf3b5553fb70372eae4b0c5000b3 (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,004   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-0.14.1-py3-none-any.whl#sha256=a3c48f9e9490ee207b75b0ab2391fa140e8999984120fd2118b5760742dabb75 (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,004   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-0.13.5-py3-none-any.whl#sha256=76f724149bc828bd0955fec0c86101b6f4e74059294ca82c125ac1409b41fd8f (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,005   Skipping link: No binaries permitted for biobakery-workflows: https://www.piwheels.org/simple/biobakery-workflows/biobakery_workflows-0.13.4-py3-none-any.whl#sha256=2a4c6e3a616edccbac0c9c4e21c61473be1830c94820aead37a54885d755dfa5 (from https://www.piwheels.org/simple/biobakery-workflows/)
2024-11-16T05:39:25,006 Skipping link: not a file: https://www.piwheels.org/simple/biobakery-workflows/
2024-11-16T05:39:25,006 Skipping link: not a file: https://pypi.org/simple/biobakery-workflows/
2024-11-16T05:39:25,028 Given no hashes to check 1 links for project 'biobakery-workflows': discarding no candidates
2024-11-16T05:39:25,030 Collecting biobakery-workflows==4.0.0a1
2024-11-16T05:39:25,032   Created temporary directory: /tmp/pip-unpack-mi1fie03
2024-11-16T05:39:25,270   Downloading biobakery_workflows-4.0.0a1.tar.gz (45.9 MB)
2024-11-16T05:39:41,759   Added biobakery-workflows==4.0.0a1 from https://files.pythonhosted.org/packages/a2/f5/b37b8eac3a57544f5891fe1a34b54dabde3ea5f763603445627cfe17ec11/biobakery_workflows-4.0.0a1.tar.gz to build tracker '/tmp/pip-build-tracker-iy_y4fyl'
2024-11-16T05:39:41,763   Running setup.py (path:/tmp/pip-wheel-nqg7op_8/biobakery-workflows_4da002643c5648fbb949b2c01a989098/setup.py) egg_info for package biobakery-workflows
2024-11-16T05:39:41,765   Created temporary directory: /tmp/pip-pip-egg-info-7o116i6m
2024-11-16T05:39:41,765   Preparing metadata (setup.py): started
2024-11-16T05:39:41,766   Running command python setup.py egg_info
2024-11-16T05:39:46,761   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
2024-11-16T05:39:46,762     warnings.warn(msg)
2024-11-16T05:39:57,284   running egg_info
2024-11-16T05:39:57,324   creating /tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info
2024-11-16T05:39:57,325   writing /tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info/PKG-INFO
2024-11-16T05:39:57,330   writing dependency_links to /tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info/dependency_links.txt
2024-11-16T05:39:57,332   writing entry points to /tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info/entry_points.txt
2024-11-16T05:39:57,334   writing requirements to /tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info/requires.txt
2024-11-16T05:39:57,336   writing top-level names to /tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info/top_level.txt
2024-11-16T05:39:57,338   writing manifest file '/tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info/SOURCES.txt'
2024-11-16T05:39:57,513   reading manifest file '/tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info/SOURCES.txt'
2024-11-16T05:39:57,515   reading manifest template 'MANIFEST.in'
2024-11-16T05:39:57,528   adding license file 'LICENSE'
2024-11-16T05:39:57,535   writing manifest file '/tmp/pip-pip-egg-info-7o116i6m/biobakery_workflows.egg-info/SOURCES.txt'
2024-11-16T05:39:57,644   Preparing metadata (setup.py): finished with status 'done'
2024-11-16T05:39:57,649   Source in /tmp/pip-wheel-nqg7op_8/biobakery-workflows_4da002643c5648fbb949b2c01a989098 has version 4.0.0a1, which satisfies requirement biobakery-workflows==4.0.0a1 from https://files.pythonhosted.org/packages/a2/f5/b37b8eac3a57544f5891fe1a34b54dabde3ea5f763603445627cfe17ec11/biobakery_workflows-4.0.0a1.tar.gz
2024-11-16T05:39:57,651   Removed biobakery-workflows==4.0.0a1 from https://files.pythonhosted.org/packages/a2/f5/b37b8eac3a57544f5891fe1a34b54dabde3ea5f763603445627cfe17ec11/biobakery_workflows-4.0.0a1.tar.gz from build tracker '/tmp/pip-build-tracker-iy_y4fyl'
2024-11-16T05:39:57,656 Created temporary directory: /tmp/pip-unpack-_5k4ed95
2024-11-16T05:39:57,658 Created temporary directory: /tmp/pip-unpack-omd84ttf
2024-11-16T05:39:57,658 Building wheels for collected packages: biobakery-workflows
2024-11-16T05:39:57,664   Created temporary directory: /tmp/pip-wheel-qh_d1olp
2024-11-16T05:39:57,664   Building wheel for biobakery-workflows (setup.py): started
2024-11-16T05:39:57,665   Destination directory: /tmp/pip-wheel-qh_d1olp
2024-11-16T05:39:57,666   Running command python setup.py bdist_wheel
2024-11-16T05:39:58,203   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/dist.py:261: UserWarning: Unknown distribution option: 'test_suite'
2024-11-16T05:39:58,203     warnings.warn(msg)
2024-11-16T05:40:00,152   running bdist_wheel
2024-11-16T05:40:01,227   running build
2024-11-16T05:40:01,227   running build_py
2024-11-16T05:40:01,262   creating build/lib/tests
2024-11-16T05:40:01,265   copying tests/test_utilities.py -> build/lib/tests
2024-11-16T05:40:01,270   copying tests/__init__.py -> build/lib/tests
2024-11-16T05:40:01,273   creating build/lib/biobakery_workflows
2024-11-16T05:40:01,274   copying biobakery_workflows/biobakery_workflows_databases.py -> build/lib/biobakery_workflows
2024-11-16T05:40:01,277   copying biobakery_workflows/visualizations.py -> build/lib/biobakery_workflows
2024-11-16T05:40:01,282   copying biobakery_workflows/biobakery_workflows.py -> build/lib/biobakery_workflows
2024-11-16T05:40:01,285   copying biobakery_workflows/biobakery_workflows_scripts.py -> build/lib/biobakery_workflows
2024-11-16T05:40:01,287   copying biobakery_workflows/__init__.py -> build/lib/biobakery_workflows
2024-11-16T05:40:01,289   copying biobakery_workflows/utilities.py -> build/lib/biobakery_workflows
2024-11-16T05:40:01,298   copying biobakery_workflows/config.py -> build/lib/biobakery_workflows
2024-11-16T05:40:01,300   copying biobakery_workflows/files.py -> build/lib/biobakery_workflows
2024-11-16T05:40:01,304   creating build/lib/biobakery_workflows/data
2024-11-16T05:40:01,306   copying biobakery_workflows/data/__init__.py -> build/lib/biobakery_workflows/data
2024-11-16T05:40:01,310   creating build/lib/biobakery_workflows/tasks
2024-11-16T05:40:01,311   copying biobakery_workflows/tasks/general.py -> build/lib/biobakery_workflows/tasks
2024-11-16T05:40:01,316   copying biobakery_workflows/tasks/__init__.py -> build/lib/biobakery_workflows/tasks
2024-11-16T05:40:01,318   copying biobakery_workflows/tasks/shotgun.py -> build/lib/biobakery_workflows/tasks
2024-11-16T05:40:01,322   copying biobakery_workflows/tasks/sixteen_s.py -> build/lib/biobakery_workflows/tasks
2024-11-16T05:40:01,326   copying biobakery_workflows/tasks/dadatwo.py -> build/lib/biobakery_workflows/tasks
2024-11-16T05:40:01,337   creating build/lib/biobakery_workflows/workflows
2024-11-16T05:40:01,338   copying biobakery_workflows/workflows/16s.py -> build/lib/biobakery_workflows/workflows
2024-11-16T05:40:01,343   copying biobakery_workflows/workflows/wmgx.py -> build/lib/biobakery_workflows/workflows
2024-11-16T05:40:01,346   copying biobakery_workflows/workflows/wmgx_wmtx.py -> build/lib/biobakery_workflows/workflows
2024-11-16T05:40:01,349   copying biobakery_workflows/workflows/vis.py -> build/lib/biobakery_workflows/workflows
2024-11-16T05:40:01,352   copying biobakery_workflows/workflows/stats.py -> build/lib/biobakery_workflows/workflows
2024-11-16T05:40:01,356   copying biobakery_workflows/workflows/isolate_assembly.py -> build/lib/biobakery_workflows/workflows
2024-11-16T05:40:01,359   creating build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,361   copying biobakery_workflows/document_templates/read_count_usearch.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,363   copying biobakery_workflows/document_templates/picard.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,366   copying biobakery_workflows/document_templates/stats_mantel_plots.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,369   copying biobakery_workflows/document_templates/quality_control_dada2.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,372   copying biobakery_workflows/document_templates/read_count_dada2.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,375   copying biobakery_workflows/document_templates/quality_control_paired_dna.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,378   copying biobakery_workflows/document_templates/stats.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,381   copying biobakery_workflows/document_templates/universal_vis.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,383   copying biobakery_workflows/document_templates/quality_control_single_dna.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,386   copying biobakery_workflows/document_templates/taxonomy.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,391   copying biobakery_workflows/document_templates/stats_permanova.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,394   copying biobakery_workflows/document_templates/stats_halla.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,396   copying biobakery_workflows/document_templates/stats_maaslin_stratified.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,399   copying biobakery_workflows/document_templates/workflow_info.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,403   copying biobakery_workflows/document_templates/16S.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,407   copying biobakery_workflows/document_templates/functional_dna.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,410   copying biobakery_workflows/document_templates/stats_maaslin.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,414   copying biobakery_workflows/document_templates/quality_control_usearch.pmd -> build/lib/biobakery_workflows/document_templates
2024-11-16T05:40:01,416   copying biobakery_workflows/data/strainphlan_species_gcf.tsv -> build/lib/biobakery_workflows/data
2024-11-16T05:40:01,434   copying biobakery_workflows/data/wmgx_methods.txt -> build/lib/biobakery_workflows/data
2024-11-16T05:40:01,439   creating build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,440   copying biobakery_workflows/Rscripts/identify_primers.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,444   copying biobakery_workflows/Rscripts/const_seq_table.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,449   copying biobakery_workflows/Rscripts/strainphlan_ordination_vis.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,453   copying biobakery_workflows/Rscripts/dada2_version.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,456   copying biobakery_workflows/Rscripts/permanova_hmp2.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,460   copying biobakery_workflows/Rscripts/beta_diversity.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,464   copying biobakery_workflows/Rscripts/filter_and_trim.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,468   copying biobakery_workflows/Rscripts/phylogeny.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,472   copying biobakery_workflows/Rscripts/alpha_diversity.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,476   copying biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,480   copying biobakery_workflows/Rscripts/assign_taxonomy.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,484   copying biobakery_workflows/Rscripts/mantel_test.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,500   copying biobakery_workflows/Rscripts/merge_paired_ends.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,504   copying biobakery_workflows/Rscripts/learn_error_rates.R -> build/lib/biobakery_workflows/Rscripts
2024-11-16T05:40:01,510   running build_scripts
2024-11-16T05:40:01,510   creating build/scripts-3.11
2024-11-16T05:40:01,512   copying and adjusting biobakery_workflows/workflows/16s.py -> build/scripts-3.11
2024-11-16T05:40:01,516   copying and adjusting biobakery_workflows/workflows/wmgx.py -> build/scripts-3.11
2024-11-16T05:40:01,519   copying and adjusting biobakery_workflows/workflows/wmgx_wmtx.py -> build/scripts-3.11
2024-11-16T05:40:01,522   copying and adjusting biobakery_workflows/workflows/vis.py -> build/scripts-3.11
2024-11-16T05:40:01,531   copying and adjusting biobakery_workflows/workflows/stats.py -> build/scripts-3.11
2024-11-16T05:40:01,534   copying and adjusting biobakery_workflows/workflows/isolate_assembly.py -> build/scripts-3.11
2024-11-16T05:40:01,538   copying and adjusting biobakery_workflows/scripts/create_subsampled_demos.py -> build/scripts-3.11
2024-11-16T05:40:01,542   copying and adjusting biobakery_workflows/scripts/annotate_genome.py -> build/scripts-3.11
2024-11-16T05:40:01,545   copying and adjusting biobakery_workflows/scripts/merge_and_rename_fastq.py -> build/scripts-3.11
2024-11-16T05:40:01,551   copying and adjusting biobakery_workflows/scripts/samtools_bam2fq_paired_gzip.py -> build/scripts-3.11
2024-11-16T05:40:01,554   copying and adjusting biobakery_workflows/scripts/join_taxonomic_profiles.py -> build/scripts-3.11
2024-11-16T05:40:01,557   copying and adjusting biobakery_workflows/scripts/create_fasta_per_taxonomy_from_alignments.py -> build/scripts-3.11
2024-11-16T05:40:01,559   copying and adjusting biobakery_workflows/scripts/create_image_tile.py -> build/scripts-3.11
2024-11-16T05:40:01,561   copying and adjusting biobakery_workflows/scripts/check_fastq_format.py -> build/scripts-3.11
2024-11-16T05:40:01,564   copying biobakery_workflows/scripts/rename_data_products.py -> build/scripts-3.11
2024-11-16T05:40:01,568   copying biobakery_workflows/scripts/remove_primers.py -> build/scripts-3.11
2024-11-16T05:40:01,572   copying and adjusting biobakery_workflows/scripts/check_for_reverse_reads.py -> build/scripts-3.11
2024-11-16T05:40:01,574   copying and adjusting biobakery_workflows/scripts/reverse_compliment_barcodes.py -> build/scripts-3.11
2024-11-16T05:40:01,576   copying and adjusting biobakery_workflows/scripts/rna_dna_norm.py -> build/scripts-3.11
2024-11-16T05:40:01,579   copying biobakery_workflows/scripts/compute_species_of_interest.py -> build/scripts-3.11
2024-11-16T05:40:01,583   copying and adjusting biobakery_workflows/scripts/get_counts_from_humann_logs.py -> build/scripts-3.11
2024-11-16T05:40:01,586   copying and adjusting biobakery_workflows/scripts/remove_if_exists.py -> build/scripts-3.11
2024-11-16T05:40:01,588   copying and adjusting biobakery_workflows/scripts/create_feature_table.py -> build/scripts-3.11
2024-11-16T05:40:01,590   copying and adjusting biobakery_workflows/scripts/burst_workflow.py -> build/scripts-3.11
2024-11-16T05:40:01,593   copying and adjusting biobakery_workflows/scripts/subset_file_by_sample_id.py -> build/scripts-3.11
2024-11-16T05:40:01,595   copying and adjusting biobakery_workflows/scripts/trim_taxonomy.py -> build/scripts-3.11
2024-11-16T05:40:01,597   copying and adjusting biobakery_workflows/scripts/create_otu_tables_from_alignments.py -> build/scripts-3.11
2024-11-16T05:40:01,601   copying and adjusting biobakery_workflows/scripts/count_features.py -> build/scripts-3.11
2024-11-16T05:40:01,603   copying and adjusting biobakery_workflows/scripts/merge_fastq.py -> build/scripts-3.11
2024-11-16T05:40:01,606   copying and adjusting biobakery_workflows/scripts/demultiplex_split_index.py -> build/scripts-3.11
2024-11-16T05:40:01,608   copying and adjusting biobakery_workflows/scripts/generate_dual_barcode.py -> build/scripts-3.11
2024-11-16T05:40:01,611   copying biobakery_workflows/scripts/rename_files_to_sample_ids.py -> build/scripts-3.11
2024-11-16T05:40:01,615   copying and adjusting biobakery_workflows/scripts/rename_fastq_files.py -> build/scripts-3.11
2024-11-16T05:40:01,618   copying biobakery_workflows/scripts/anadama2_add_files_to_database.py -> build/scripts-3.11
2024-11-16T05:40:01,621   copying biobakery_workflows/scripts/pull_out_reads_by_species_metaphlan2_results.py -> build/scripts-3.11
2024-11-16T05:40:01,624   copying and adjusting biobakery_workflows/scripts/extract_orphan_reads.py -> build/scripts-3.11
2024-11-16T05:40:01,627   copying biobakery_workflows/scripts/use_seqtk_to_downsample.py -> build/scripts-3.11
2024-11-16T05:40:01,629   changing mode of build/scripts-3.11/16s.py from 644 to 755
2024-11-16T05:40:01,630   changing mode of build/scripts-3.11/wmgx.py from 644 to 755
2024-11-16T05:40:01,630   changing mode of build/scripts-3.11/wmgx_wmtx.py from 644 to 755
2024-11-16T05:40:01,631   changing mode of build/scripts-3.11/vis.py from 644 to 755
2024-11-16T05:40:01,632   changing mode of build/scripts-3.11/stats.py from 644 to 755
2024-11-16T05:40:01,632   changing mode of build/scripts-3.11/isolate_assembly.py from 644 to 755
2024-11-16T05:40:01,633   changing mode of build/scripts-3.11/create_subsampled_demos.py from 644 to 755
2024-11-16T05:40:01,633   changing mode of build/scripts-3.11/annotate_genome.py from 644 to 755
2024-11-16T05:40:01,634   changing mode of build/scripts-3.11/merge_and_rename_fastq.py from 644 to 755
2024-11-16T05:40:01,634   changing mode of build/scripts-3.11/samtools_bam2fq_paired_gzip.py from 644 to 755
2024-11-16T05:40:01,635   changing mode of build/scripts-3.11/join_taxonomic_profiles.py from 644 to 755
2024-11-16T05:40:01,635   changing mode of build/scripts-3.11/create_fasta_per_taxonomy_from_alignments.py from 644 to 755
2024-11-16T05:40:01,636   changing mode of build/scripts-3.11/create_image_tile.py from 644 to 755
2024-11-16T05:40:01,637   changing mode of build/scripts-3.11/check_fastq_format.py from 644 to 755
2024-11-16T05:40:01,638   changing mode of build/scripts-3.11/rename_data_products.py from 644 to 755
2024-11-16T05:40:01,638   changing mode of build/scripts-3.11/remove_primers.py from 644 to 755
2024-11-16T05:40:01,639   changing mode of build/scripts-3.11/check_for_reverse_reads.py from 644 to 755
2024-11-16T05:40:01,640   changing mode of build/scripts-3.11/reverse_compliment_barcodes.py from 644 to 755
2024-11-16T05:40:01,641   changing mode of build/scripts-3.11/rna_dna_norm.py from 644 to 755
2024-11-16T05:40:01,642   changing mode of build/scripts-3.11/compute_species_of_interest.py from 644 to 755
2024-11-16T05:40:01,642   changing mode of build/scripts-3.11/get_counts_from_humann_logs.py from 644 to 755
2024-11-16T05:40:01,643   changing mode of build/scripts-3.11/remove_if_exists.py from 644 to 755
2024-11-16T05:40:01,644   changing mode of build/scripts-3.11/create_feature_table.py from 644 to 755
2024-11-16T05:40:01,644   changing mode of build/scripts-3.11/burst_workflow.py from 644 to 755
2024-11-16T05:40:01,645   changing mode of build/scripts-3.11/subset_file_by_sample_id.py from 644 to 755
2024-11-16T05:40:01,646   changing mode of build/scripts-3.11/trim_taxonomy.py from 644 to 755
2024-11-16T05:40:01,646   changing mode of build/scripts-3.11/create_otu_tables_from_alignments.py from 644 to 755
2024-11-16T05:40:01,647   changing mode of build/scripts-3.11/count_features.py from 644 to 755
2024-11-16T05:40:01,648   changing mode of build/scripts-3.11/merge_fastq.py from 644 to 755
2024-11-16T05:40:01,649   changing mode of build/scripts-3.11/demultiplex_split_index.py from 644 to 755
2024-11-16T05:40:01,649   changing mode of build/scripts-3.11/generate_dual_barcode.py from 644 to 755
2024-11-16T05:40:01,650   changing mode of build/scripts-3.11/rename_files_to_sample_ids.py from 644 to 755
2024-11-16T05:40:01,651   changing mode of build/scripts-3.11/rename_fastq_files.py from 644 to 755
2024-11-16T05:40:01,652   changing mode of build/scripts-3.11/anadama2_add_files_to_database.py from 644 to 755
2024-11-16T05:40:01,653   changing mode of build/scripts-3.11/pull_out_reads_by_species_metaphlan2_results.py from 644 to 755
2024-11-16T05:40:01,653   changing mode of build/scripts-3.11/extract_orphan_reads.py from 644 to 755
2024-11-16T05:40:01,654   changing mode of build/scripts-3.11/use_seqtk_to_downsample.py from 644 to 755
2024-11-16T05:40:01,685   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2024-11-16T05:40:01,686   !!

2024-11-16T05:40:01,687           ********************************************************************************
2024-11-16T05:40:01,688           Please avoid running ``setup.py`` directly.
2024-11-16T05:40:01,689           Instead, use pypa/build, pypa/installer or other
2024-11-16T05:40:01,689           standards-based tools.

2024-11-16T05:40:01,690           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2024-11-16T05:40:01,691           ********************************************************************************

2024-11-16T05:40:01,692   !!
2024-11-16T05:40:01,693     self.initialize_options()
2024-11-16T05:40:01,718   installing to build/bdist.linux-armv7l/wheel
2024-11-16T05:40:01,718   running install
2024-11-16T05:40:01,743   running install_lib
2024-11-16T05:40:01,774   creating build/bdist.linux-armv7l/wheel
2024-11-16T05:40:01,777   creating build/bdist.linux-armv7l/wheel/tests
2024-11-16T05:40:01,779   copying build/lib/tests/test_utilities.py -> build/bdist.linux-armv7l/wheel/./tests
2024-11-16T05:40:01,783   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/./tests
2024-11-16T05:40:01,786   creating build/bdist.linux-armv7l/wheel/biobakery_workflows
2024-11-16T05:40:01,788   copying build/lib/biobakery_workflows/biobakery_workflows_databases.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows
2024-11-16T05:40:01,792   copying build/lib/biobakery_workflows/visualizations.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows
2024-11-16T05:40:01,797   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/data
2024-11-16T05:40:01,798   copying build/lib/biobakery_workflows/data/strainphlan_species_gcf.tsv -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/data
2024-11-16T05:40:01,817   copying build/lib/biobakery_workflows/data/wmgx_methods.txt -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/data
2024-11-16T05:40:01,819   copying build/lib/biobakery_workflows/data/__init__.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/data
2024-11-16T05:40:01,822   copying build/lib/biobakery_workflows/biobakery_workflows.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows
2024-11-16T05:40:01,824   copying build/lib/biobakery_workflows/biobakery_workflows_scripts.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows
2024-11-16T05:40:01,828   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2024-11-16T05:40:01,829   copying build/lib/biobakery_workflows/tasks/general.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/tasks
2024-11-16T05:40:01,832   copying build/lib/biobakery_workflows/tasks/__init__.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/tasks
2024-11-16T05:40:01,834   copying build/lib/biobakery_workflows/tasks/shotgun.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/tasks
2024-11-16T05:40:01,838   copying build/lib/biobakery_workflows/tasks/sixteen_s.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/tasks
2024-11-16T05:40:01,842   copying build/lib/biobakery_workflows/tasks/dadatwo.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/tasks
2024-11-16T05:40:01,846   copying build/lib/biobakery_workflows/__init__.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows
2024-11-16T05:40:01,848   copying build/lib/biobakery_workflows/utilities.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows
2024-11-16T05:40:01,854   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2024-11-16T05:40:01,856   copying build/lib/biobakery_workflows/Rscripts/identify_primers.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,859   copying build/lib/biobakery_workflows/Rscripts/const_seq_table.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,862   copying build/lib/biobakery_workflows/Rscripts/strainphlan_ordination_vis.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,865   copying build/lib/biobakery_workflows/Rscripts/dada2_version.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,874   copying build/lib/biobakery_workflows/Rscripts/permanova_hmp2.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,877   copying build/lib/biobakery_workflows/Rscripts/beta_diversity.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,880   copying build/lib/biobakery_workflows/Rscripts/filter_and_trim.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,882   copying build/lib/biobakery_workflows/Rscripts/phylogeny.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,885   copying build/lib/biobakery_workflows/Rscripts/alpha_diversity.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,887   copying build/lib/biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,890   copying build/lib/biobakery_workflows/Rscripts/assign_taxonomy.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,892   copying build/lib/biobakery_workflows/Rscripts/mantel_test.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,896   copying build/lib/biobakery_workflows/Rscripts/merge_paired_ends.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,899   copying build/lib/biobakery_workflows/Rscripts/learn_error_rates.R -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/Rscripts
2024-11-16T05:40:01,902   copying build/lib/biobakery_workflows/config.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows
2024-11-16T05:40:01,906   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2024-11-16T05:40:01,907   copying build/lib/biobakery_workflows/workflows/16s.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/workflows
2024-11-16T05:40:01,911   copying build/lib/biobakery_workflows/workflows/wmgx.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/workflows
2024-11-16T05:40:01,916   copying build/lib/biobakery_workflows/workflows/wmgx_wmtx.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/workflows
2024-11-16T05:40:01,921   copying build/lib/biobakery_workflows/workflows/vis.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/workflows
2024-11-16T05:40:01,926   copying build/lib/biobakery_workflows/workflows/stats.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/workflows
2024-11-16T05:40:01,930   copying build/lib/biobakery_workflows/workflows/isolate_assembly.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/workflows
2024-11-16T05:40:01,935   copying build/lib/biobakery_workflows/files.py -> build/bdist.linux-armv7l/wheel/./biobakery_workflows
2024-11-16T05:40:01,940   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2024-11-16T05:40:01,942   copying build/lib/biobakery_workflows/document_templates/read_count_usearch.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,945   copying build/lib/biobakery_workflows/document_templates/picard.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,948   copying build/lib/biobakery_workflows/document_templates/stats_mantel_plots.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,950   copying build/lib/biobakery_workflows/document_templates/quality_control_dada2.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,954   copying build/lib/biobakery_workflows/document_templates/read_count_dada2.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,957   copying build/lib/biobakery_workflows/document_templates/quality_control_paired_dna.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,959   copying build/lib/biobakery_workflows/document_templates/stats.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,962   copying build/lib/biobakery_workflows/document_templates/universal_vis.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,966   copying build/lib/biobakery_workflows/document_templates/quality_control_single_dna.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,969   copying build/lib/biobakery_workflows/document_templates/taxonomy.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,972   copying build/lib/biobakery_workflows/document_templates/stats_permanova.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,975   copying build/lib/biobakery_workflows/document_templates/stats_halla.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,978   copying build/lib/biobakery_workflows/document_templates/stats_maaslin_stratified.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,981   copying build/lib/biobakery_workflows/document_templates/workflow_info.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,983   copying build/lib/biobakery_workflows/document_templates/16S.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,987   copying build/lib/biobakery_workflows/document_templates/functional_dna.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,990   copying build/lib/biobakery_workflows/document_templates/stats_maaslin.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,993   copying build/lib/biobakery_workflows/document_templates/quality_control_usearch.pmd -> build/bdist.linux-armv7l/wheel/./biobakery_workflows/document_templates
2024-11-16T05:40:01,995   running install_data
2024-11-16T05:40:02,041   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data
2024-11-16T05:40:02,044   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,045   copying images/tutorial_taxa_barplot.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,052   copying images/4005903235-DADA2Workflow_75percent.jpg -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,056   copying images/tutorial_halla_heatmap.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,063   copying images/2782656604-isolate_workflow.jpg -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,068   copying images/4071512812-wms_wtx_workflow.jpg -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,073   copying images/tutorial_pcoa.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,084   copying images/tutorial_maaslin_heatmap.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,090   copying images/tutorial_alpha_diversity.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,093   copying images/tutorial_table_of_contents.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,097   copying images/wms_workflow.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,102   copying images/tutoral_workflow_info.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,107   copying images/tutorial_pathway_heatmap.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,112   copying images/1618113365-16s_workflow_with_fasttree_merge_truncate_filter.jpg -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,117   copying images/tutorial_mantel_test.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,120   copying images/tutorial_halla_heatmap_metadata.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,126   copying images/tutorial_qc_barplot.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,130   copying images/tutorial_humann_stratified_barplot.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,135   copying images/tutorial_permanova.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/images
2024-11-16T05:40:02,139   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/input
2024-11-16T05:40:02,141   copying examples/tutorial/input/LV20R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/input
2024-11-16T05:40:02,244   copying examples/tutorial/input/HD32R1_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/input
2024-11-16T05:40:02,329   copying examples/tutorial/input/LD96R2_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/input
2024-11-16T05:40:02,482   copying examples/tutorial/input/HD42R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/input
2024-11-16T05:40:02,524   copying examples/tutorial/input/LV16R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/input
2024-11-16T05:40:05,103   copying examples/tutorial/input/HD48R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/input
2024-11-16T05:40:05,156   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2024-11-16T05:40:05,158   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2024-11-16T05:40:05,226   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2024-11-16T05:40:05,229   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.3.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2024-11-16T05:40:05,231   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.4.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2024-11-16T05:40:05,234   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2024-11-16T05:40:05,297   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2024-11-16T05:40:05,301   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2024-11-16T05:40:05,303   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2024-11-16T05:40:05,385   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.4.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2024-11-16T05:40:05,388   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2024-11-16T05:40:05,391   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2024-11-16T05:40:05,625   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2024-11-16T05:40:05,629   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.3.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2024-11-16T05:40:05,630   running install_egg_info
2024-11-16T05:40:05,723   running egg_info
2024-11-16T05:40:06,406   writing biobakery_workflows.egg-info/PKG-INFO
2024-11-16T05:40:06,411   writing dependency_links to biobakery_workflows.egg-info/dependency_links.txt
2024-11-16T05:40:06,414   writing entry points to biobakery_workflows.egg-info/entry_points.txt
2024-11-16T05:40:06,416   writing requirements to biobakery_workflows.egg-info/requires.txt
2024-11-16T05:40:06,418   writing top-level names to biobakery_workflows.egg-info/top_level.txt
2024-11-16T05:40:06,489   reading manifest file 'biobakery_workflows.egg-info/SOURCES.txt'
2024-11-16T05:40:06,504   reading manifest template 'MANIFEST.in'
2024-11-16T05:40:06,515   adding license file 'LICENSE'
2024-11-16T05:40:06,524   writing manifest file 'biobakery_workflows.egg-info/SOURCES.txt'
2024-11-16T05:40:06,526   Copying biobakery_workflows.egg-info to build/bdist.linux-armv7l/wheel/./biobakery_workflows-4.0.0a1-py3.11.egg-info
2024-11-16T05:40:06,546   running install_scripts
2024-11-16T05:40:06,547   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,549   copying build/scripts-3.11/create_subsampled_demos.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,552   copying build/scripts-3.11/annotate_genome.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,555   copying build/scripts-3.11/merge_and_rename_fastq.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,558   copying build/scripts-3.11/samtools_bam2fq_paired_gzip.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,560   copying build/scripts-3.11/join_taxonomic_profiles.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,563   copying build/scripts-3.11/create_fasta_per_taxonomy_from_alignments.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,566   copying build/scripts-3.11/create_image_tile.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,569   copying build/scripts-3.11/check_fastq_format.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,572   copying build/scripts-3.11/16s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,575   copying build/scripts-3.11/rename_data_products.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,578   copying build/scripts-3.11/remove_primers.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,580   copying build/scripts-3.11/check_for_reverse_reads.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,583   copying build/scripts-3.11/reverse_compliment_barcodes.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,585   copying build/scripts-3.11/rna_dna_norm.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,588   copying build/scripts-3.11/compute_species_of_interest.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,591   copying build/scripts-3.11/get_counts_from_humann_logs.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,596   copying build/scripts-3.11/wmgx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,599   copying build/scripts-3.11/remove_if_exists.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,602   copying build/scripts-3.11/create_feature_table.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,606   copying build/scripts-3.11/burst_workflow.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,609   copying build/scripts-3.11/subset_file_by_sample_id.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,612   copying build/scripts-3.11/trim_taxonomy.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,614   copying build/scripts-3.11/wmgx_wmtx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,617   copying build/scripts-3.11/create_otu_tables_from_alignments.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,620   copying build/scripts-3.11/vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,623   copying build/scripts-3.11/count_features.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,626   copying build/scripts-3.11/merge_fastq.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,628   copying build/scripts-3.11/demultiplex_split_index.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,631   copying build/scripts-3.11/generate_dual_barcode.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,634   copying build/scripts-3.11/rename_files_to_sample_ids.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,636   copying build/scripts-3.11/stats.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,639   copying build/scripts-3.11/rename_fastq_files.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,642   copying build/scripts-3.11/anadama2_add_files_to_database.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,644   copying build/scripts-3.11/pull_out_reads_by_species_metaphlan2_results.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,647   copying build/scripts-3.11/extract_orphan_reads.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,650   copying build/scripts-3.11/use_seqtk_to_downsample.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,652   copying build/scripts-3.11/isolate_assembly.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts
2024-11-16T05:40:06,656   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/create_subsampled_demos.py to 755
2024-11-16T05:40:06,656   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/annotate_genome.py to 755
2024-11-16T05:40:06,657   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/merge_and_rename_fastq.py to 755
2024-11-16T05:40:06,657   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/samtools_bam2fq_paired_gzip.py to 755
2024-11-16T05:40:06,658   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/join_taxonomic_profiles.py to 755
2024-11-16T05:40:06,658   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/create_fasta_per_taxonomy_from_alignments.py to 755
2024-11-16T05:40:06,658   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/create_image_tile.py to 755
2024-11-16T05:40:06,659   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/check_fastq_format.py to 755
2024-11-16T05:40:06,659   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/16s.py to 755
2024-11-16T05:40:06,660   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/rename_data_products.py to 755
2024-11-16T05:40:06,661   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/remove_primers.py to 755
2024-11-16T05:40:06,661   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/check_for_reverse_reads.py to 755
2024-11-16T05:40:06,662   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/reverse_compliment_barcodes.py to 755
2024-11-16T05:40:06,662   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/rna_dna_norm.py to 755
2024-11-16T05:40:06,663   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/compute_species_of_interest.py to 755
2024-11-16T05:40:06,663   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/get_counts_from_humann_logs.py to 755
2024-11-16T05:40:06,664   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/wmgx.py to 755
2024-11-16T05:40:06,664   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/remove_if_exists.py to 755
2024-11-16T05:40:06,665   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/create_feature_table.py to 755
2024-11-16T05:40:06,665   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/burst_workflow.py to 755
2024-11-16T05:40:06,666   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/subset_file_by_sample_id.py to 755
2024-11-16T05:40:06,666   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/trim_taxonomy.py to 755
2024-11-16T05:40:06,667   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/wmgx_wmtx.py to 755
2024-11-16T05:40:06,668   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/create_otu_tables_from_alignments.py to 755
2024-11-16T05:40:06,668   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/vis.py to 755
2024-11-16T05:40:06,669   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/count_features.py to 755
2024-11-16T05:40:06,669   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/merge_fastq.py to 755
2024-11-16T05:40:06,670   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/demultiplex_split_index.py to 755
2024-11-16T05:40:06,671   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/generate_dual_barcode.py to 755
2024-11-16T05:40:06,671   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/rename_files_to_sample_ids.py to 755
2024-11-16T05:40:06,672   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/stats.py to 755
2024-11-16T05:40:06,672   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/rename_fastq_files.py to 755
2024-11-16T05:40:06,673   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/anadama2_add_files_to_database.py to 755
2024-11-16T05:40:06,673   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/pull_out_reads_by_species_metaphlan2_results.py to 755
2024-11-16T05:40:06,674   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/extract_orphan_reads.py to 755
2024-11-16T05:40:06,674   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/use_seqtk_to_downsample.py to 755
2024-11-16T05:40:06,675   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.data/scripts/isolate_assembly.py to 755
2024-11-16T05:40:06,691   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-4.0.0a1.dist-info/WHEEL
2024-11-16T05:40:06,694   creating '/tmp/pip-wheel-qh_d1olp/biobakery_workflows-4.0.0a1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2024-11-16T05:40:06,696   adding 'biobakery_workflows/__init__.py'
2024-11-16T05:40:06,698   adding 'biobakery_workflows/biobakery_workflows.py'
2024-11-16T05:40:06,700   adding 'biobakery_workflows/biobakery_workflows_databases.py'
2024-11-16T05:40:06,702   adding 'biobakery_workflows/biobakery_workflows_scripts.py'
2024-11-16T05:40:06,703   adding 'biobakery_workflows/config.py'
2024-11-16T05:40:06,705   adding 'biobakery_workflows/files.py'
2024-11-16T05:40:06,719   adding 'biobakery_workflows/utilities.py'
2024-11-16T05:40:06,726   adding 'biobakery_workflows/visualizations.py'
2024-11-16T05:40:06,729   adding 'biobakery_workflows/Rscripts/alpha_diversity.R'
2024-11-16T05:40:06,730   adding 'biobakery_workflows/Rscripts/assign_taxonomy.R'
2024-11-16T05:40:06,732   adding 'biobakery_workflows/Rscripts/beta_diversity.R'
2024-11-16T05:40:06,734   adding 'biobakery_workflows/Rscripts/const_seq_table.R'
2024-11-16T05:40:06,735   adding 'biobakery_workflows/Rscripts/dada2_version.R'
2024-11-16T05:40:06,736   adding 'biobakery_workflows/Rscripts/filter_and_trim.R'
2024-11-16T05:40:06,738   adding 'biobakery_workflows/Rscripts/identify_primers.R'
2024-11-16T05:40:06,739   adding 'biobakery_workflows/Rscripts/learn_error_rates.R'
2024-11-16T05:40:06,741   adding 'biobakery_workflows/Rscripts/mantel_test.R'
2024-11-16T05:40:06,743   adding 'biobakery_workflows/Rscripts/merge_paired_ends.R'
2024-11-16T05:40:06,746   adding 'biobakery_workflows/Rscripts/permanova_hmp2.R'
2024-11-16T05:40:06,747   adding 'biobakery_workflows/Rscripts/phylogeny.R'
2024-11-16T05:40:06,748   adding 'biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R'
2024-11-16T05:40:06,750   adding 'biobakery_workflows/Rscripts/strainphlan_ordination_vis.R'
2024-11-16T05:40:06,752   adding 'biobakery_workflows/data/__init__.py'
2024-11-16T05:40:06,832   adding 'biobakery_workflows/data/strainphlan_species_gcf.tsv'
2024-11-16T05:40:06,838   adding 'biobakery_workflows/data/wmgx_methods.txt'
2024-11-16T05:40:06,840   adding 'biobakery_workflows/document_templates/16S.pmd'
2024-11-16T05:40:06,843   adding 'biobakery_workflows/document_templates/functional_dna.pmd'
2024-11-16T05:40:06,844   adding 'biobakery_workflows/document_templates/picard.pmd'
2024-11-16T05:40:06,847   adding 'biobakery_workflows/document_templates/quality_control_dada2.pmd'
2024-11-16T05:40:06,848   adding 'biobakery_workflows/document_templates/quality_control_paired_dna.pmd'
2024-11-16T05:40:06,850   adding 'biobakery_workflows/document_templates/quality_control_single_dna.pmd'
2024-11-16T05:40:06,851   adding 'biobakery_workflows/document_templates/quality_control_usearch.pmd'
2024-11-16T05:40:06,852   adding 'biobakery_workflows/document_templates/read_count_dada2.pmd'
2024-11-16T05:40:06,854   adding 'biobakery_workflows/document_templates/read_count_usearch.pmd'
2024-11-16T05:40:06,855   adding 'biobakery_workflows/document_templates/stats.pmd'
2024-11-16T05:40:06,856   adding 'biobakery_workflows/document_templates/stats_halla.pmd'
2024-11-16T05:40:06,858   adding 'biobakery_workflows/document_templates/stats_maaslin.pmd'
2024-11-16T05:40:06,859   adding 'biobakery_workflows/document_templates/stats_maaslin_stratified.pmd'
2024-11-16T05:40:06,860   adding 'biobakery_workflows/document_templates/stats_mantel_plots.pmd'
2024-11-16T05:40:06,862   adding 'biobakery_workflows/document_templates/stats_permanova.pmd'
2024-11-16T05:40:06,864   adding 'biobakery_workflows/document_templates/taxonomy.pmd'
2024-11-16T05:40:06,866   adding 'biobakery_workflows/document_templates/universal_vis.pmd'
2024-11-16T05:40:06,867   adding 'biobakery_workflows/document_templates/workflow_info.pmd'
2024-11-16T05:40:06,868   adding 'biobakery_workflows/tasks/__init__.py'
2024-11-16T05:40:06,871   adding 'biobakery_workflows/tasks/dadatwo.py'
2024-11-16T05:40:06,873   adding 'biobakery_workflows/tasks/general.py'
2024-11-16T05:40:06,880   adding 'biobakery_workflows/tasks/shotgun.py'
2024-11-16T05:40:06,885   adding 'biobakery_workflows/tasks/sixteen_s.py'
2024-11-16T05:40:06,888   adding 'biobakery_workflows/workflows/16s.py'
2024-11-16T05:40:06,890   adding 'biobakery_workflows/workflows/isolate_assembly.py'
2024-11-16T05:40:06,892   adding 'biobakery_workflows/workflows/stats.py'
2024-11-16T05:40:06,894   adding 'biobakery_workflows/workflows/vis.py'
2024-11-16T05:40:06,896   adding 'biobakery_workflows/workflows/wmgx.py'
2024-11-16T05:40:06,898   adding 'biobakery_workflows/workflows/wmgx_wmtx.py'
2024-11-16T05:40:06,910   adding 'biobakery_workflows-4.0.0a1.data/data/images/1618113365-16s_workflow_with_fasttree_merge_truncate_filter.jpg'
2024-11-16T05:40:06,914   adding 'biobakery_workflows-4.0.0a1.data/data/images/2782656604-isolate_workflow.jpg'
2024-11-16T05:40:06,920   adding 'biobakery_workflows-4.0.0a1.data/data/images/4005903235-DADA2Workflow_75percent.jpg'
2024-11-16T05:40:06,925   adding 'biobakery_workflows-4.0.0a1.data/data/images/4071512812-wms_wtx_workflow.jpg'
2024-11-16T05:40:06,929   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutoral_workflow_info.png'
2024-11-16T05:40:06,931   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_alpha_diversity.png'
2024-11-16T05:40:06,950   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_halla_heatmap.png'
2024-11-16T05:40:06,965   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_halla_heatmap_metadata.png'
2024-11-16T05:40:06,977   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_humann_stratified_barplot.png'
2024-11-16T05:40:06,991   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_maaslin_heatmap.png'
2024-11-16T05:40:06,995   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_mantel_test.png'
2024-11-16T05:40:07,004   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_pathway_heatmap.png'
2024-11-16T05:40:07,036   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_pcoa.png'
2024-11-16T05:40:07,041   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_permanova.png'
2024-11-16T05:40:07,044   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_qc_barplot.png'
2024-11-16T05:40:07,047   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_table_of_contents.png'
2024-11-16T05:40:07,057   adding 'biobakery_workflows-4.0.0a1.data/data/images/tutorial_taxa_barplot.png'
2024-11-16T05:40:07,068   adding 'biobakery_workflows-4.0.0a1.data/data/images/wms_workflow.png'
2024-11-16T05:40:07,419   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/input/HD32R1_subsample.fastq.gz'
2024-11-16T05:40:07,695   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/input/HD42R4_subsample.fastq.gz'
2024-11-16T05:40:08,038   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/input/HD48R4_subsample.fastq.gz'
2024-11-16T05:40:09,118   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/input/LD96R2_subsample.fastq.gz'
2024-11-16T05:40:10,198   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/input/LV16R4_subsample.fastq.gz'
2024-11-16T05:40:10,867   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/input/LV20R4_subsample.fastq.gz'
2024-11-16T05:40:11,043   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.1.bt2'
2024-11-16T05:40:11,073   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.2.bt2'
2024-11-16T05:40:11,075   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.3.bt2'
2024-11-16T05:40:11,078   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.4.bt2'
2024-11-16T05:40:11,218   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.1.bt2'
2024-11-16T05:40:11,517   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.2.bt2'
2024-11-16T05:40:11,629   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.1.bt2'
2024-11-16T05:40:11,659   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.2.bt2'
2024-11-16T05:40:11,661   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.3.bt2'
2024-11-16T05:40:11,664   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.4.bt2'
2024-11-16T05:40:11,775   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.1.bt2'
2024-11-16T05:40:11,806   adding 'biobakery_workflows-4.0.0a1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.2.bt2'
2024-11-16T05:40:11,810   adding 'biobakery_workflows-4.0.0a1.data/scripts/16s.py'
2024-11-16T05:40:11,812   adding 'biobakery_workflows-4.0.0a1.data/scripts/anadama2_add_files_to_database.py'
2024-11-16T05:40:11,813   adding 'biobakery_workflows-4.0.0a1.data/scripts/annotate_genome.py'
2024-11-16T05:40:11,815   adding 'biobakery_workflows-4.0.0a1.data/scripts/burst_workflow.py'
2024-11-16T05:40:11,817   adding 'biobakery_workflows-4.0.0a1.data/scripts/check_fastq_format.py'
2024-11-16T05:40:11,819   adding 'biobakery_workflows-4.0.0a1.data/scripts/check_for_reverse_reads.py'
2024-11-16T05:40:11,821   adding 'biobakery_workflows-4.0.0a1.data/scripts/compute_species_of_interest.py'
2024-11-16T05:40:11,823   adding 'biobakery_workflows-4.0.0a1.data/scripts/count_features.py'
2024-11-16T05:40:11,825   adding 'biobakery_workflows-4.0.0a1.data/scripts/create_fasta_per_taxonomy_from_alignments.py'
2024-11-16T05:40:11,827   adding 'biobakery_workflows-4.0.0a1.data/scripts/create_feature_table.py'
2024-11-16T05:40:11,829   adding 'biobakery_workflows-4.0.0a1.data/scripts/create_image_tile.py'
2024-11-16T05:40:11,831   adding 'biobakery_workflows-4.0.0a1.data/scripts/create_otu_tables_from_alignments.py'
2024-11-16T05:40:11,834   adding 'biobakery_workflows-4.0.0a1.data/scripts/create_subsampled_demos.py'
2024-11-16T05:40:11,837   adding 'biobakery_workflows-4.0.0a1.data/scripts/demultiplex_split_index.py'
2024-11-16T05:40:11,838   adding 'biobakery_workflows-4.0.0a1.data/scripts/extract_orphan_reads.py'
2024-11-16T05:40:11,841   adding 'biobakery_workflows-4.0.0a1.data/scripts/generate_dual_barcode.py'
2024-11-16T05:40:11,843   adding 'biobakery_workflows-4.0.0a1.data/scripts/get_counts_from_humann_logs.py'
2024-11-16T05:40:11,845   adding 'biobakery_workflows-4.0.0a1.data/scripts/isolate_assembly.py'
2024-11-16T05:40:11,847   adding 'biobakery_workflows-4.0.0a1.data/scripts/join_taxonomic_profiles.py'
2024-11-16T05:40:11,849   adding 'biobakery_workflows-4.0.0a1.data/scripts/merge_and_rename_fastq.py'
2024-11-16T05:40:11,851   adding 'biobakery_workflows-4.0.0a1.data/scripts/merge_fastq.py'
2024-11-16T05:40:11,853   adding 'biobakery_workflows-4.0.0a1.data/scripts/pull_out_reads_by_species_metaphlan2_results.py'
2024-11-16T05:40:11,855   adding 'biobakery_workflows-4.0.0a1.data/scripts/remove_if_exists.py'
2024-11-16T05:40:11,856   adding 'biobakery_workflows-4.0.0a1.data/scripts/remove_primers.py'
2024-11-16T05:40:11,858   adding 'biobakery_workflows-4.0.0a1.data/scripts/rename_data_products.py'
2024-11-16T05:40:11,860   adding 'biobakery_workflows-4.0.0a1.data/scripts/rename_fastq_files.py'
2024-11-16T05:40:11,862   adding 'biobakery_workflows-4.0.0a1.data/scripts/rename_files_to_sample_ids.py'
2024-11-16T05:40:11,864   adding 'biobakery_workflows-4.0.0a1.data/scripts/reverse_compliment_barcodes.py'
2024-11-16T05:40:11,866   adding 'biobakery_workflows-4.0.0a1.data/scripts/rna_dna_norm.py'
2024-11-16T05:40:11,868   adding 'biobakery_workflows-4.0.0a1.data/scripts/samtools_bam2fq_paired_gzip.py'
2024-11-16T05:40:11,871   adding 'biobakery_workflows-4.0.0a1.data/scripts/stats.py'
2024-11-16T05:40:11,873   adding 'biobakery_workflows-4.0.0a1.data/scripts/subset_file_by_sample_id.py'
2024-11-16T05:40:11,875   adding 'biobakery_workflows-4.0.0a1.data/scripts/trim_taxonomy.py'
2024-11-16T05:40:11,877   adding 'biobakery_workflows-4.0.0a1.data/scripts/use_seqtk_to_downsample.py'
2024-11-16T05:40:11,879   adding 'biobakery_workflows-4.0.0a1.data/scripts/vis.py'
2024-11-16T05:40:11,882   adding 'biobakery_workflows-4.0.0a1.data/scripts/wmgx.py'
2024-11-16T05:40:11,884   adding 'biobakery_workflows-4.0.0a1.data/scripts/wmgx_wmtx.py'
2024-11-16T05:40:11,888   adding 'tests/__init__.py'
2024-11-16T05:40:11,891   adding 'tests/test_utilities.py'
2024-11-16T05:40:11,893   adding 'biobakery_workflows-4.0.0a1.dist-info/LICENSE'
2024-11-16T05:40:11,894   adding 'biobakery_workflows-4.0.0a1.dist-info/METADATA'
2024-11-16T05:40:11,896   adding 'biobakery_workflows-4.0.0a1.dist-info/WHEEL'
2024-11-16T05:40:11,898   adding 'biobakery_workflows-4.0.0a1.dist-info/entry_points.txt'
2024-11-16T05:40:11,899   adding 'biobakery_workflows-4.0.0a1.dist-info/top_level.txt'
2024-11-16T05:40:11,902   adding 'biobakery_workflows-4.0.0a1.dist-info/RECORD'
2024-11-16T05:40:13,584   removing build/bdist.linux-armv7l/wheel
2024-11-16T05:40:13,778   Building wheel for biobakery-workflows (setup.py): finished with status 'done'
2024-11-16T05:40:14,553   Created wheel for biobakery-workflows: filename=biobakery_workflows-4.0.0a1-py3-none-any.whl size=33738494 sha256=e199eaec8f39d4ae7ebc62f3c582a1b422b647d61ff04285a9138122bb6071a6
2024-11-16T05:40:14,791   Stored in directory: /tmp/pip-ephem-wheel-cache-xpiwhmnt/wheels/f2/a0/60/b6b9cedd7ed1fceaf61b6c288288d0508fd17f429bb87e9fe4
2024-11-16T05:40:15,127 Successfully built biobakery-workflows
2024-11-16T05:40:16,197 Removed build tracker: '/tmp/pip-build-tracker-iy_y4fyl'