2021-02-19T21:50:13,509 DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
2021-02-19T21:50:14,195 Created temporary directory: /tmp/pip-ephem-wheel-cache-fi1f_tl3
2021-02-19T21:50:14,200 Created temporary directory: /tmp/pip-req-tracker-9j6_6rhb
2021-02-19T21:50:14,201 Initialized build tracking at /tmp/pip-req-tracker-9j6_6rhb
2021-02-19T21:50:14,201 Created build tracker: /tmp/pip-req-tracker-9j6_6rhb
2021-02-19T21:50:14,202 Entered build tracker: /tmp/pip-req-tracker-9j6_6rhb
2021-02-19T21:50:14,203 Created temporary directory: /tmp/pip-wheel-q1zpsd31
2021-02-19T21:50:14,280 1 location(s) to search for versions of biobakery-workflows:
2021-02-19T21:50:14,280 * https://pypi.org/simple/biobakery-workflows/
2021-02-19T21:50:14,280 Fetching project page and analyzing links: https://pypi.org/simple/biobakery-workflows/
2021-02-19T21:50:14,283 Getting page https://pypi.org/simple/biobakery-workflows/
2021-02-19T21:50:14,287 Found index url https://pypi.org/simple
2021-02-19T21:50:14,643   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
2021-02-19T21:50:14,644   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
2021-02-19T21:50:14,645   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
2021-02-19T21:50:14,646   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
2021-02-19T21:50:14,647   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
2021-02-19T21:50:14,648   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
2021-02-19T21:50:14,649   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
2021-02-19T21:50:14,650   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
2021-02-19T21:50:14,651   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
2021-02-19T21:50:14,652   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
2021-02-19T21:50:14,653   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
2021-02-19T21:50:14,654   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
2021-02-19T21:50:14,655   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
2021-02-19T21:50:14,655   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
2021-02-19T21:50:14,656   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
2021-02-19T21:50:14,657   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
2021-02-19T21:50:14,658   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
2021-02-19T21:50:14,659   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
2021-02-19T21:50:14,660   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
2021-02-19T21:50:14,661   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
2021-02-19T21:50:14,662   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
2021-02-19T21:50:14,663   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
2021-02-19T21:50:14,664   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
2021-02-19T21:50:14,705 Given no hashes to check 1 links for project 'biobakery-workflows': discarding no candidates
2021-02-19T21:50:14,740 Collecting biobakery-workflows==3.0.0a7
2021-02-19T21:50:14,743   Created temporary directory: /tmp/pip-unpack-fj9smw5k
2021-02-19T21:50:16,161   Downloading biobakery_workflows-3.0.0a7.tar.gz (44.7 MB)
2021-02-19T21:50:35,986   Added biobakery-workflows==3.0.0a7 from https://files.pythonhosted.org/packages/c0/04/503cf382ef99894d05171a39ca39ee70866ce815cb369ca6b6215538df5e/biobakery_workflows-3.0.0a7.tar.gz#sha256=8819d6a110d01005d5c855a5f6a906b0a6b75e33d20b96471ae41c5ab354203f to build tracker '/tmp/pip-req-tracker-9j6_6rhb'
2021-02-19T21:50:35,990     Running setup.py (path:/tmp/pip-wheel-q1zpsd31/biobakery-workflows_ecfedf6fb2564a77a2e6833552a9fc0d/setup.py) egg_info for package biobakery-workflows
2021-02-19T21:50:35,992     Created temporary directory: /tmp/pip-pip-egg-info-zienayt0
2021-02-19T21:50:35,993     Running command python setup.py egg_info
2021-02-19T21:50:38,187     running egg_info
2021-02-19T21:50:38,193     creating /tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info
2021-02-19T21:50:38,197     writing entry points to /tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info/entry_points.txt
2021-02-19T21:50:38,200     writing /tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info/PKG-INFO
2021-02-19T21:50:38,205     writing dependency_links to /tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info/dependency_links.txt
2021-02-19T21:50:38,208     writing top-level names to /tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info/top_level.txt
2021-02-19T21:50:38,211     writing requirements to /tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info/requires.txt
2021-02-19T21:50:38,215     writing manifest file '/tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info/SOURCES.txt'
2021-02-19T21:50:38,615     reading manifest file '/tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info/SOURCES.txt'
2021-02-19T21:50:38,619     reading manifest template 'MANIFEST.in'
2021-02-19T21:50:38,668     writing manifest file '/tmp/pip-pip-egg-info-zienayt0/biobakery_workflows.egg-info/SOURCES.txt'
2021-02-19T21:50:38,671     /usr/local/lib/python3.5/dist-packages/setuptools/dist.py:452: UserWarning: Normalizing '3.0.0-alpha.7' to '3.0.0a7'
2021-02-19T21:50:38,672       warnings.warn(tmpl.format(**locals()))
2021-02-19T21:50:38,806   Source in /tmp/pip-wheel-q1zpsd31/biobakery-workflows_ecfedf6fb2564a77a2e6833552a9fc0d has version 3.0.0a7, which satisfies requirement biobakery-workflows==3.0.0a7 from https://files.pythonhosted.org/packages/c0/04/503cf382ef99894d05171a39ca39ee70866ce815cb369ca6b6215538df5e/biobakery_workflows-3.0.0a7.tar.gz#sha256=8819d6a110d01005d5c855a5f6a906b0a6b75e33d20b96471ae41c5ab354203f
2021-02-19T21:50:38,808   Removed biobakery-workflows==3.0.0a7 from https://files.pythonhosted.org/packages/c0/04/503cf382ef99894d05171a39ca39ee70866ce815cb369ca6b6215538df5e/biobakery_workflows-3.0.0a7.tar.gz#sha256=8819d6a110d01005d5c855a5f6a906b0a6b75e33d20b96471ae41c5ab354203f from build tracker '/tmp/pip-req-tracker-9j6_6rhb'
2021-02-19T21:50:38,817 Created temporary directory: /tmp/pip-unpack-rx4wqplu
2021-02-19T21:50:38,818 Building wheels for collected packages: biobakery-workflows
2021-02-19T21:50:38,827   Created temporary directory: /tmp/pip-wheel-t2q3ziyn
2021-02-19T21:50:38,828   Building wheel for biobakery-workflows (setup.py): started
2021-02-19T21:50:38,829   Destination directory: /tmp/pip-wheel-t2q3ziyn
2021-02-19T21:50:38,829   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-q1zpsd31/biobakery-workflows_ecfedf6fb2564a77a2e6833552a9fc0d/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-q1zpsd31/biobakery-workflows_ecfedf6fb2564a77a2e6833552a9fc0d/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-t2q3ziyn
2021-02-19T21:50:40,904   /usr/local/lib/python3.5/dist-packages/setuptools/dist.py:452: UserWarning: Normalizing '3.0.0-alpha.7' to '3.0.0a7'
2021-02-19T21:50:40,905     warnings.warn(tmpl.format(**locals()))
2021-02-19T21:50:41,001   running bdist_wheel
2021-02-19T21:50:41,017   running build
2021-02-19T21:50:41,017   running build_py
2021-02-19T21:50:41,361   creating build
2021-02-19T21:50:41,362   creating build/lib
2021-02-19T21:50:41,364   creating build/lib/tests
2021-02-19T21:50:41,367   copying tests/__init__.py -> build/lib/tests
2021-02-19T21:50:41,371   copying tests/test_utilities.py -> build/lib/tests
2021-02-19T21:50:41,381   creating build/lib/biobakery_workflows
2021-02-19T21:50:41,383   copying biobakery_workflows/visualizations.py -> build/lib/biobakery_workflows
2021-02-19T21:50:41,394   copying biobakery_workflows/utilities.py -> build/lib/biobakery_workflows
2021-02-19T21:50:41,409   copying biobakery_workflows/biobakery_workflows_scripts.py -> build/lib/biobakery_workflows
2021-02-19T21:50:41,416   copying biobakery_workflows/files.py -> build/lib/biobakery_workflows
2021-02-19T21:50:41,426   copying biobakery_workflows/config.py -> build/lib/biobakery_workflows
2021-02-19T21:50:41,433   copying biobakery_workflows/biobakery_workflows.py -> build/lib/biobakery_workflows
2021-02-19T21:50:41,439   copying biobakery_workflows/biobakery_workflows_databases.py -> build/lib/biobakery_workflows
2021-02-19T21:50:41,445   copying biobakery_workflows/__init__.py -> build/lib/biobakery_workflows
2021-02-19T21:50:41,454   creating build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,459   copying biobakery_workflows/document_templates/quality_control_single_dna.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,467   copying biobakery_workflows/document_templates/header.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,473   copying biobakery_workflows/document_templates/header_author.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,478   copying biobakery_workflows/document_templates/workflow_info.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,484   copying biobakery_workflows/document_templates/16S.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,492   copying biobakery_workflows/document_templates/quality_control_paired_dna_rna.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,499   copying biobakery_workflows/document_templates/stats.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,507   copying biobakery_workflows/document_templates/quality_control_paired_dna.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,513   copying biobakery_workflows/document_templates/taxonomy.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,520   copying biobakery_workflows/document_templates/functional_dna_rna.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,528   copying biobakery_workflows/document_templates/functional_dna.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,533   copying biobakery_workflows/document_templates/__init__.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,537   copying biobakery_workflows/document_templates/header_image.template.py -> build/lib/biobakery_workflows/document_templates
2021-02-19T21:50:41,543   creating build/lib/biobakery_workflows/data
2021-02-19T21:50:41,545   copying biobakery_workflows/data/__init__.py -> build/lib/biobakery_workflows/data
2021-02-19T21:50:41,551   creating build/lib/biobakery_workflows/tasks
2021-02-19T21:50:41,555   copying biobakery_workflows/tasks/dadatwo.py -> build/lib/biobakery_workflows/tasks
2021-02-19T21:50:41,563   copying biobakery_workflows/tasks/general.py -> build/lib/biobakery_workflows/tasks
2021-02-19T21:50:41,571   copying biobakery_workflows/tasks/sixteen_s.py -> build/lib/biobakery_workflows/tasks
2021-02-19T21:50:41,580   copying biobakery_workflows/tasks/shotgun.py -> build/lib/biobakery_workflows/tasks
2021-02-19T21:50:41,590   copying biobakery_workflows/tasks/__init__.py -> build/lib/biobakery_workflows/tasks
2021-02-19T21:50:41,622   creating build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,624   copying biobakery_workflows/workflows/wmgx_wmtx.py -> build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,630   copying biobakery_workflows/workflows/16s_vis.py -> build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,637   copying biobakery_workflows/workflows/wmgx_wmtx_vis.py -> build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,643   copying biobakery_workflows/workflows/isolate_assembly.py -> build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,649   copying biobakery_workflows/workflows/stats.py -> build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,657   copying biobakery_workflows/workflows/16s.py -> build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,666   copying biobakery_workflows/workflows/wmgx.py -> build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,674   copying biobakery_workflows/workflows/wmgx_vis.py -> build/lib/biobakery_workflows/workflows
2021-02-19T21:50:41,700   copying biobakery_workflows/data/strainphlan_species_gcf.tsv -> build/lib/biobakery_workflows/data
2021-02-19T21:50:41,771   creating build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,773   copying biobakery_workflows/Rscripts/assign_taxonomy.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,781   copying biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,788   copying biobakery_workflows/Rscripts/filter_and_trim.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,796   copying biobakery_workflows/Rscripts/permanova_hmp2.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,804   copying biobakery_workflows/Rscripts/phylogeny.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,809   copying biobakery_workflows/Rscripts/identify_primers.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,814   copying biobakery_workflows/Rscripts/strainphlan_ordination_vis.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,821   copying biobakery_workflows/Rscripts/beta_diversity.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,829   copying biobakery_workflows/Rscripts/merge_paired_ends.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,836   copying biobakery_workflows/Rscripts/dada2_version.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,841   copying biobakery_workflows/Rscripts/mantel_test.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,848   copying biobakery_workflows/Rscripts/learn_error_rates.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,853   copying biobakery_workflows/Rscripts/const_seq_table.R -> build/lib/biobakery_workflows/Rscripts
2021-02-19T21:50:41,873   running build_scripts
2021-02-19T21:50:41,874   creating build/scripts-3.5
2021-02-19T21:50:41,877   copying and adjusting biobakery_workflows/workflows/wmgx_wmtx.py -> build/scripts-3.5
2021-02-19T21:50:41,882   copying and adjusting biobakery_workflows/workflows/16s_vis.py -> build/scripts-3.5
2021-02-19T21:50:41,887   copying and adjusting biobakery_workflows/workflows/wmgx_wmtx_vis.py -> build/scripts-3.5
2021-02-19T21:50:41,891   copying and adjusting biobakery_workflows/workflows/isolate_assembly.py -> build/scripts-3.5
2021-02-19T21:50:41,896   copying and adjusting biobakery_workflows/workflows/stats.py -> build/scripts-3.5
2021-02-19T21:50:41,901   copying and adjusting biobakery_workflows/workflows/16s.py -> build/scripts-3.5
2021-02-19T21:50:41,906   copying and adjusting biobakery_workflows/workflows/wmgx.py -> build/scripts-3.5
2021-02-19T21:50:41,911   copying and adjusting biobakery_workflows/workflows/wmgx_vis.py -> build/scripts-3.5
2021-02-19T21:50:41,916   copying and adjusting biobakery_workflows/scripts/create_otu_tables_from_alignments.py -> build/scripts-3.5
2021-02-19T21:50:41,922   copying and adjusting biobakery_workflows/scripts/annotate_genome.py -> build/scripts-3.5
2021-02-19T21:50:41,926   copying and adjusting biobakery_workflows/scripts/count_features.py -> build/scripts-3.5
2021-02-19T21:50:41,931   copying and adjusting biobakery_workflows/scripts/create_subsampled_demos.py -> build/scripts-3.5
2021-02-19T21:50:41,938   copying and adjusting biobakery_workflows/scripts/rename_fastq_files.py -> build/scripts-3.5
2021-02-19T21:50:41,942   copying and adjusting biobakery_workflows/scripts/merge_fastq.py -> build/scripts-3.5
2021-02-19T21:50:41,946   copying and adjusting biobakery_workflows/scripts/create_image_tile.py -> build/scripts-3.5
2021-02-19T21:50:41,950   copying biobakery_workflows/scripts/rename_data_products.py -> build/scripts-3.5
2021-02-19T21:50:41,955   copying and adjusting biobakery_workflows/scripts/merge_and_rename_fastq.py -> build/scripts-3.5
2021-02-19T21:50:41,960   copying and adjusting biobakery_workflows/scripts/create_fasta_per_taxonomy_from_alignments.py -> build/scripts-3.5
2021-02-19T21:50:41,966   copying biobakery_workflows/scripts/anadama2_add_files_to_database.py -> build/scripts-3.5
2021-02-19T21:50:41,972   copying biobakery_workflows/scripts/remove_primers.py -> build/scripts-3.5
2021-02-19T21:50:41,977   copying and adjusting biobakery_workflows/scripts/check_fastq_format.py -> build/scripts-3.5
2021-02-19T21:50:41,982   copying and adjusting biobakery_workflows/scripts/demultiplex_split_index.py -> build/scripts-3.5
2021-02-19T21:50:41,989   copying and adjusting biobakery_workflows/scripts/trim_taxonomy.py -> build/scripts-3.5
2021-02-19T21:50:41,995   copying and adjusting biobakery_workflows/scripts/generate_dual_barcode.py -> build/scripts-3.5
2021-02-19T21:50:42,000   copying and adjusting biobakery_workflows/scripts/reverse_compliment_barcodes.py -> build/scripts-3.5
2021-02-19T21:50:42,005   copying biobakery_workflows/scripts/rename_files_to_sample_ids.py -> build/scripts-3.5
2021-02-19T21:50:42,010   copying and adjusting biobakery_workflows/scripts/remove_if_exists.py -> build/scripts-3.5
2021-02-19T21:50:42,014   copying and adjusting biobakery_workflows/scripts/rna_dna_norm.py -> build/scripts-3.5
2021-02-19T21:50:42,020   copying and adjusting biobakery_workflows/scripts/get_counts_from_humann_logs.py -> build/scripts-3.5
2021-02-19T21:50:42,027   copying biobakery_workflows/scripts/pull_out_reads_by_species_metaphlan2_results.py -> build/scripts-3.5
2021-02-19T21:50:42,034   copying and adjusting biobakery_workflows/scripts/create_feature_table.py -> build/scripts-3.5
2021-02-19T21:50:42,039   copying and adjusting biobakery_workflows/scripts/burst_workflow.py -> build/scripts-3.5
2021-02-19T21:50:42,044   copying and adjusting biobakery_workflows/scripts/join_taxonomic_profiles.py -> build/scripts-3.5
2021-02-19T21:50:42,049   copying and adjusting biobakery_workflows/scripts/extract_orphan_reads.py -> build/scripts-3.5
2021-02-19T21:50:42,051   changing mode of build/scripts-3.5/wmgx_wmtx.py from 644 to 755
2021-02-19T21:50:42,052   changing mode of build/scripts-3.5/16s_vis.py from 644 to 755
2021-02-19T21:50:42,053   changing mode of build/scripts-3.5/wmgx_wmtx_vis.py from 644 to 755
2021-02-19T21:50:42,053   changing mode of build/scripts-3.5/isolate_assembly.py from 644 to 755
2021-02-19T21:50:42,054   changing mode of build/scripts-3.5/stats.py from 644 to 755
2021-02-19T21:50:42,055   changing mode of build/scripts-3.5/16s.py from 644 to 755
2021-02-19T21:50:42,056   changing mode of build/scripts-3.5/wmgx.py from 644 to 755
2021-02-19T21:50:42,056   changing mode of build/scripts-3.5/wmgx_vis.py from 644 to 755
2021-02-19T21:50:42,057   changing mode of build/scripts-3.5/create_otu_tables_from_alignments.py from 644 to 755
2021-02-19T21:50:42,058   changing mode of build/scripts-3.5/annotate_genome.py from 644 to 755
2021-02-19T21:50:42,058   changing mode of build/scripts-3.5/count_features.py from 644 to 755
2021-02-19T21:50:42,059   changing mode of build/scripts-3.5/create_subsampled_demos.py from 644 to 755
2021-02-19T21:50:42,060   changing mode of build/scripts-3.5/rename_fastq_files.py from 644 to 755
2021-02-19T21:50:42,060   changing mode of build/scripts-3.5/merge_fastq.py from 644 to 755
2021-02-19T21:50:42,061   changing mode of build/scripts-3.5/create_image_tile.py from 644 to 755
2021-02-19T21:50:42,062   changing mode of build/scripts-3.5/rename_data_products.py from 644 to 755
2021-02-19T21:50:42,063   changing mode of build/scripts-3.5/merge_and_rename_fastq.py from 644 to 755
2021-02-19T21:50:42,063   changing mode of build/scripts-3.5/create_fasta_per_taxonomy_from_alignments.py from 644 to 755
2021-02-19T21:50:42,064   changing mode of build/scripts-3.5/anadama2_add_files_to_database.py from 644 to 755
2021-02-19T21:50:42,065   changing mode of build/scripts-3.5/remove_primers.py from 644 to 755
2021-02-19T21:50:42,066   changing mode of build/scripts-3.5/check_fastq_format.py from 644 to 755
2021-02-19T21:50:42,066   changing mode of build/scripts-3.5/demultiplex_split_index.py from 644 to 755
2021-02-19T21:50:42,067   changing mode of build/scripts-3.5/trim_taxonomy.py from 644 to 755
2021-02-19T21:50:42,068   changing mode of build/scripts-3.5/generate_dual_barcode.py from 644 to 755
2021-02-19T21:50:42,069   changing mode of build/scripts-3.5/reverse_compliment_barcodes.py from 644 to 755
2021-02-19T21:50:42,069   changing mode of build/scripts-3.5/rename_files_to_sample_ids.py from 644 to 755
2021-02-19T21:50:42,070   changing mode of build/scripts-3.5/remove_if_exists.py from 644 to 755
2021-02-19T21:50:42,071   changing mode of build/scripts-3.5/rna_dna_norm.py from 644 to 755
2021-02-19T21:50:42,072   changing mode of build/scripts-3.5/get_counts_from_humann_logs.py from 644 to 755
2021-02-19T21:50:42,072   changing mode of build/scripts-3.5/pull_out_reads_by_species_metaphlan2_results.py from 644 to 755
2021-02-19T21:50:42,073   changing mode of build/scripts-3.5/create_feature_table.py from 644 to 755
2021-02-19T21:50:42,074   changing mode of build/scripts-3.5/burst_workflow.py from 644 to 755
2021-02-19T21:50:42,074   changing mode of build/scripts-3.5/join_taxonomic_profiles.py from 644 to 755
2021-02-19T21:50:42,075   changing mode of build/scripts-3.5/extract_orphan_reads.py from 644 to 755
2021-02-19T21:50:42,082   installing to build/bdist.linux-armv7l/wheel
2021-02-19T21:50:42,083   running install
2021-02-19T21:50:42,085   running install_lib
2021-02-19T21:50:42,093   creating build/bdist.linux-armv7l
2021-02-19T21:50:42,093   creating build/bdist.linux-armv7l/wheel
2021-02-19T21:50:42,098   creating build/bdist.linux-armv7l/wheel/tests
2021-02-19T21:50:42,100   copying build/lib/tests/__init__.py -> build/bdist.linux-armv7l/wheel/tests
2021-02-19T21:50:42,105   copying build/lib/tests/test_utilities.py -> build/bdist.linux-armv7l/wheel/tests
2021-02-19T21:50:42,114   creating build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,116   copying build/lib/biobakery_workflows/visualizations.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,126   copying build/lib/biobakery_workflows/utilities.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,140   copying build/lib/biobakery_workflows/biobakery_workflows_scripts.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,146   copying build/lib/biobakery_workflows/files.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,153   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,155   copying build/lib/biobakery_workflows/Rscripts/assign_taxonomy.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,161   copying build/lib/biobakery_workflows/Rscripts/strainphlan_ggtree_vis.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,166   copying build/lib/biobakery_workflows/Rscripts/filter_and_trim.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,172   copying build/lib/biobakery_workflows/Rscripts/permanova_hmp2.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,181   copying build/lib/biobakery_workflows/Rscripts/phylogeny.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,187   copying build/lib/biobakery_workflows/Rscripts/identify_primers.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,193   copying build/lib/biobakery_workflows/Rscripts/strainphlan_ordination_vis.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,199   copying build/lib/biobakery_workflows/Rscripts/beta_diversity.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,206   copying build/lib/biobakery_workflows/Rscripts/merge_paired_ends.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,212   copying build/lib/biobakery_workflows/Rscripts/dada2_version.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,218   copying build/lib/biobakery_workflows/Rscripts/mantel_test.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,225   copying build/lib/biobakery_workflows/Rscripts/learn_error_rates.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,231   copying build/lib/biobakery_workflows/Rscripts/const_seq_table.R -> build/bdist.linux-armv7l/wheel/biobakery_workflows/Rscripts
2021-02-19T21:50:42,237   copying build/lib/biobakery_workflows/config.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,246   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,248   copying build/lib/biobakery_workflows/document_templates/quality_control_single_dna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,255   copying build/lib/biobakery_workflows/document_templates/header.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,261   copying build/lib/biobakery_workflows/document_templates/header_author.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,267   copying build/lib/biobakery_workflows/document_templates/workflow_info.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,272   copying build/lib/biobakery_workflows/document_templates/16S.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,280   copying build/lib/biobakery_workflows/document_templates/quality_control_paired_dna_rna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,287   copying build/lib/biobakery_workflows/document_templates/stats.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,292   copying build/lib/biobakery_workflows/document_templates/quality_control_paired_dna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,297   copying build/lib/biobakery_workflows/document_templates/taxonomy.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,302   copying build/lib/biobakery_workflows/document_templates/functional_dna_rna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,309   copying build/lib/biobakery_workflows/document_templates/functional_dna.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,316   copying build/lib/biobakery_workflows/document_templates/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,321   copying build/lib/biobakery_workflows/document_templates/header_image.template.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/document_templates
2021-02-19T21:50:42,328   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/data
2021-02-19T21:50:42,331   copying build/lib/biobakery_workflows/data/strainphlan_species_gcf.tsv -> build/bdist.linux-armv7l/wheel/biobakery_workflows/data
2021-02-19T21:50:42,402   copying build/lib/biobakery_workflows/data/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/data
2021-02-19T21:50:42,408   copying build/lib/biobakery_workflows/biobakery_workflows.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,413   copying build/lib/biobakery_workflows/biobakery_workflows_databases.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,422   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,425   copying build/lib/biobakery_workflows/workflows/wmgx_wmtx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,432   copying build/lib/biobakery_workflows/workflows/16s_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,439   copying build/lib/biobakery_workflows/workflows/wmgx_wmtx_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,446   copying build/lib/biobakery_workflows/workflows/isolate_assembly.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,452   copying build/lib/biobakery_workflows/workflows/stats.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,459   copying build/lib/biobakery_workflows/workflows/16s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,466   copying build/lib/biobakery_workflows/workflows/wmgx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,473   copying build/lib/biobakery_workflows/workflows/wmgx_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/workflows
2021-02-19T21:50:42,480   copying build/lib/biobakery_workflows/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows
2021-02-19T21:50:42,486   creating build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2021-02-19T21:50:42,488   copying build/lib/biobakery_workflows/tasks/dadatwo.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2021-02-19T21:50:42,495   copying build/lib/biobakery_workflows/tasks/general.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2021-02-19T21:50:42,500   copying build/lib/biobakery_workflows/tasks/sixteen_s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2021-02-19T21:50:42,509   copying build/lib/biobakery_workflows/tasks/shotgun.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2021-02-19T21:50:42,521   copying build/lib/biobakery_workflows/tasks/__init__.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows/tasks
2021-02-19T21:50:42,525   running install_data
2021-02-19T21:50:42,532   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data
2021-02-19T21:50:42,533   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data
2021-02-19T21:50:42,536   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial
2021-02-19T21:50:42,537   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/input
2021-02-19T21:50:42,540   copying examples/tutorial/input/LV16R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/input/
2021-02-19T21:50:43,276   copying examples/tutorial/input/HD42R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/input/
2021-02-19T21:50:43,497   copying examples/tutorial/input/HD32R1_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/input/
2021-02-19T21:50:43,793   copying examples/tutorial/input/LV20R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/input/
2021-02-19T21:50:44,328   copying examples/tutorial/input/LD96R2_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/input/
2021-02-19T21:50:45,237   copying examples/tutorial/input/HD48R4_subsample.fastq.gz -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/input/
2021-02-19T21:50:45,485   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db
2021-02-19T21:50:45,486   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo
2021-02-19T21:50:45,489   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.3.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2021-02-19T21:50:45,494   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2021-02-19T21:50:45,502   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2021-02-19T21:50:45,904   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2021-02-19T21:50:45,912   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.4.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2021-02-19T21:50:45,920   copying examples/tutorial/kneaddata_demo_db/Homo_sapiens_demo/Homo_sapiens_demo.rev.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/Homo_sapiens_demo/
2021-02-19T21:50:46,318   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/SILVA_demo
2021-02-19T21:50:46,321   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.1.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2021-02-19T21:50:46,713   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.3.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2021-02-19T21:50:46,720   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.4.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2021-02-19T21:50:46,728   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-3.0.0a7.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2021-02-19T21:50:47,129   copying examples/tutorial/kneaddata_demo_db/SILVA_demo/SILVA_128_LSUParc_SSUParc_ribosomal_RNA_demo.2.bt2 -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2021-02-19T21:50:47,137   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-3.0.0a7.data/data/tutorial/kneaddata_demo_db/SILVA_demo/
2021-02-19T21:50:47,144   running install_egg_info
2021-02-19T21:50:47,192   running egg_info
2021-02-19T21:50:47,193   writing biobakery_workflows.egg-info/PKG-INFO
2021-02-19T21:50:47,197   writing requirements to biobakery_workflows.egg-info/requires.txt
2021-02-19T21:50:47,200   writing entry points to biobakery_workflows.egg-info/entry_points.txt
2021-02-19T21:50:47,202   writing dependency_links to biobakery_workflows.egg-info/dependency_links.txt
2021-02-19T21:50:47,205   writing top-level names to biobakery_workflows.egg-info/top_level.txt
2021-02-19T21:50:47,226   reading manifest file 'biobakery_workflows.egg-info/SOURCES.txt'
2021-02-19T21:50:47,241   reading manifest template 'MANIFEST.in'
2021-02-19T21:50:47,292   writing manifest file 'biobakery_workflows.egg-info/SOURCES.txt'
2021-02-19T21:50:47,296   Copying biobakery_workflows.egg-info to build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7-py3.5.egg-info
2021-02-19T21:50:47,335   running install_scripts
2021-02-19T21:50:47,475   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,477   copying build/scripts-3.5/wmgx_wmtx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,483   copying build/scripts-3.5/create_otu_tables_from_alignments.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,489   copying build/scripts-3.5/annotate_genome.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,495   copying build/scripts-3.5/count_features.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,501   copying build/scripts-3.5/create_subsampled_demos.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,509   copying build/scripts-3.5/rename_fastq_files.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,515   copying build/scripts-3.5/merge_fastq.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,519   copying build/scripts-3.5/create_image_tile.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,523   copying build/scripts-3.5/16s_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,528   copying build/scripts-3.5/rename_data_products.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,533   copying build/scripts-3.5/merge_and_rename_fastq.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,540   copying build/scripts-3.5/create_fasta_per_taxonomy_from_alignments.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,547   copying build/scripts-3.5/wmgx_wmtx_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,553   copying build/scripts-3.5/isolate_assembly.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,560   copying build/scripts-3.5/anadama2_add_files_to_database.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,566   copying build/scripts-3.5/stats.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,573   copying build/scripts-3.5/remove_primers.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,579   copying build/scripts-3.5/16s.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,586   copying build/scripts-3.5/wmgx.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,593   copying build/scripts-3.5/check_fastq_format.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,605   copying build/scripts-3.5/demultiplex_split_index.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,611   copying build/scripts-3.5/trim_taxonomy.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,617   copying build/scripts-3.5/generate_dual_barcode.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,623   copying build/scripts-3.5/reverse_compliment_barcodes.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,629   copying build/scripts-3.5/rename_files_to_sample_ids.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,634   copying build/scripts-3.5/remove_if_exists.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,640   copying build/scripts-3.5/rna_dna_norm.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,647   copying build/scripts-3.5/get_counts_from_humann_logs.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,653   copying build/scripts-3.5/wmgx_vis.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,659   copying build/scripts-3.5/pull_out_reads_by_species_metaphlan2_results.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,665   copying build/scripts-3.5/create_feature_table.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,671   copying build/scripts-3.5/burst_workflow.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,677   copying build/scripts-3.5/join_taxonomic_profiles.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,684   copying build/scripts-3.5/extract_orphan_reads.py -> build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts
2021-02-19T21:50:47,689   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/wmgx_wmtx.py to 755
2021-02-19T21:50:47,690   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/create_otu_tables_from_alignments.py to 755
2021-02-19T21:50:47,692   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/annotate_genome.py to 755
2021-02-19T21:50:47,693   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/count_features.py to 755
2021-02-19T21:50:47,694   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/create_subsampled_demos.py to 755
2021-02-19T21:50:47,696   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/rename_fastq_files.py to 755
2021-02-19T21:50:47,697   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/merge_fastq.py to 755
2021-02-19T21:50:47,698   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/create_image_tile.py to 755
2021-02-19T21:50:47,699   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/16s_vis.py to 755
2021-02-19T21:50:47,700   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/rename_data_products.py to 755
2021-02-19T21:50:47,700   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/merge_and_rename_fastq.py to 755
2021-02-19T21:50:47,701   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/create_fasta_per_taxonomy_from_alignments.py to 755
2021-02-19T21:50:47,702   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/wmgx_wmtx_vis.py to 755
2021-02-19T21:50:47,702   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/isolate_assembly.py to 755
2021-02-19T21:50:47,703   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/anadama2_add_files_to_database.py to 755
2021-02-19T21:50:47,704   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/stats.py to 755
2021-02-19T21:50:47,705   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/remove_primers.py to 755
2021-02-19T21:50:47,705   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/16s.py to 755
2021-02-19T21:50:47,706   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/wmgx.py to 755
2021-02-19T21:50:47,707   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/check_fastq_format.py to 755
2021-02-19T21:50:47,708   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/demultiplex_split_index.py to 755
2021-02-19T21:50:47,708   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/trim_taxonomy.py to 755
2021-02-19T21:50:47,709   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/generate_dual_barcode.py to 755
2021-02-19T21:50:47,710   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/reverse_compliment_barcodes.py to 755
2021-02-19T21:50:47,710   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/rename_files_to_sample_ids.py to 755
2021-02-19T21:50:47,711   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/remove_if_exists.py to 755
2021-02-19T21:50:47,712   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/rna_dna_norm.py to 755
2021-02-19T21:50:47,713   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/get_counts_from_humann_logs.py to 755
2021-02-19T21:50:47,713   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/wmgx_vis.py to 755
2021-02-19T21:50:47,714   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/pull_out_reads_by_species_metaphlan2_results.py to 755
2021-02-19T21:50:47,715   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/create_feature_table.py to 755
2021-02-19T21:50:47,715   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/burst_workflow.py to 755
2021-02-19T21:50:47,716   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/join_taxonomic_profiles.py to 755
2021-02-19T21:50:47,717   changing mode of build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.data/scripts/extract_orphan_reads.py to 755
2021-02-19T21:50:47,768   creating build/bdist.linux-armv7l/wheel/biobakery_workflows-3.0.0a7.dist-info/WHEEL
2021-02-19T21:50:58,889   Building wheel for biobakery-workflows (setup.py): finished with status 'done'
2021-02-19T21:50:59,424   Created wheel for biobakery-workflows: filename=biobakery_workflows-3.0.0a7-py3-none-any.whl size=32457069 sha256=3dc1f34656c0d1c4390b9102b73ec613ae32bad3d1b399a6a572c9c21af41acc
2021-02-19T21:50:59,425   Stored in directory: /tmp/pip-ephem-wheel-cache-fi1f_tl3/wheels/33/d1/fd/6d7faf16f3cdde63cc8b8dafc7696b6b9e3d33f2db71e577b8
2021-02-19T21:50:59,467 Successfully built biobakery-workflows
2021-02-19T21:51:05,359 Removed build tracker: '/tmp/pip-req-tracker-9j6_6rhb'