2022-09-27T13:56:44,183 Created temporary directory: /tmp/pip-ephem-wheel-cache-t0knnld6
2022-09-27T13:56:44,189 Created temporary directory: /tmp/pip-build-tracker-vqfsywiv
2022-09-27T13:56:44,190 Initialized build tracking at /tmp/pip-build-tracker-vqfsywiv
2022-09-27T13:56:44,190 Created build tracker: /tmp/pip-build-tracker-vqfsywiv
2022-09-27T13:56:44,191 Entered build tracker: /tmp/pip-build-tracker-vqfsywiv
2022-09-27T13:56:44,192 Created temporary directory: /tmp/pip-wheel-pmkgjznk
2022-09-27T13:56:44,264 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2022-09-27T13:56:44,273 2 location(s) to search for versions of biobakery-workflows:
2022-09-27T13:56:44,273 * https://pypi.org/simple/biobakery-workflows/
2022-09-27T13:56:44,273 * https://www.piwheels.org/simple/biobakery-workflows/
2022-09-27T13:56:44,274 Fetching project page and analyzing links: https://pypi.org/simple/biobakery-workflows/
2022-09-27T13:56:44,275 Getting page https://pypi.org/simple/biobakery-workflows/
2022-09-27T13:56:44,279 Found index url https://pypi.org/simple
2022-09-27T13:56:44,479   Found link https://files.pythonhosted.org/packages/1c/b8/2d49305112ddce416e9f37d6bbd9cdd50eeda669d91954e9b4188b00aa9c/biobakery_workflows-0.3.0.tar.gz#sha256=40fb7921f8bf721b0179672ea42220e43627e2fbf2cc9ec71225f1b405406e05 (from https://pypi.org/simple/biobakery-workflows/), version: 0.3.0
2022-09-27T13:56:44,480   Found link https://files.pythonhosted.org/packages/70/7c/64769accee73cfba802fd536ca6b19990bfd444dc429038a0b0e970d4707/biobakery_workflows-0.3.1.tar.gz#sha256=8ffadeb2c57595a33a01a3f1d341191eff0dcc1acd33280496fe220ceb02ebe9 (from https://pypi.org/simple/biobakery-workflows/), version: 0.3.1
2022-09-27T13:56:44,481   Found link https://files.pythonhosted.org/packages/10/51/511c7456972a3e51fb98416e153eaaf2f2e091683763a9030bcfd9278dee/biobakery_workflows-0.9.0.tar.gz#sha256=80496a31a267472bdfc434ad52f4a38d896fece5817f87cf37f9010882d75298 (from https://pypi.org/simple/biobakery-workflows/), version: 0.9.0
2022-09-27T13:56:44,482   Found link https://files.pythonhosted.org/packages/26/56/14a401341149cc14532ab03e8e327c21518b3e03c07ab4f8b9469abc4d11/biobakery_workflows-0.12.1.tar.gz#sha256=d5f6f0a73e5e30d0fb5ef198296ac8ad7d63813e098b6963ee27b6f606d12042 (from https://pypi.org/simple/biobakery-workflows/), version: 0.12.1
2022-09-27T13:56:44,483   Found link https://files.pythonhosted.org/packages/10/5f/a627ee61e221c02dc272c5d77c2208be7f47e274f0241cc4a6052b5c17eb/biobakery_workflows-0.13.0.tar.gz#sha256=6cbf6df4e2cf77f6c8ddb21ac03137747ce1561775464eab8dc74b8b91c4b729 (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.0
2022-09-27T13:56:44,483   Found link https://files.pythonhosted.org/packages/51/63/a9f0055e5c798017111b959383b92a79d77716a8aae668353f46985f48da/biobakery_workflows-0.13.1.tar.gz#sha256=8d57bffdd3d67bef378537046f0a4c54bb855d0ae8dab8c97d027b680e9050ab (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.1
2022-09-27T13:56:44,484   Found link https://files.pythonhosted.org/packages/4b/5f/e8a487a22758156034d8a9ecd9846f10383e610780cd8b5d90ecfb32faf9/biobakery_workflows-0.13.2.tar.gz#sha256=93b5ecf1f5395149a9021516a0cc3e2a7cb2c9c4c5c1ebefc5f5822bcfdbf6b4 (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.2
2022-09-27T13:56:44,485   Found link https://files.pythonhosted.org/packages/cc/87/d006df9363f78ade3e5c766c61113ad96d18036e2cca432c6f174fa87340/biobakery_workflows-0.13.3.tar.gz#sha256=211e600d24e0ef0c654265b914b2181b92a635d2a4bbab4773c890ab5aa06574 (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.3
2022-09-27T13:56:44,486   Found link https://files.pythonhosted.org/packages/cb/c6/ff6d693a51709e1a48870184ad3390ee690fd9f240a557e373755829cb4d/biobakery_workflows-0.13.4.tar.gz#sha256=7f5d6637ca83ec1df74277110fc65bc8bc75aed5ff10c923b6f5fb15cb7fec3f (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.4
2022-09-27T13:56:44,486   Found link https://files.pythonhosted.org/packages/a8/07/8fca14b4626560e71b8c43dc209c0f6c0b028d0be5633d681fa3176c1b8d/biobakery_workflows-0.13.5.tar.gz#sha256=d755c443d58897c2514a62a2e65c2692bfe7999bab249ee6674acef6131ba68f (from https://pypi.org/simple/biobakery-workflows/), version: 0.13.5
2022-09-27T13:56:44,487   Found link https://files.pythonhosted.org/packages/e1/de/5b3da5aca1d31c8a68642e94663e3e23e037397ab6397af891ae388c95ca/biobakery_workflows-0.14.1.tar.gz#sha256=a6a4f59351e43e3a18e8b6cafa3de970af1922aaddd6cf86ba316bbdddf2a2f2 (from https://pypi.org/simple/biobakery-workflows/), version: 0.14.1
2022-09-27T13:56:44,488   Found link https://files.pythonhosted.org/packages/56/fd/8c492771a384b1ee53db56903eff6d850f5bbb3059784f5f205d5a8dc297/biobakery_workflows-0.14.2.tar.gz#sha256=7c6a539b1c673dbf96235956b51e75f5f9a66d07d4104eac92c3d1d3a56d57a5 (from https://pypi.org/simple/biobakery-workflows/), version: 0.14.2
2022-09-27T13:56:44,489   Found link https://files.pythonhosted.org/packages/97/44/dc0bdd6b40a5ea79a6b0fac53d119644ebeb61daefb3fe4756cd5eed2cea/biobakery_workflows-0.14.3.tar.gz#sha256=99d09d8ebc2689d80162ed152d8ab6d840950dd52e278d6c055a27cc5540610a (from https://pypi.org/simple/biobakery-workflows/), version: 0.14.3
2022-09-27T13:56:44,489   Found link https://files.pythonhosted.org/packages/52/24/2fcc8032cb2f3ac6e62b9f7c0fc3e23ff2eb644a7962c9e1c4ac6a717f11/biobakery_workflows-0.15.0.tar.gz#sha256=205a4711d9167e41a4fd8bb286b6650db4989e5e3a849ae64fce3138029ceb83 (from https://pypi.org/simple/biobakery-workflows/), version: 0.15.0
2022-09-27T13:56:44,490   Found link https://files.pythonhosted.org/packages/2f/4e/992ed567f8094c64e39cb5728d2f899678415ac398cc8346e1b2750d14c9/biobakery_workflows-0.15.1.tar.gz#sha256=4fa73ef5641b8b9531d4b8da09ed76a2d4d36c5cbe2a49ae257679cafd15fd5c (from https://pypi.org/simple/biobakery-workflows/), version: 0.15.1
2022-09-27T13:56:44,491   Found link https://files.pythonhosted.org/packages/f5/4c/5e631276b617f23bd0fdd6569bd5a8223936c1f4230acd48fdb28d8772be/biobakery_workflows-3.0.0a0.tar.gz#sha256=cb050a3cf356522185e8badd2bc599d1cb2d3e2d4d29b47531807b3e685bda8d (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a0
2022-09-27T13:56:44,492   Found link https://files.pythonhosted.org/packages/19/55/22b8a4c499049c4e3abeda7dbe0998e9fb773b38943c862afb64786295e9/biobakery_workflows-3.0.0a1.tar.gz#sha256=e7d1a948fd3c447665e95a10441ca7320db91aad2962a70b60ae184a37cff15a (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a1
2022-09-27T13:56:44,492   Found link https://files.pythonhosted.org/packages/6a/4d/2775b25e75bfe3c769b3ead36eff1ef3d7bb2aee8142a74492b1d3c63d70/biobakery_workflows-3.0.0a2.tar.gz#sha256=2c42fb5cbbf9bdf19a01cccb14ecf5876b69a5c1c2cb92bf4e14590c4f22a9fd (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a2
2022-09-27T13:56:44,493   Found link https://files.pythonhosted.org/packages/90/c2/6b34fa5d6bfad28790eae27778468c7092b0e29a501ba1eb6265b771cbf7/biobakery_workflows-3.0.0a3.tar.gz#sha256=de2afa9747db28482f46031dfc3192e6f170ff1fb81e4efc325cd07500862b1b (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a3
2022-09-27T13:56:44,494   Found link https://files.pythonhosted.org/packages/e9/76/ba376c1958d671c238f1198a934b117c8d133ef9b1558f82fc7f494495ef/biobakery_workflows-3.0.0a4.tar.gz#sha256=bfd73d442ed99402e61f87774b123746b6a3161574997654cdceb4bd258a5518 (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a4
2022-09-27T13:56:44,495   Found link https://files.pythonhosted.org/packages/f7/66/714144f76398d9055b80803d04c20a5dc5cc25059514786caaf7454389a0/biobakery_workflows-3.0.0a5.tar.gz#sha256=0127302c678e4fd3952efd9a6907660703907900dafe015291d6c3fd2ec2922d (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a5
2022-09-27T13:56:44,495   Found link https://files.pythonhosted.org/packages/2d/94/a35b04d3a7202fea932bffdeca372c13fc45b6d463c62dcb8293e0893e95/biobakery_workflows-3.0.0-alpha.6.tar.gz#sha256=686481c6b638fc718cd295e893cd6eae40bd7d4e2e3009862a8958f410f17242 (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0-alpha.6
2022-09-27T13:56:44,496   Found link https://files.pythonhosted.org/packages/c0/04/503cf382ef99894d05171a39ca39ee70866ce815cb369ca6b6215538df5e/biobakery_workflows-3.0.0a7.tar.gz#sha256=8819d6a110d01005d5c855a5f6a906b0a6b75e33d20b96471ae41c5ab354203f (from https://pypi.org/simple/biobakery-workflows/), version: 3.0.0a7
2022-09-27T13:56:44,497   Found link https://files.pythonhosted.org/packages/9e/7c/8b19b9e18cff1aebd3087871ce06563761d4946715f4fc28d99af7b99b07/biobakery_workflows-3.1.tar.gz#sha256=c11a00192aa0bd6a6978eabef768c483dd240281991ce2a31bfaf291fe3d0e2b (from https://pypi.org/simple/biobakery-workflows/), version: 3.1
2022-09-27T13:56:44,498 Fetching project page and analyzing links: https://www.piwheels.org/simple/biobakery-workflows/
2022-09-27T13:56:44,499 Getting page https://www.piwheels.org/simple/biobakery-workflows/
2022-09-27T13:56:44,501 Found index url https://www.piwheels.org/simple
2022-09-27T13:56:44,761   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/)
2022-09-27T13:56:44,762   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/)
2022-09-27T13:56:44,763   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/)
2022-09-27T13:56:44,763   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/)
2022-09-27T13:56:44,764   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/)
2022-09-27T13:56:44,764   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/)
2022-09-27T13:56:44,765   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/)
2022-09-27T13:56:44,766   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/)
2022-09-27T13:56:44,766   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/)
2022-09-27T13:56:44,767   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/)
2022-09-27T13:56:44,767   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/)
2022-09-27T13:56:44,768   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/)
2022-09-27T13:56:44,768   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/)
2022-09-27T13:56:44,769   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/)
2022-09-27T13:56:44,769   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/)
2022-09-27T13:56:44,770 Skipping link: not a file: https://www.piwheels.org/simple/biobakery-workflows/
2022-09-27T13:56:44,771 Skipping link: not a file: https://pypi.org/simple/biobakery-workflows/
2022-09-27T13:56:44,812 Given no hashes to check 1 links for project 'biobakery-workflows': discarding no candidates
2022-09-27T13:56:44,843 Collecting biobakery-workflows==3.1
2022-09-27T13:56:44,847   Created temporary directory: /tmp/pip-unpack-qrdh6f74
2022-09-27T13:56:47,085   Downloading biobakery_workflows-3.1.tar.gz (45.9 MB)
2022-09-27T13:57:01,860   Added biobakery-workflows==3.1 from https://files.pythonhosted.org/packages/9e/7c/8b19b9e18cff1aebd3087871ce06563761d4946715f4fc28d99af7b99b07/biobakery_workflows-3.1.tar.gz#sha256=c11a00192aa0bd6a6978eabef768c483dd240281991ce2a31bfaf291fe3d0e2b to build tracker '/tmp/pip-build-tracker-vqfsywiv'
2022-09-27T13:57:01,864   Running setup.py (path:/tmp/pip-wheel-pmkgjznk/biobakery-workflows_3aa7592ca5e8447a814aaa9614911ce2/setup.py) egg_info for package biobakery-workflows
2022-09-27T13:57:01,865   Created temporary directory: /tmp/pip-pip-egg-info-8mm6ol0k
2022-09-27T13:57:01,866   Preparing metadata (setup.py): started
2022-09-27T13:57:01,868   Running command python setup.py egg_info
2022-09-27T13:57:10,582   running egg_info
2022-09-27T13:57:10,587   creating /tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info
2022-09-27T13:57:11,305   writing /tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info/PKG-INFO
2022-09-27T13:57:11,901   writing dependency_links to /tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info/dependency_links.txt
2022-09-27T13:57:13,676   writing entry points to /tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info/entry_points.txt
2022-09-27T13:57:14,862   writing requirements to /tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info/requires.txt
2022-09-27T13:57:15,457   writing top-level names to /tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info/top_level.txt
2022-09-27T13:57:15,459   writing manifest file '/tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info/SOURCES.txt'
2022-09-27T13:57:16,634   reading manifest file '/tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info/SOURCES.txt'
2022-09-27T13:57:16,637   reading manifest template 'MANIFEST.in'
2022-09-27T13:57:16,656   adding license file 'LICENSE'
2022-09-27T13:57:16,673   writing manifest file '/tmp/pip-pip-egg-info-8mm6ol0k/biobakery_workflows.egg-info/SOURCES.txt'
2022-09-27T13:57:16,894   Preparing metadata (setup.py): finished with status 'done'
2022-09-27T13:57:16,905   Source in /tmp/pip-wheel-pmkgjznk/biobakery-workflows_3aa7592ca5e8447a814aaa9614911ce2 has version 3.1, which satisfies requirement biobakery-workflows==3.1 from https://files.pythonhosted.org/packages/9e/7c/8b19b9e18cff1aebd3087871ce06563761d4946715f4fc28d99af7b99b07/biobakery_workflows-3.1.tar.gz#sha256=c11a00192aa0bd6a6978eabef768c483dd240281991ce2a31bfaf291fe3d0e2b
2022-09-27T13:57:16,907   Removed biobakery-workflows==3.1 from https://files.pythonhosted.org/packages/9e/7c/8b19b9e18cff1aebd3087871ce06563761d4946715f4fc28d99af7b99b07/biobakery_workflows-3.1.tar.gz#sha256=c11a00192aa0bd6a6978eabef768c483dd240281991ce2a31bfaf291fe3d0e2b from build tracker '/tmp/pip-build-tracker-vqfsywiv'
2022-09-27T13:57:16,916 Created temporary directory: /tmp/pip-unpack-p7en4qir
2022-09-27T13:57:16,917 Building wheels for collected packages: biobakery-workflows
2022-09-27T13:57:16,926   Created temporary directory: /tmp/pip-wheel-t_jghu3c
2022-09-27T13:57:16,927   Building wheel for biobakery-workflows (setup.py): started
2022-09-27T13:57:16,929   Destination directory: /tmp/pip-wheel-t_jghu3c
2022-09-27T13:57:16,930   Running command python setup.py bdist_wheel
2022-09-27T13:57:25,187   running bdist_wheel
2022-09-27T13:57:25,577   running build
2022-09-27T13:57:25,578   running build_py
2022-09-27T13:57:26,324   creating build
2022-09-27T13:57:26,325   creating build/lib
2022-09-27T13:57:26,326   creating build/lib/biobakery_workflows
2022-09-27T13:57:26,328   copying biobakery_workflows/__init__.py -> build/lib/biobakery_workflows
2022-09-27T13:57:26,331   copying biobakery_workflows/config.py -> build/lib/biobakery_workflows
2022-09-27T13:57:26,335   copying biobakery_workflows/files.py -> build/lib/biobakery_workflows
2022-09-27T13:57:26,340   copying biobakery_workflows/visualizations.py -> build/lib/biobakery_workflows
2022-09-27T13:57:26,347   copying biobakery_workflows/biobakery_workflows_databases.py -> build/lib/biobakery_workflows
2022-09-27T13:57:26,352   copying biobakery_workflows/utilities.py -> build/lib/biobakery_workflows
2022-09-27T13:57:26,363   copying biobakery_workflows/biobakery_workflows_scripts.py -> build/lib/biobakery_workflows
2022-09-27T13:57:26,366   copying biobakery_workflows/biobakery_workflows.py -> build/lib/biobakery_workflows
2022-09-27T13:57:26,371   creating build/lib/tests
2022-09-27T13:57:26,372   copying tests/__init__.py -> build/lib/tests
2022-09-27T13:57:26,376   copying tests/test_utilities.py -> build/lib/tests
2022-09-27T13:57:26,383   creating build/lib/biobakery_workflows/tasks
2022-09-27T13:57:26,384   copying biobakery_workflows/tasks/sixteen_s.py -> build/lib/biobakery_workflows/tasks
2022-09-27T13:57:26,390   copying biobakery_workflows/tasks/__init__.py -> build/lib/biobakery_workflows/tasks
2022-09-27T13:57:26,393   copying biobakery_workflows/tasks/general.py -> build/lib/biobakery_workflows/tasks
2022-09-27T13:57:26,397   copying biobakery_workflows/tasks/dadatwo.py -> build/lib/biobakery_workflows/tasks
2022-09-27T13:57:26,401   copying biobakery_workflows/tasks/shotgun.py -> build/lib/biobakery_workflows/tasks
2022-09-27T13:57:26,409   creating build/lib/biobakery_workflows/data
2022-09-27T13:57:26,410   copying biobakery_workflows/data/__init__.py -> build/lib/biobakery_workflows/data
2022-09-27T13:57:26,438   creating build/lib/biobakery_workflows/workflows
2022-09-27T13:57:26,439   copying biobakery_workflows/workflows/isolate_assembly.py -> build/lib/biobakery_workflows/workflows
2022-09-27T13:57:26,444   copying biobakery_workflows/workflows/wmgx.py -> build/lib/biobakery_workflows/workflows
2022-09-27T13:57:26,449   copying biobakery_workflows/workflows/16s.py -> build/lib/biobakery_workflows/workflows
2022-09-27T13:57:26,454   copying biobakery_workflows/workflows/stats.py -> build/lib/biobakery_workflows/workflows
2022-09-27T13:57:26,459   copying biobakery_workflows/workflows/wmgx_wmtx.py -> build/lib/biobakery_workflows/workflows
2022-09-27T13:57:26,464   copying biobakery_workflows/workflows/vis.py -> build/lib/biobakery_workflows/workflows
2022-09-27T13:57:26,469   creating build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,470   copying biobakery_workflows/document_templates/read_count_usearch.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,474   copying biobakery_workflows/document_templates/stats_permanova.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,478   copying biobakery_workflows/document_templates/quality_control_usearch.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,482   copying biobakery_workflows/document_templates/functional_dna.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,487   copying biobakery_workflows/document_templates/stats.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,491   copying biobakery_workflows/document_templates/read_count_dada2.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,494   copying biobakery_workflows/document_templates/stats_halla.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,498   copying biobakery_workflows/document_templates/quality_control_dada2.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,502   copying biobakery_workflows/document_templates/quality_control_single_dna.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,506   copying biobakery_workflows/document_templates/picard.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,509   copying biobakery_workflows/document_templates/stats_maaslin_stratified.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,513   copying biobakery_workflows/document_templates/stats_maaslin.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,517   copying biobakery_workflows/document_templates/stats_mantel_plots.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,521   copying biobakery_workflows/document_templates/taxonomy.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,525   copying biobakery_workflows/document_templates/quality_control_paired_dna.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,530   copying biobakery_workflows/document_templates/workflow_info.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,533   copying biobakery_workflows/document_templates/universal_vis.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,537   copying biobakery_workflows/document_templates/16S.pmd -> build/lib/biobakery_workflows/document_templates
2022-09-27T13:57:26,542   copying biobakery_workflows/data/strainphlan_species_gcf.tsv -> build/lib/biobakery_workflows/data
2022-09-27T13:57:26,574   copying biobakery_workflows/data/wmgx_methods.txt -> build/lib/biobakery_workflows/data
2022-09-27T13:57:26,578   creating build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,580   copying biobakery_workflows/Rscripts/permanova_hmp2.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,585   copying biobakery_workflows/Rscripts/mantel_test.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,590   copying biobakery_workflows/Rscripts/dada2_version.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,594   copying biobakery_workflows/Rscripts/strainphlan_ordination_vis.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,598   copying biobakery_workflows/Rscripts/alpha_diversity.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,602   copying biobakery_workflows/Rscripts/const_seq_table.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,606   copying biobakery_workflows/Rscripts/merge_paired_ends.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,610   copying biobakery_workflows/Rscripts/assign_taxonomy.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,615   copying biobakery_workflows/Rscripts/identify_primers.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,620   copying biobakery_workflows/Rscripts/phylogeny.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,624   copying biobakery_workflows/Rscripts/filter_and_trim.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,629   copying biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,634   copying biobakery_workflows/Rscripts/beta_diversity.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,639   copying biobakery_workflows/Rscripts/learn_error_rates.R -> build/lib/biobakery_workflows/Rscripts
2022-09-27T13:57:26,648   running build_scripts
2022-09-27T13:57:26,650   creating build/scripts-3.7
2022-09-27T13:57:26,652   copying and adjusting biobakery_workflows/workflows/isolate_assembly.py -> build/scripts-3.7
2022-09-27T13:57:26,657   copying and adjusting biobakery_workflows/workflows/wmgx.py -> build/scripts-3.7
2022-09-27T13:57:26,662   copying and adjusting biobakery_workflows/workflows/16s.py -> build/scripts-3.7
2022-09-27T13:57:26,666   copying and adjusting biobakery_workflows/workflows/stats.py -> build/scripts-3.7
2022-09-27T13:57:26,671   copying and adjusting biobakery_workflows/workflows/wmgx_wmtx.py -> build/scripts-3.7
2022-09-27T13:57:26,675   copying and adjusting biobakery_workflows/workflows/vis.py -> build/scripts-3.7
2022-09-27T13:57:26,680   copying and adjusting biobakery_workflows/scripts/burst_workflow.py -> build/scripts-3.7
2022-09-27T13:57:26,684   copying and adjusting biobakery_workflows/scripts/count_features.py -> build/scripts-3.7
2022-09-27T13:57:26,688   copying and adjusting biobakery_workflows/scripts/rna_dna_norm.py -> build/scripts-3.7
2022-09-27T13:57:26,693   copying and adjusting biobakery_workflows/scripts/create_fasta_per_taxonomy_from_alignments.py -> build/scripts-3.7
2022-09-27T13:57:26,698   copying and adjusting biobakery_workflows/scripts/subset_file_by_sample_id.py -> build/scripts-3.7
2022-09-27T13:57:26,701   copying and adjusting biobakery_workflows/scripts/remove_if_exists.py -> build/scripts-3.7
2022-09-27T13:57:26,705   copying and adjusting biobakery_workflows/scripts/check_for_reverse_reads.py -> build/scripts-3.7
2022-09-27T13:57:26,708   copying and adjusting biobakery_workflows/scripts/check_fastq_format.py -> build/scripts-3.7
2022-09-27T13:57:26,712   copying and adjusting biobakery_workflows/scripts/create_subsampled_demos.py -> build/scripts-3.7
2022-09-27T13:57:26,718   copying and adjusting biobakery_workflows/scripts/create_otu_tables_from_alignments.py -> build/scripts-3.7
2022-09-27T13:57:26,723   copying and adjusting biobakery_workflows/scripts/merge_and_rename_fastq.py -> build/scripts-3.7
2022-09-27T13:57:26,728   copying and adjusting biobakery_workflows/scripts/reverse_compliment_barcodes.py -> build/scripts-3.7
2022-09-27T13:57:26,732   copying and adjusting biobakery_workflows/scripts/merge_fastq.py -> build/scripts-3.7
2022-09-27T13:57:26,735   copying biobakery_workflows/scripts/anadama2_add_files_to_database.py -> build/scripts-3.7
2022-09-27T13:57:26,740   copying biobakery_workflows/scripts/compute_species_of_interest.py -> build/scripts-3.7
2022-09-27T13:57:26,746   copying and adjusting biobakery_workflows/scripts/trim_taxonomy.py -> build/scripts-3.7
2022-09-27T13:57:26,750   copying biobakery_workflows/scripts/pull_out_reads_by_species_metaphlan2_results.py -> build/scripts-3.7
2022-09-27T13:57:26,754   copying and adjusting biobakery_workflows/scripts/join_taxonomic_profiles.py -> build/scripts-3.7
2022-09-27T13:57:26,758   copying and adjusting biobakery_workflows/scripts/get_counts_from_humann_logs.py -> build/scripts-3.7
2022-09-27T13:57:26,761   copying and adjusting biobakery_workflows/scripts/annotate_genome.py -> build/scripts-3.7
2022-09-27T13:57:26,765   copying biobakery_workflows/scripts/rename_data_products.py -> build/scripts-3.7
2022-09-27T13:57:26,769   copying and adjusting biobakery_workflows/scripts/generate_dual_barcode.py -> build/scripts-3.7
2022-09-27T13:57:26,772   copying and adjusting biobakery_workflows/scripts/rename_fastq_files.py -> build/scripts-3.7
2022-09-27T13:57:26,776   copying and adjusting biobakery_workflows/scripts/demultiplex_split_index.py -> build/scripts-3.7
2022-09-27T13:57:26,781   copying and adjusting biobakery_workflows/scripts/extract_orphan_reads.py -> build/scripts-3.7
2022-09-27T13:57:26,784   copying and adjusting biobakery_workflows/scripts/create_feature_table.py -> build/scripts-3.7
2022-09-27T13:57:26,787   copying biobakery_workflows/scripts/remove_primers.py -> build/scripts-3.7
2022-09-27T13:57:26,791   copying and adjusting biobakery_workflows/scripts/create_image_tile.py -> build/scripts-3.7
2022-09-27T13:57:26,794   copying biobakery_workflows/scripts/rename_files_to_sample_ids.py -> build/scripts-3.7
2022-09-27T13:57:26,797   changing mode of build/scripts-3.7/isolate_assembly.py from 644 to 755
2022-09-27T13:57:26,797   changing mode of build/scripts-3.7/wmgx.py from 644 to 755
2022-09-27T13:57:26,798   changing mode of build/scripts-3.7/16s.py from 644 to 755
2022-09-27T13:57:26,798   changing mode of build/scripts-3.7/stats.py from 644 to 755
2022-09-27T13:57:26,799   changing mode of build/scripts-3.7/wmgx_wmtx.py from 644 to 755
2022-09-27T13:57:26,799   changing mode of build/scripts-3.7/vis.py from 644 to 755
2022-09-27T13:57:26,799   changing mode of build/scripts-3.7/burst_workflow.py from 644 to 755
2022-09-27T13:57:26,800   changing mode of build/scripts-3.7/count_features.py from 644 to 755
2022-09-27T13:57:26,800   changing mode of build/scripts-3.7/rna_dna_norm.py from 644 to 755
2022-09-27T13:57:26,801   changing mode of build/scripts-3.7/create_fasta_per_taxonomy_from_alignments.py from 644 to 755
2022-09-27T13:57:26,801   changing mode of build/scripts-3.7/subset_file_by_sample_id.py from 644 to 755
2022-09-27T13:57:26,802   changing mode of build/scripts-3.7/remove_if_exists.py from 644 to 755
2022-09-27T13:57:26,802   changing mode of build/scripts-3.7/check_for_reverse_reads.py from 644 to 755
2022-09-27T13:57:26,803   changing mode of build/scripts-3.7/check_fastq_format.py from 644 to 755
2022-09-27T13:57:26,803   changing mode of build/scripts-3.7/create_subsampled_demos.py from 644 to 755
2022-09-27T13:57:26,804   changing mode of build/scripts-3.7/create_otu_tables_from_alignments.py from 644 to 755
2022-09-27T13:57:26,804   changing mode of build/scripts-3.7/merge_and_rename_fastq.py from 644 to 755
2022-09-27T13:57:26,804   changing mode of build/scripts-3.7/reverse_compliment_barcodes.py from 644 to 755
2022-09-27T13:57:26,805   changing mode of build/scripts-3.7/merge_fastq.py from 644 to 755
2022-09-27T13:57:26,805   changing mode of build/scripts-3.7/anadama2_add_files_to_database.py from 644 to 755
2022-09-27T13:57:26,806   changing mode of build/scripts-3.7/compute_species_of_interest.py from 644 to 755
2022-09-27T13:57:26,806   changing mode of build/scripts-3.7/trim_taxonomy.py from 644 to 755
2022-09-27T13:57:26,807   changing mode of build/scripts-3.7/pull_out_reads_by_species_metaphlan2_results.py from 644 to 755
2022-09-27T13:57:26,807   changing mode of build/scripts-3.7/join_taxonomic_profiles.py from 644 to 755
2022-09-27T13:57:26,808   changing mode of build/scripts-3.7/get_counts_from_humann_logs.py from 644 to 755
2022-09-27T13:57:26,808   changing mode of build/scripts-3.7/annotate_genome.py from 644 to 755
2022-09-27T13:57:26,809   changing mode of build/scripts-3.7/rename_data_products.py from 644 to 755
2022-09-27T13:57:26,809   changing mode of build/scripts-3.7/generate_dual_barcode.py from 644 to 755
2022-09-27T13:57:26,810   changing mode of build/scripts-3.7/rename_fastq_files.py from 644 to 755
2022-09-27T13:57:26,810   changing mode of build/scripts-3.7/demultiplex_split_index.py from 644 to 755
2022-09-27T13:57:26,810   changing mode of build/scripts-3.7/extract_orphan_reads.py from 644 to 755
2022-09-27T13:57:26,811   changing mode of build/scripts-3.7/create_feature_table.py from 644 to 755
2022-09-27T13:57:26,811   changing mode of build/scripts-3.7/remove_primers.py from 644 to 755
2022-09-27T13:57:26,812   changing mode of build/scripts-3.7/create_image_tile.py from 644 to 755
2022-09-27T13:57:26,812   changing mode of build/scripts-3.7/rename_files_to_sample_ids.py from 644 to 755
2022-09-27T13:57:27,556   /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.
2022-09-27T13:57:27,557     setuptools.SetuptoolsDeprecationWarning,
2022-09-27T13:57:28,299   installing to build/bdist.linux-armv7l/wheel
2022-09-27T13:57:28,299   running install
2022-09-27T13:57:28,360   running install_lib
2022-09-27T13:57:29,104   creating build/bdist.linux-armv7l
2022-09-27T13:57:29,104   creating build/bdist.linux-armv7l/wheel
2022-09-27T13:57:29,107   creating build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,109   copying build/lib/biobakery_workflows/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,113   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,115   copying build/lib/biobakery_workflows/document_templates/read_count_usearch.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,118   copying build/lib/biobakery_workflows/document_templates/stats_permanova.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,121   copying build/lib/biobakery_workflows/document_templates/quality_control_usearch.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,124   copying build/lib/biobakery_workflows/document_templates/functional_dna.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,129   copying build/lib/biobakery_workflows/document_templates/stats.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,132   copying build/lib/biobakery_workflows/document_templates/read_count_dada2.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,135   copying build/lib/biobakery_workflows/document_templates/stats_halla.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,138   copying build/lib/biobakery_workflows/document_templates/quality_control_dada2.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,141   copying build/lib/biobakery_workflows/document_templates/quality_control_single_dna.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,144   copying build/lib/biobakery_workflows/document_templates/picard.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,147   copying build/lib/biobakery_workflows/document_templates/stats_maaslin_stratified.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,150   copying build/lib/biobakery_workflows/document_templates/stats_maaslin.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,153   copying build/lib/biobakery_workflows/document_templates/stats_mantel_plots.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,156   copying build/lib/biobakery_workflows/document_templates/taxonomy.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,160   copying build/lib/biobakery_workflows/document_templates/quality_control_paired_dna.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,164   copying build/lib/biobakery_workflows/document_templates/workflow_info.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,167   copying build/lib/biobakery_workflows/document_templates/universal_vis.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,170   copying build/lib/biobakery_workflows/document_templates/16S.pmd -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2022-09-27T13:57:29,174   copying build/lib/biobakery_workflows/config.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,178   copying build/lib/biobakery_workflows/files.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,183   copying build/lib/biobakery_workflows/visualizations.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,190   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2022-09-27T13:57:29,191   copying build/lib/biobakery_workflows/tasks/sixteen_s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2022-09-27T13:57:29,197   copying build/lib/biobakery_workflows/tasks/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2022-09-27T13:57:29,200   copying build/lib/biobakery_workflows/tasks/general.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2022-09-27T13:57:29,204   copying build/lib/biobakery_workflows/tasks/dadatwo.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2022-09-27T13:57:29,208   copying build/lib/biobakery_workflows/tasks/shotgun.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2022-09-27T13:57:29,215   copying build/lib/biobakery_workflows/biobakery_workflows_databases.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,220   copying build/lib/biobakery_workflows/utilities.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,229   copying build/lib/biobakery_workflows/biobakery_workflows_scripts.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,232   copying build/lib/biobakery_workflows/biobakery_workflows.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2022-09-27T13:57:29,236   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/data
2022-09-27T13:57:29,238   copying build/lib/biobakery_workflows/data/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/data
2022-09-27T13:57:29,241   copying build/lib/biobakery_workflows/data/strainphlan_species_gcf.tsv -> build/bdist.linux-armv7l/wheel/biobakery_workflows/data
2022-09-27T13:57:29,278   copying build/lib/biobakery_workflows/data/wmgx_methods.txt -> build/bdist.linux-armv7l/wheel/biobakery_workflows/data
2022-09-27T13:57:29,282   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2022-09-27T13:57:29,284   copying build/lib/biobakery_workflows/workflows/isolate_assembly.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2022-09-27T13:57:29,288   copying build/lib/biobakery_workflows/workflows/wmgx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2022-09-27T13:57:29,292   copying build/lib/biobakery_workflows/workflows/16s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2022-09-27T13:57:29,297   copying build/lib/biobakery_workflows/workflows/stats.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2022-09-27T13:57:29,301   copying build/lib/biobakery_workflows/workflows/wmgx_wmtx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2022-09-27T13:57:29,305   copying build/lib/biobakery_workflows/workflows/vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2022-09-27T13:57:29,311   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,312   copying build/lib/biobakery_workflows/Rscripts/permanova_hmp2.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,318   copying build/lib/biobakery_workflows/Rscripts/mantel_test.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,323   copying build/lib/biobakery_workflows/Rscripts/dada2_version.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,326   copying build/lib/biobakery_workflows/Rscripts/strainphlan_ordination_vis.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,329   copying build/lib/biobakery_workflows/Rscripts/alpha_diversity.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,333   copying build/lib/biobakery_workflows/Rscripts/const_seq_table.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,337   copying build/lib/biobakery_workflows/Rscripts/merge_paired_ends.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,340   copying build/lib/biobakery_workflows/Rscripts/assign_taxonomy.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,344   copying build/lib/biobakery_workflows/Rscripts/identify_primers.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,347   copying build/lib/biobakery_workflows/Rscripts/phylogeny.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,351   copying build/lib/biobakery_workflows/Rscripts/filter_and_trim.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,354   copying build/lib/biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,357   copying build/lib/biobakery_workflows/Rscripts/beta_diversity.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,362   copying build/lib/biobakery_workflows/Rscripts/learn_error_rates.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2022-09-27T13:57:29,366   creating build/bdist.linux-armv7l/wheel/tests
2022-09-27T13:57:29,367   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests
2022-09-27T13:57:29,371   copying build/lib/tests/test_utilities.py -> build/bdist.linux-armv7l/wheel/tests
2022-09-27T13:57:29,375   running install_data
2022-09-27T13:57:29,506   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data
2022-09-27T13:57:29,506   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data
2022-09-27T13:57:29,508   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images
2022-09-27T13:57:29,510   copying images/tutorial_pathway_heatmap.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,519   copying images/tutorial_permanova.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,524   copying images/4071512812-wms_wtx_workflow.jpg -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,530   copying images/tutorial_mantel_test.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,535   copying images/1618113365-16s_workflow_with_fasttree_merge_truncate_filter.jpg -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,543   copying images/tutorial_humann_stratified_barplot.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,551   copying images/tutorial_taxa_barplot.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,559   copying images/tutorial_qc_barplot.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,564   copying images/tutorial_table_of_contents.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,570   copying images/tutorial_halla_heatmap.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,584   copying images/tutoral_workflow_info.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,590   copying images/tutorial_maaslin_heatmap.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,600   copying images/2782656604-isolate_workflow.jpg -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,606   copying images/tutorial_pcoa.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,630   copying images/tutorial_halla_heatmap_metadata.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,640   copying images/4005903235-DADA2Workflow_75percent.jpg -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,648   copying images/wms_workflow.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,658   copying images/tutorial_alpha_diversity.png -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/images/
2022-09-27T13:57:29,663   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial
2022-09-27T13:57:29,663   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/input
2022-09-27T13:57:29,666   copying examples/tutorial/input/HD48R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/input/
2022-09-27T13:57:29,775   copying examples/tutorial/input/LD96R2_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/input/
2022-09-27T13:57:30,243   copying examples/tutorial/input/HD32R1_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/input/
2022-09-27T13:57:30,415   copying examples/tutorial/input/LV16R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/input/
2022-09-27T13:57:30,825   copying examples/tutorial/input/LV20R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/input/
2022-09-27T13:57:31,124   copying examples/tutorial/input/HD42R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/input/
2022-09-27T13:57:31,251   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db
2022-09-27T13:57:31,251   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2022-09-27T13:57:31,253   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2022-09-27T13:57:31,469   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2022-09-27T13:57:31,473   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.4.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2022-09-27T13:57:31,478   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.3.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2022-09-27T13:57:31,481   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2022-09-27T13:57:31,485   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2022-09-27T13:57:31,699   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2022-09-27T13:57:31,701   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.4.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2022-09-27T13:57:31,706   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2022-09-27T13:57:31,922   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.3.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2022-09-27T13:57:31,926   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-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2022-09-27T13:57:32,134   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-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2022-09-27T13:57:32,139   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2022-09-27T13:57:32,144   running install_egg_info
2022-09-27T13:57:33,661   running egg_info
2022-09-27T13:57:34,394   writing biobakery_workflows.egg-info/PKG-INFO
2022-09-27T13:57:35,004   writing dependency_links to biobakery_workflows.egg-info/dependency_links.txt
2022-09-27T13:57:36,827   writing entry points to biobakery_workflows.egg-info/entry_points.txt
2022-09-27T13:57:38,094   writing requirements to biobakery_workflows.egg-info/requires.txt
2022-09-27T13:57:38,702   writing top-level names to biobakery_workflows.egg-info/top_level.txt
2022-09-27T13:57:38,877   reading manifest file 'biobakery_workflows.egg-info/SOURCES.txt'
2022-09-27T13:57:38,895   reading manifest template 'MANIFEST.in'
2022-09-27T13:57:38,912   adding license file 'LICENSE'
2022-09-27T13:57:38,935   writing manifest file 'biobakery_workflows.egg-info/SOURCES.txt'
2022-09-27T13:57:38,938   Copying biobakery_workflows.egg-info to build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1-py3.7.egg-info
2022-09-27T13:57:38,967   running install_scripts
2022-09-27T13:57:39,076   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,077   copying build/scripts-3.7/burst_workflow.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,081   copying build/scripts-3.7/isolate_assembly.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,085   copying build/scripts-3.7/count_features.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,089   copying build/scripts-3.7/rna_dna_norm.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,093   copying build/scripts-3.7/create_fasta_per_taxonomy_from_alignments.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,097   copying build/scripts-3.7/subset_file_by_sample_id.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,101   copying build/scripts-3.7/remove_if_exists.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,104   copying build/scripts-3.7/check_for_reverse_reads.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,107   copying build/scripts-3.7/check_fastq_format.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,110   copying build/scripts-3.7/wmgx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,114   copying build/scripts-3.7/create_subsampled_demos.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,119   copying build/scripts-3.7/create_otu_tables_from_alignments.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,124   copying build/scripts-3.7/merge_and_rename_fastq.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,128   copying build/scripts-3.7/reverse_compliment_barcodes.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,132   copying build/scripts-3.7/merge_fastq.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,135   copying build/scripts-3.7/16s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,139   copying build/scripts-3.7/anadama2_add_files_to_database.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,142   copying build/scripts-3.7/compute_species_of_interest.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,146   copying build/scripts-3.7/stats.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,150   copying build/scripts-3.7/trim_taxonomy.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,153   copying build/scripts-3.7/pull_out_reads_by_species_metaphlan2_results.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,157   copying build/scripts-3.7/join_taxonomic_profiles.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,161   copying build/scripts-3.7/wmgx_wmtx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,164   copying build/scripts-3.7/get_counts_from_humann_logs.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,168   copying build/scripts-3.7/annotate_genome.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,171   copying build/scripts-3.7/rename_data_products.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,174   copying build/scripts-3.7/generate_dual_barcode.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,177   copying build/scripts-3.7/rename_fastq_files.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,181   copying build/scripts-3.7/demultiplex_split_index.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,185   copying build/scripts-3.7/extract_orphan_reads.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,188   copying build/scripts-3.7/create_feature_table.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,191   copying build/scripts-3.7/vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,196   copying build/scripts-3.7/remove_primers.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,199   copying build/scripts-3.7/create_image_tile.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,202   copying build/scripts-3.7/rename_files_to_sample_ids.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts
2022-09-27T13:57:39,205   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/burst_workflow.py to 755
2022-09-27T13:57:39,205   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/isolate_assembly.py to 755
2022-09-27T13:57:39,206   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/count_features.py to 755
2022-09-27T13:57:39,206   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/rna_dna_norm.py to 755
2022-09-27T13:57:39,207   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/create_fasta_per_taxonomy_from_alignments.py to 755
2022-09-27T13:57:39,207   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/subset_file_by_sample_id.py to 755
2022-09-27T13:57:39,208   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/remove_if_exists.py to 755
2022-09-27T13:57:39,208   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/check_for_reverse_reads.py to 755
2022-09-27T13:57:39,209   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/check_fastq_format.py to 755
2022-09-27T13:57:39,209   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/wmgx.py to 755
2022-09-27T13:57:39,210   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/create_subsampled_demos.py to 755
2022-09-27T13:57:39,210   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/create_otu_tables_from_alignments.py to 755
2022-09-27T13:57:39,211   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/merge_and_rename_fastq.py to 755
2022-09-27T13:57:39,211   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/reverse_compliment_barcodes.py to 755
2022-09-27T13:57:39,211   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/merge_fastq.py to 755
2022-09-27T13:57:39,212   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/16s.py to 755
2022-09-27T13:57:39,212   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/anadama2_add_files_to_database.py to 755
2022-09-27T13:57:39,213   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/compute_species_of_interest.py to 755
2022-09-27T13:57:39,213   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/stats.py to 755
2022-09-27T13:57:39,214   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/trim_taxonomy.py to 755
2022-09-27T13:57:39,214   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/pull_out_reads_by_species_metaphlan2_results.py to 755
2022-09-27T13:57:39,215   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/join_taxonomic_profiles.py to 755
2022-09-27T13:57:39,215   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/wmgx_wmtx.py to 755
2022-09-27T13:57:39,215   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/get_counts_from_humann_logs.py to 755
2022-09-27T13:57:39,216   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/annotate_genome.py to 755
2022-09-27T13:57:39,216   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/rename_data_products.py to 755
2022-09-27T13:57:39,217   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/generate_dual_barcode.py to 755
2022-09-27T13:57:39,217   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/rename_fastq_files.py to 755
2022-09-27T13:57:39,218   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/demultiplex_split_index.py to 755
2022-09-27T13:57:39,218   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/extract_orphan_reads.py to 755
2022-09-27T13:57:39,219   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/create_feature_table.py to 755
2022-09-27T13:57:39,219   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/vis.py to 755
2022-09-27T13:57:39,220   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/remove_primers.py to 755
2022-09-27T13:57:39,220   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/create_image_tile.py to 755
2022-09-27T13:57:39,220   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.data/scripts/rename_files_to_sample_ids.py to 755
2022-09-27T13:57:39,255   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2022-09-27T13:57:39,264   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.1.dist-info/WHEEL
2022-09-27T13:57:39,269   creating '/tmp/pip-wheel-t_jghu3c/biobakery_workflows-3.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2022-09-27T13:57:39,273   adding 'biobakery_workflows/__init__.py'
2022-09-27T13:57:39,276   adding 'biobakery_workflows/biobakery_workflows.py'
2022-09-27T13:57:39,280   adding 'biobakery_workflows/biobakery_workflows_databases.py'
2022-09-27T13:57:39,283   adding 'biobakery_workflows/biobakery_workflows_scripts.py'
2022-09-27T13:57:39,286   adding 'biobakery_workflows/config.py'
2022-09-27T13:57:39,290   adding 'biobakery_workflows/files.py'
2022-09-27T13:57:39,325   adding 'biobakery_workflows/utilities.py'
2022-09-27T13:57:39,342   adding 'biobakery_workflows/visualizations.py'
2022-09-27T13:57:39,347   adding 'biobakery_workflows/Rscripts/alpha_diversity.R'
2022-09-27T13:57:39,351   adding 'biobakery_workflows/Rscripts/assign_taxonomy.R'
2022-09-27T13:57:39,354   adding 'biobakery_workflows/Rscripts/beta_diversity.R'
2022-09-27T13:57:39,357   adding 'biobakery_workflows/Rscripts/const_seq_table.R'
2022-09-27T13:57:39,359   adding 'biobakery_workflows/Rscripts/dada2_version.R'
2022-09-27T13:57:39,362   adding 'biobakery_workflows/Rscripts/filter_and_trim.R'
2022-09-27T13:57:39,365   adding 'biobakery_workflows/Rscripts/identify_primers.R'
2022-09-27T13:57:39,367   adding 'biobakery_workflows/Rscripts/learn_error_rates.R'
2022-09-27T13:57:39,371   adding 'biobakery_workflows/Rscripts/mantel_test.R'
2022-09-27T13:57:39,374   adding 'biobakery_workflows/Rscripts/merge_paired_ends.R'
2022-09-27T13:57:39,381   adding 'biobakery_workflows/Rscripts/permanova_hmp2.R'
2022-09-27T13:57:39,384   adding 'biobakery_workflows/Rscripts/phylogeny.R'
2022-09-27T13:57:39,387   adding 'biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R'
2022-09-27T13:57:39,389   adding 'biobakery_workflows/Rscripts/strainphlan_ordination_vis.R'
2022-09-27T13:57:39,392   adding 'biobakery_workflows/data/__init__.py'
2022-09-27T13:57:39,591   adding 'biobakery_workflows/data/strainphlan_species_gcf.tsv'
2022-09-27T13:57:39,607   adding 'biobakery_workflows/data/wmgx_methods.txt'
2022-09-27T13:57:39,612   adding 'biobakery_workflows/document_templates/16S.pmd'
2022-09-27T13:57:39,616   adding 'biobakery_workflows/document_templates/functional_dna.pmd'
2022-09-27T13:57:39,618   adding 'biobakery_workflows/document_templates/picard.pmd'
2022-09-27T13:57:39,620   adding 'biobakery_workflows/document_templates/quality_control_dada2.pmd'
2022-09-27T13:57:39,623   adding 'biobakery_workflows/document_templates/quality_control_paired_dna.pmd'
2022-09-27T13:57:39,625   adding 'biobakery_workflows/document_templates/quality_control_single_dna.pmd'
2022-09-27T13:57:39,627   adding 'biobakery_workflows/document_templates/quality_control_usearch.pmd'
2022-09-27T13:57:39,630   adding 'biobakery_workflows/document_templates/read_count_dada2.pmd'
2022-09-27T13:57:39,632   adding 'biobakery_workflows/document_templates/read_count_usearch.pmd'
2022-09-27T13:57:39,634   adding 'biobakery_workflows/document_templates/stats.pmd'
2022-09-27T13:57:39,636   adding 'biobakery_workflows/document_templates/stats_halla.pmd'
2022-09-27T13:57:39,639   adding 'biobakery_workflows/document_templates/stats_maaslin.pmd'
2022-09-27T13:57:39,641   adding 'biobakery_workflows/document_templates/stats_maaslin_stratified.pmd'
2022-09-27T13:57:39,643   adding 'biobakery_workflows/document_templates/stats_mantel_plots.pmd'
2022-09-27T13:57:39,645   adding 'biobakery_workflows/document_templates/stats_permanova.pmd'
2022-09-27T13:57:39,649   adding 'biobakery_workflows/document_templates/taxonomy.pmd'
2022-09-27T13:57:39,651   adding 'biobakery_workflows/document_templates/universal_vis.pmd'
2022-09-27T13:57:39,653   adding 'biobakery_workflows/document_templates/workflow_info.pmd'
2022-09-27T13:57:39,656   adding 'biobakery_workflows/tasks/__init__.py'
2022-09-27T13:57:39,661   adding 'biobakery_workflows/tasks/dadatwo.py'
2022-09-27T13:57:39,666   adding 'biobakery_workflows/tasks/general.py'
2022-09-27T13:57:39,680   adding 'biobakery_workflows/tasks/shotgun.py'
2022-09-27T13:57:39,691   adding 'biobakery_workflows/tasks/sixteen_s.py'
2022-09-27T13:57:39,697   adding 'biobakery_workflows/workflows/16s.py'
2022-09-27T13:57:39,701   adding 'biobakery_workflows/workflows/isolate_assembly.py'
2022-09-27T13:57:39,705   adding 'biobakery_workflows/workflows/stats.py'
2022-09-27T13:57:39,709   adding 'biobakery_workflows/workflows/vis.py'
2022-09-27T13:57:39,713   adding 'biobakery_workflows/workflows/wmgx.py'
2022-09-27T13:57:39,716   adding 'biobakery_workflows/workflows/wmgx_wmtx.py'
2022-09-27T13:57:39,740   adding 'biobakery_workflows-3.1.data/data/images/1618113365-16s_workflow_with_fasttree_merge_truncate_filter.jpg'
2022-09-27T13:57:39,751   adding 'biobakery_workflows-3.1.data/data/images/2782656604-isolate_workflow.jpg'
2022-09-27T13:57:39,766   adding 'biobakery_workflows-3.1.data/data/images/4005903235-DADA2Workflow_75percent.jpg'
2022-09-27T13:57:39,776   adding 'biobakery_workflows-3.1.data/data/images/4071512812-wms_wtx_workflow.jpg'
2022-09-27T13:57:39,786   adding 'biobakery_workflows-3.1.data/data/images/tutoral_workflow_info.png'
2022-09-27T13:57:39,791   adding 'biobakery_workflows-3.1.data/data/images/tutorial_alpha_diversity.png'
2022-09-27T13:57:39,840   adding 'biobakery_workflows-3.1.data/data/images/tutorial_halla_heatmap.png'
2022-09-27T13:57:39,878   adding 'biobakery_workflows-3.1.data/data/images/tutorial_halla_heatmap_metadata.png'
2022-09-27T13:57:39,909   adding 'biobakery_workflows-3.1.data/data/images/tutorial_humann_stratified_barplot.png'
2022-09-27T13:57:39,945   adding 'biobakery_workflows-3.1.data/data/images/tutorial_maaslin_heatmap.png'
2022-09-27T13:57:39,954   adding 'biobakery_workflows-3.1.data/data/images/tutorial_mantel_test.png'
2022-09-27T13:57:39,975   adding 'biobakery_workflows-3.1.data/data/images/tutorial_pathway_heatmap.png'
2022-09-27T13:57:40,056   adding 'biobakery_workflows-3.1.data/data/images/tutorial_pcoa.png'
2022-09-27T13:57:40,070   adding 'biobakery_workflows-3.1.data/data/images/tutorial_permanova.png'
2022-09-27T13:57:40,077   adding 'biobakery_workflows-3.1.data/data/images/tutorial_qc_barplot.png'
2022-09-27T13:57:40,084   adding 'biobakery_workflows-3.1.data/data/images/tutorial_table_of_contents.png'
2022-09-27T13:57:40,109   adding 'biobakery_workflows-3.1.data/data/images/tutorial_taxa_barplot.png'
2022-09-27T13:57:40,136   adding 'biobakery_workflows-3.1.data/data/images/wms_workflow.png'
2022-09-27T13:57:41,011   adding 'biobakery_workflows-3.1.data/data/tutorial/input/HD32R1_subsample.fastq.gz'
2022-09-27T13:57:41,715   adding 'biobakery_workflows-3.1.data/data/tutorial/input/HD42R4_subsample.fastq.gz'
2022-09-27T13:57:42,492   adding 'biobakery_workflows-3.1.data/data/tutorial/input/HD48R4_subsample.fastq.gz'
2022-09-27T13:57:45,195   adding 'biobakery_workflows-3.1.data/data/tutorial/input/LD96R2_subsample.fastq.gz'
2022-09-27T13:57:47,574   adding 'biobakery_workflows-3.1.data/data/tutorial/input/LV16R4_subsample.fastq.gz'
2022-09-27T13:57:49,277   adding 'biobakery_workflows-3.1.data/data/tutorial/input/LV20R4_subsample.fastq.gz'
2022-09-27T13:57:49,749   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.1.bt2'
2022-09-27T13:57:49,841   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.2.bt2'
2022-09-27T13:57:49,843   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.3.bt2'
2022-09-27T13:57:49,848   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.4.bt2'
2022-09-27T13:57:50,204   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.1.bt2'
2022-09-27T13:57:50,297   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.2.bt2'
2022-09-27T13:57:50,576   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.1.bt2'
2022-09-27T13:57:50,671   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.2.bt2'
2022-09-27T13:57:50,674   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.3.bt2'
2022-09-27T13:57:50,679   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.4.bt2'
2022-09-27T13:57:50,958   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.1.bt2'
2022-09-27T13:57:51,053   adding 'biobakery_workflows-3.1.data/data/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.rev.2.bt2'
2022-09-27T13:57:51,059   adding 'biobakery_workflows-3.1.data/scripts/16s.py'
2022-09-27T13:57:51,062   adding 'biobakery_workflows-3.1.data/scripts/anadama2_add_files_to_database.py'
2022-09-27T13:57:51,064   adding 'biobakery_workflows-3.1.data/scripts/annotate_genome.py'
2022-09-27T13:57:51,067   adding 'biobakery_workflows-3.1.data/scripts/burst_workflow.py'
2022-09-27T13:57:51,070   adding 'biobakery_workflows-3.1.data/scripts/check_fastq_format.py'
2022-09-27T13:57:51,072   adding 'biobakery_workflows-3.1.data/scripts/check_for_reverse_reads.py'
2022-09-27T13:57:51,075   adding 'biobakery_workflows-3.1.data/scripts/compute_species_of_interest.py'
2022-09-27T13:57:51,078   adding 'biobakery_workflows-3.1.data/scripts/count_features.py'
2022-09-27T13:57:51,081   adding 'biobakery_workflows-3.1.data/scripts/create_fasta_per_taxonomy_from_alignments.py'
2022-09-27T13:57:51,084   adding 'biobakery_workflows-3.1.data/scripts/create_feature_table.py'
2022-09-27T13:57:51,086   adding 'biobakery_workflows-3.1.data/scripts/create_image_tile.py'
2022-09-27T13:57:51,090   adding 'biobakery_workflows-3.1.data/scripts/create_otu_tables_from_alignments.py'
2022-09-27T13:57:51,096   adding 'biobakery_workflows-3.1.data/scripts/create_subsampled_demos.py'
2022-09-27T13:57:51,100   adding 'biobakery_workflows-3.1.data/scripts/demultiplex_split_index.py'
2022-09-27T13:57:51,102   adding 'biobakery_workflows-3.1.data/scripts/extract_orphan_reads.py'
2022-09-27T13:57:51,105   adding 'biobakery_workflows-3.1.data/scripts/generate_dual_barcode.py'
2022-09-27T13:57:51,107   adding 'biobakery_workflows-3.1.data/scripts/get_counts_from_humann_logs.py'
2022-09-27T13:57:51,110   adding 'biobakery_workflows-3.1.data/scripts/isolate_assembly.py'
2022-09-27T13:57:51,113   adding 'biobakery_workflows-3.1.data/scripts/join_taxonomic_profiles.py'
2022-09-27T13:57:51,116   adding 'biobakery_workflows-3.1.data/scripts/merge_and_rename_fastq.py'
2022-09-27T13:57:51,119   adding 'biobakery_workflows-3.1.data/scripts/merge_fastq.py'
2022-09-27T13:57:51,121   adding 'biobakery_workflows-3.1.data/scripts/pull_out_reads_by_species_metaphlan2_results.py'
2022-09-27T13:57:51,124   adding 'biobakery_workflows-3.1.data/scripts/remove_if_exists.py'
2022-09-27T13:57:51,126   adding 'biobakery_workflows-3.1.data/scripts/remove_primers.py'
2022-09-27T13:57:51,128   adding 'biobakery_workflows-3.1.data/scripts/rename_data_products.py'
2022-09-27T13:57:51,131   adding 'biobakery_workflows-3.1.data/scripts/rename_fastq_files.py'
2022-09-27T13:57:51,133   adding 'biobakery_workflows-3.1.data/scripts/rename_files_to_sample_ids.py'
2022-09-27T13:57:51,135   adding 'biobakery_workflows-3.1.data/scripts/reverse_compliment_barcodes.py'
2022-09-27T13:57:51,139   adding 'biobakery_workflows-3.1.data/scripts/rna_dna_norm.py'
2022-09-27T13:57:51,144   adding 'biobakery_workflows-3.1.data/scripts/stats.py'
2022-09-27T13:57:51,146   adding 'biobakery_workflows-3.1.data/scripts/subset_file_by_sample_id.py'
2022-09-27T13:57:51,149   adding 'biobakery_workflows-3.1.data/scripts/trim_taxonomy.py'
2022-09-27T13:57:51,153   adding 'biobakery_workflows-3.1.data/scripts/vis.py'
2022-09-27T13:57:51,157   adding 'biobakery_workflows-3.1.data/scripts/wmgx.py'
2022-09-27T13:57:51,160   adding 'biobakery_workflows-3.1.data/scripts/wmgx_wmtx.py'
2022-09-27T13:57:51,166   adding 'tests/__init__.py'
2022-09-27T13:57:51,172   adding 'tests/test_utilities.py'
2022-09-27T13:57:51,174   adding 'biobakery_workflows-3.1.dist-info/LICENSE'
2022-09-27T13:57:51,176   adding 'biobakery_workflows-3.1.dist-info/METADATA'
2022-09-27T13:57:51,178   adding 'biobakery_workflows-3.1.dist-info/WHEEL'
2022-09-27T13:57:51,179   adding 'biobakery_workflows-3.1.dist-info/entry_points.txt'
2022-09-27T13:57:51,181   adding 'biobakery_workflows-3.1.dist-info/top_level.txt'
2022-09-27T13:57:51,185   adding 'biobakery_workflows-3.1.dist-info/RECORD'
2022-09-27T13:57:52,236   removing build/bdist.linux-armv7l/wheel
2022-09-27T13:57:52,595   Building wheel for biobakery-workflows (setup.py): finished with status 'done'
2022-09-27T13:57:53,595   Created wheel for biobakery-workflows: filename=biobakery_workflows-3.1-py3-none-any.whl size=33733563 sha256=cd6f19db7a54407ce0596dcf273e53cf5a3221255d6ac9092e646bbdf7a653ed
2022-09-27T13:57:53,598   Stored in directory: /tmp/pip-ephem-wheel-cache-t0knnld6/wheels/93/fd/2d/41c750950e63b3cb54648aee89b401380a39e3274752e0f53f
2022-09-27T13:57:53,669 Successfully built biobakery-workflows
2022-09-27T13:57:56,203 Removed build tracker: '/tmp/pip-build-tracker-vqfsywiv'