2020-05-29T05:47:17,761 Created temporary directory: /tmp/pip-ephem-wheel-cache-pauh8_3f
2020-05-29T05:47:17,765 Created temporary directory: /tmp/pip-req-tracker-fsl117m3
2020-05-29T05:47:17,766 Initialized build tracking at /tmp/pip-req-tracker-fsl117m3
2020-05-29T05:47:17,767 Created build tracker: /tmp/pip-req-tracker-fsl117m3
2020-05-29T05:47:17,767 Entered build tracker: /tmp/pip-req-tracker-fsl117m3
2020-05-29T05:47:17,768 Created temporary directory: /tmp/pip-wheel-9zxnbad9
2020-05-29T05:47:17,782 1 location(s) to search for versions of gtdbtk:
2020-05-29T05:47:17,782 * https://pypi.org/simple/gtdbtk/
2020-05-29T05:47:17,783 Fetching project page and analyzing links: https://pypi.org/simple/gtdbtk/
2020-05-29T05:47:17,784 Getting page https://pypi.org/simple/gtdbtk/
2020-05-29T05:47:17,786 Found index url https://pypi.org/simple
2020-05-29T05:47:17,790 Getting credentials from keyring for https://pypi.org/simple
2020-05-29T05:47:17,790 Getting credentials from keyring for pypi.org
2020-05-29T05:47:18,012   Found link https://files.pythonhosted.org/packages/77/1d/a47e727062761ea6108b1be340d24c711131df11415d82cdb30bcb51738b/gtdbtk-0.0.1.tar.gz#sha256=3f9a367bf64dc907226c2ac5f39204080fa5f305a995dcfa183ec0da6f4187a8 (from https://pypi.org/simple/gtdbtk/), version: 0.0.1
2020-05-29T05:47:18,013   Found link https://files.pythonhosted.org/packages/78/fc/021b3e4fc9fc1a8d8596ccf703ee4f5abd97b496bc714a9bfc69332e913e/gtdbtk-0.0.2.tar.gz#sha256=b350aa8766a772509197a361646104b17dd106cf834fb9ea517c1924f5a8d345 (from https://pypi.org/simple/gtdbtk/), version: 0.0.2
2020-05-29T05:47:18,013   Found link https://files.pythonhosted.org/packages/b8/55/a62d05d6a2d35a6e9f2247586a77f8033eaeeffb8e8d4db6511252c8a59b/gtdbtk-0.0.3.tar.gz#sha256=55d6be274b732fa9bda5682892900ad0edc06a32f44db1fd5990910c206692b8 (from https://pypi.org/simple/gtdbtk/), version: 0.0.3
2020-05-29T05:47:18,014   Found link https://files.pythonhosted.org/packages/88/3d/2dedbfdce682d2c73aebb1182835889222aecefac4072e205e885b601be5/gtdbtk-0.0.4b0.tar.gz#sha256=39e82b23287c42e89b097b7aa163425a46b8616f2ec356d6b9fa5b1dccd85984 (from https://pypi.org/simple/gtdbtk/), version: 0.0.4b0
2020-05-29T05:47:18,014   Found link https://files.pythonhosted.org/packages/e7/21/7b30d68267c9ed81610a37c8fdac4b53f7090f9511d963a54754ec49d521/gtdbtk-0.0.4b1.tar.gz#sha256=eb4de226ccd8f266cc31fe11f2df8d8582cfd7164d7b3b4bf08cf97e0acf5004 (from https://pypi.org/simple/gtdbtk/), version: 0.0.4b1
2020-05-29T05:47:18,015   Found link https://files.pythonhosted.org/packages/d1/f0/970559d46438a2004ccaa4199491188afc1bb13304fb899b26a3530ed841/gtdbtk-0.0.4b2.tar.gz#sha256=a92edcfd6f7e15b3aad5154d10f08798417d49df4634b7e9165c0e0fe55f35f0 (from https://pypi.org/simple/gtdbtk/), version: 0.0.4b2
2020-05-29T05:47:18,016   Found link https://files.pythonhosted.org/packages/e0/47/a9610df19e2bcf2782fc1ee29e5f85452b20a22d6f80581a23e3c0111c52/gtdbtk-0.0.4b3.tar.gz#sha256=c98f0847a434e9f88cfaaa33b11b99f97123e6982a59d90a7291370f3cc2cc46 (from https://pypi.org/simple/gtdbtk/), version: 0.0.4b3
2020-05-29T05:47:18,016   Found link https://files.pythonhosted.org/packages/bf/f1/ebd7ba5d9ac68fc00ec0f7a69b52111d945a70f836dd4ba975600b088a98/gtdbtk-0.0.5.tar.gz#sha256=116c8aff980e2af0d18cf79a5ce452cb78cee11c226425554c9b6f2b2969ec27 (from https://pypi.org/simple/gtdbtk/), version: 0.0.5
2020-05-29T05:47:18,017   Found link https://files.pythonhosted.org/packages/ca/7c/fc51570da6722bd31e310bb1ac218cb9d839dfae5d5e94d0ea3666402812/gtdbtk-0.0.6.tar.gz#sha256=e83a8ec329637753a4f7fc4672ae89442aa464a7daba55067cbf05ff195ae8c9 (from https://pypi.org/simple/gtdbtk/), version: 0.0.6
2020-05-29T05:47:18,017   Found link https://files.pythonhosted.org/packages/68/72/fdfc81336d6a94e8f286f562bc265e5d215f653f5d08d91689b6cb69a6cb/gtdbtk-0.0.7.tar.gz#sha256=6fa59cd7cb19aee52b82b179bb6efa7ba00a22b9c2317f9d01837e1e35d4a1e0 (from https://pypi.org/simple/gtdbtk/), version: 0.0.7
2020-05-29T05:47:18,018   Found link https://files.pythonhosted.org/packages/00/bb/2c2c4a00d4ca637be0daa7ac6bca99011afa8c42de7148c4e5dd6fc28141/gtdbtk-0.0.8b1.tar.gz#sha256=09183582b140dd0f40bda9db70e1f49347934c61cc2deab7214a183b915a0057 (from https://pypi.org/simple/gtdbtk/), version: 0.0.8b1
2020-05-29T05:47:18,019   Found link https://files.pythonhosted.org/packages/c0/3e/4a7f207340198fb69fe0764236f9cfb562840796cca457317024f1bcfb65/gtdbtk-0.1.0.tar.gz#sha256=4970c3a740f9d40142b81104ededd65cf109b57b11ab6ca66b6b21ed0ea40307 (from https://pypi.org/simple/gtdbtk/), version: 0.1.0
2020-05-29T05:47:18,019   Found link https://files.pythonhosted.org/packages/5f/c1/f028b36863e2b27d0a4191f4033eec25cfff898abceb97b0ccfa1352e1f0/gtdbtk-0.1.1.tar.gz#sha256=acfaed6f97b88b5a4cc327f956d408f6a0f8b49c0088f6222f992e179c1a8b89 (from https://pypi.org/simple/gtdbtk/), version: 0.1.1
2020-05-29T05:47:18,020   Found link https://files.pythonhosted.org/packages/1f/40/6a7cae5b58902ff5add1db17bf0dd24857bfedacd73f47096e3ef5789899/gtdbtk-0.1.2.tar.gz#sha256=2702d6b289e93ef725d01b6fe13d55abbe00711cb6704de8b2ad20604d8d2267 (from https://pypi.org/simple/gtdbtk/), version: 0.1.2
2020-05-29T05:47:18,020   Found link https://files.pythonhosted.org/packages/e4/e7/481464381afdf57da5e920a1713a73627373583c57d292ad7155e8b4f32c/gtdbtk-0.1.3.tar.gz#sha256=1063a8cdb0f72164fbba0f41e3df12ab23e944b0b15fc9e264bb0a2903b8978e (from https://pypi.org/simple/gtdbtk/), version: 0.1.3
2020-05-29T05:47:18,021   Found link https://files.pythonhosted.org/packages/29/6d/e9dc39898e8cc79fe54b5109ca7ed03842bcab51368cc6dbf05c2b2c6f39/gtdbtk-0.1.6.tar.gz#sha256=d30abfb59a1d9180bdbdb6d07d26b0baaa6fdf70f5ef08576bf284854cf3b262 (from https://pypi.org/simple/gtdbtk/), version: 0.1.6
2020-05-29T05:47:18,022   Found link https://files.pythonhosted.org/packages/db/c8/b052434152065efc0d209401041a7f7ba51c153832f4fe0a424fe0990cfa/gtdbtk-0.2.1.tar.gz#sha256=043118d31a94902eed5d623cc94ed3eb941c397411084d3909e3b504e0d1c4ca (from https://pypi.org/simple/gtdbtk/), version: 0.2.1
2020-05-29T05:47:18,022   Found link https://files.pythonhosted.org/packages/0a/74/8cbe8afea3aa0f7d6b948210b8937f3edcf541b3212cae2ce6aa560276a9/gtdbtk-0.2.2.tar.gz#sha256=23f6dd77e0102cfbc88d0e1c1cc4ba61a1df64ec71848a160ac4d9b5d2e81d1d (from https://pypi.org/simple/gtdbtk/), version: 0.2.2
2020-05-29T05:47:18,023   Found link https://files.pythonhosted.org/packages/45/de/019db6634299b4086a49646891c9e99347e2908713baa14641e15687e4af/gtdbtk-0.3.0.tar.gz#sha256=1048113616b37e30201b6b85cb80bdd952644c6c42240f4f876f6249cff9c41c (from https://pypi.org/simple/gtdbtk/), version: 0.3.0
2020-05-29T05:47:18,023   Found link https://files.pythonhosted.org/packages/6e/46/14181ed7f443fd8f70353250d09c94d2a2d867e68cc687167a8546ef4926/gtdbtk-0.3.1.tar.gz#sha256=ac6329774211953e431b449788ac0bfbf16a6485eb33b4d4559e84a7cc080bda (from https://pypi.org/simple/gtdbtk/), version: 0.3.1
2020-05-29T05:47:18,024   Found link https://files.pythonhosted.org/packages/91/64/06be7ada30b1895a1205feac310a92929a5e135b5821036632aa36d1354c/gtdbtk-0.3.2.tar.gz#sha256=8df3b941df5aa1a4bd0e0344da179d73f756a20b5f28610f3837efacbb019f4a (from https://pypi.org/simple/gtdbtk/), version: 0.3.2
2020-05-29T05:47:18,025   Found link https://files.pythonhosted.org/packages/7d/90/a62620e2c5c5799d0271f097a83c356dd7d458bf85651da24a353e93d669/gtdbtk-0.3.3.tar.gz#sha256=32283b128e438fa7924b302d8189c61656ac5cefcfa49269d0eade997034015a (from https://pypi.org/simple/gtdbtk/), version: 0.3.3
2020-05-29T05:47:18,026   Found link https://files.pythonhosted.org/packages/48/b3/ce025d246df8196fbb18ac4ef9b3f09b430d8a71627b3b49dd7f33647b95/gtdbtk-1.0.0.tar.gz#sha256=e6e13437d76d6e3ac48b5860790f74a3394b13392c099b98c05fa1b2473697d6 (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.0.0
2020-05-29T05:47:18,027   Found link https://files.pythonhosted.org/packages/87/bc/dcfb65d65adda7952adf9251cb7e86c2cc3143804932d2a6cbdc04f4249e/gtdbtk-1.0.1.tar.gz#sha256=5f849a4f53db03fcffe832ee82b3816c3aca0c69e2dc16733608bdd1ca1781f0 (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.0.1
2020-05-29T05:47:18,028   Found link https://files.pythonhosted.org/packages/cd/3b/c70443baef1058d1955bfe476d521a4ad423958bf349527cf75cb3e892a5/gtdbtk-1.0.2.tar.gz#sha256=b8fb65555d86301c55bef0f4722f6ae0d0bd974d2a04cbb71973b51dc0013655 (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.0.2
2020-05-29T05:47:18,029   Found link https://files.pythonhosted.org/packages/f0/28/78411977ec02799a3a16a08ba9ea036851fd23d26126a583d7a4dbd7e129/gtdbtk-1.1.0.tar.gz#sha256=ffee0895b016c173ad043853a7d5111154f7e04194d2a2bc05a150acf9669f8a (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.1.0
2020-05-29T05:47:18,030   Found link https://files.pythonhosted.org/packages/68/d0/bcdb38880ed7e0d0ae563c62b1f192b1d77a35a0d00b193f9e5a01817454/gtdbtk-1.1.1.tar.gz#sha256=b1ee2e8c0a75132b8061b454676f9dd68acfeaf6ee71fab48db005b6eed57263 (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.1.1
2020-05-29T05:47:18,030   Skipping link: No binaries permitted for gtdbtk: https://files.pythonhosted.org/packages/f3/56/60ff2a296580b4e5741592ad17ca874ba024f7f5c9c225d7cadfb9cfd54f/gtdbtk-1.2.0-py3-none-any.whl#sha256=ab384e5e12dd2a8abe3882778963d6eabc09964a254c57730df308091e7953f3 (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6)
2020-05-29T05:47:18,031   Found link https://files.pythonhosted.org/packages/fd/9d/2060d8cdefde94050a969360e8b1343d6c441b35f57ca3000ec2b8c0c950/gtdbtk-1.2.0.tar.gz#sha256=1eda0b342b090f7c03ddcacee0ef249fcaa0a05e664b06a88fcf57b65d990cb5 (from https://pypi.org/simple/gtdbtk/) (requires-python:>=3.6), version: 1.2.0
2020-05-29T05:47:18,048 Given no hashes to check 1 links for project 'gtdbtk': discarding no candidates
2020-05-29T05:47:18,049 Using version 1.2.0 (newest of versions: 1.2.0)
2020-05-29T05:47:18,055 Collecting gtdbtk==1.2.0
2020-05-29T05:47:18,059   Created temporary directory: /tmp/pip-unpack-a0nm65lh
2020-05-29T05:47:18,062   Getting credentials from keyring for files.pythonhosted.org
2020-05-29T05:47:18,325   Downloading gtdbtk-1.2.0.tar.gz (1.7 MB)
2020-05-29T05:47:19,904   Added gtdbtk==1.2.0 from https://files.pythonhosted.org/packages/fd/9d/2060d8cdefde94050a969360e8b1343d6c441b35f57ca3000ec2b8c0c950/gtdbtk-1.2.0.tar.gz#sha256=1eda0b342b090f7c03ddcacee0ef249fcaa0a05e664b06a88fcf57b65d990cb5 to build tracker '/tmp/pip-req-tracker-fsl117m3'
2020-05-29T05:47:19,907     Running setup.py (path:/tmp/pip-wheel-9zxnbad9/gtdbtk/setup.py) egg_info for package gtdbtk
2020-05-29T05:47:19,909     Created temporary directory: /tmp/pip-pip-egg-info-r4cg58m1
2020-05-29T05:47:19,910     Running command python setup.py egg_info
2020-05-29T05:47:21,830     running egg_info
2020-05-29T05:47:21,834     creating /tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info
2020-05-29T05:47:21,836     writing /tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info/PKG-INFO
2020-05-29T05:47:21,841     writing dependency_links to /tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info/dependency_links.txt
2020-05-29T05:47:21,845     writing entry points to /tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info/entry_points.txt
2020-05-29T05:47:21,847     writing requirements to /tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info/requires.txt
2020-05-29T05:47:21,849     writing top-level names to /tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info/top_level.txt
2020-05-29T05:47:21,854     writing manifest file '/tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info/SOURCES.txt'
2020-05-29T05:47:22,157     package init file 'gtdbtk/tests/__init__.py' not found (or not a regular file)
2020-05-29T05:47:22,177     reading manifest file '/tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info/SOURCES.txt'
2020-05-29T05:47:22,180     reading manifest template 'MANIFEST.in'
2020-05-29T05:47:22,182     warning: no files found matching 'genome_1.fna'
2020-05-29T05:47:22,183     warning: no files found matching 'genome_2.fna'
2020-05-29T05:47:22,184     warning: no files found matching 'genome_3.fna'
2020-05-29T05:47:22,185     warning: no previously-included files matching 'genome_*_protein.fna' found anywhere in distribution
2020-05-29T05:47:22,193     writing manifest file '/tmp/pip-pip-egg-info-r4cg58m1/gtdbtk.egg-info/SOURCES.txt'
2020-05-29T05:47:22,315   Source in /tmp/pip-wheel-9zxnbad9/gtdbtk has version 1.2.0, which satisfies requirement gtdbtk==1.2.0 from https://files.pythonhosted.org/packages/fd/9d/2060d8cdefde94050a969360e8b1343d6c441b35f57ca3000ec2b8c0c950/gtdbtk-1.2.0.tar.gz#sha256=1eda0b342b090f7c03ddcacee0ef249fcaa0a05e664b06a88fcf57b65d990cb5
2020-05-29T05:47:22,316   Removed gtdbtk==1.2.0 from https://files.pythonhosted.org/packages/fd/9d/2060d8cdefde94050a969360e8b1343d6c441b35f57ca3000ec2b8c0c950/gtdbtk-1.2.0.tar.gz#sha256=1eda0b342b090f7c03ddcacee0ef249fcaa0a05e664b06a88fcf57b65d990cb5 from build tracker '/tmp/pip-req-tracker-fsl117m3'
2020-05-29T05:47:22,321 Building wheels for collected packages: gtdbtk
2020-05-29T05:47:22,329   Created temporary directory: /tmp/pip-wheel-d7ezxqfj
2020-05-29T05:47:22,330   Building wheel for gtdbtk (setup.py): started
2020-05-29T05:47:22,331   Destination directory: /tmp/pip-wheel-d7ezxqfj
2020-05-29T05:47:22,331   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-9zxnbad9/gtdbtk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-9zxnbad9/gtdbtk/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-d7ezxqfj
2020-05-29T05:47:24,257   running bdist_wheel
2020-05-29T05:47:24,614   running build
2020-05-29T05:47:24,615   running build_py
2020-05-29T05:47:24,883   creating build
2020-05-29T05:47:24,883   creating build/lib
2020-05-29T05:47:24,885   creating build/lib/gtdbtk
2020-05-29T05:47:24,887   copying gtdbtk/reroot_tree.py -> build/lib/gtdbtk
2020-05-29T05:47:24,893   copying gtdbtk/decorate.py -> build/lib/gtdbtk
2020-05-29T05:47:24,898   copying gtdbtk/ani_rep.py -> build/lib/gtdbtk
2020-05-29T05:47:24,904   copying gtdbtk/infer_ranks.py -> build/lib/gtdbtk
2020-05-29T05:47:24,911   copying gtdbtk/relative_distance.py -> build/lib/gtdbtk
2020-05-29T05:47:24,918   copying gtdbtk/classify.py -> build/lib/gtdbtk
2020-05-29T05:47:24,933   copying gtdbtk/trim_msa.py -> build/lib/gtdbtk
2020-05-29T05:47:24,940   copying gtdbtk/markers.py -> build/lib/gtdbtk
2020-05-29T05:47:24,948   copying gtdbtk/misc.py -> build/lib/gtdbtk
2020-05-29T05:47:24,954   copying gtdbtk/main.py -> build/lib/gtdbtk
2020-05-29T05:47:24,963   copying gtdbtk/tools.py -> build/lib/gtdbtk
2020-05-29T05:47:24,969   copying gtdbtk/__init__.py -> build/lib/gtdbtk
2020-05-29T05:47:24,974   copying gtdbtk/exceptions.py -> build/lib/gtdbtk
2020-05-29T05:47:24,980   copying gtdbtk/__main__.py -> build/lib/gtdbtk
2020-05-29T05:47:24,992   creating build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:24,995   copying gtdbtk/biolib_lite/prodigal_biolib.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,002   copying gtdbtk/biolib_lite/execute.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,008   copying gtdbtk/biolib_lite/logger.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,015   copying gtdbtk/biolib_lite/common.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,021   copying gtdbtk/biolib_lite/seq_io.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,027   copying gtdbtk/biolib_lite/parallel.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,034   copying gtdbtk/biolib_lite/custom_help_formatter.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,040   copying gtdbtk/biolib_lite/taxonomy.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,049   copying gtdbtk/biolib_lite/__init__.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,053   copying gtdbtk/biolib_lite/exceptions.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,058   copying gtdbtk/biolib_lite/newick.py -> build/lib/gtdbtk/biolib_lite
2020-05-29T05:47:25,065   creating build/lib/gtdbtk/config
2020-05-29T05:47:25,068   copying gtdbtk/config/output.py -> build/lib/gtdbtk/config
2020-05-29T05:47:25,074   copying gtdbtk/config/config.py -> build/lib/gtdbtk/config
2020-05-29T05:47:25,081   copying gtdbtk/config/config_template.py -> build/lib/gtdbtk/config
2020-05-29T05:47:25,088   copying gtdbtk/config/__init__.py -> build/lib/gtdbtk/config
2020-05-29T05:47:25,095   creating build/lib/gtdbtk/external
2020-05-29T05:47:25,097   copying gtdbtk/external/prodigal.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,104   copying gtdbtk/external/hmm_aligner.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,110   copying gtdbtk/external/tigrfam_search.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,115   copying gtdbtk/external/fasttree.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,120   copying gtdbtk/external/mash.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,125   copying gtdbtk/external/pplacer.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,132   copying gtdbtk/external/fastani.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,139   copying gtdbtk/external/__init__.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,144   copying gtdbtk/external/pfam_search.py -> build/lib/gtdbtk/external
2020-05-29T05:47:25,150   package init file 'gtdbtk/tests/__init__.py' not found (or not a regular file)
2020-05-29T05:47:25,155   creating build/lib/gtdbtk/external/pypfam
2020-05-29T05:47:25,157   copying gtdbtk/external/pypfam/__init__.py -> build/lib/gtdbtk/external/pypfam
2020-05-29T05:47:25,165   creating build/lib/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:25,168   copying gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:25,176   copying gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:25,180   copying gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:25,185   copying gtdbtk/external/pypfam/HMM/__init__.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:25,189   copying gtdbtk/external/pypfam/HMM/HMMResults.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:25,196   copying gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:25,204   creating build/lib/gtdbtk/external/pypfam/Scan
2020-05-29T05:47:25,207   copying gtdbtk/external/pypfam/Scan/PfamScan.py -> build/lib/gtdbtk/external/pypfam/Scan
2020-05-29T05:47:25,216   copying gtdbtk/external/pypfam/Scan/__init__.py -> build/lib/gtdbtk/external/pypfam/Scan
2020-05-29T05:47:25,222   creating build/lib/gtdbtk/io
2020-05-29T05:47:25,225   copying gtdbtk/io/__init__.py -> build/lib/gtdbtk/io
2020-05-29T05:47:25,232   creating build/lib/gtdbtk/io/marker
2020-05-29T05:47:25,234   copying gtdbtk/io/marker/tophit.py -> build/lib/gtdbtk/io/marker
2020-05-29T05:47:25,242   copying gtdbtk/io/marker/copy_number.py -> build/lib/gtdbtk/io/marker
2020-05-29T05:47:25,249   copying gtdbtk/io/marker/__init__.py -> build/lib/gtdbtk/io/marker
2020-05-29T05:47:25,255   creating build/lib/gtdbtk/io/prodigal
2020-05-29T05:47:25,258   copying gtdbtk/io/prodigal/tln_table_summary.py -> build/lib/gtdbtk/io/prodigal
2020-05-29T05:47:25,264   copying gtdbtk/io/prodigal/tln_table.py -> build/lib/gtdbtk/io/prodigal
2020-05-29T05:47:25,270   copying gtdbtk/io/prodigal/__init__.py -> build/lib/gtdbtk/io/prodigal
2020-05-29T05:47:25,278   copying gtdbtk/VERSION -> build/lib/gtdbtk
2020-05-29T05:47:25,283   creating build/lib/gtdbtk/tests
2020-05-29T05:47:25,284   creating build/lib/gtdbtk/tests/data
2020-05-29T05:47:25,285   creating build/lib/gtdbtk/tests/data/genomes
2020-05-29T05:47:25,288   copying gtdbtk/tests/data/genomes/genome_3.fna -> build/lib/gtdbtk/tests/data/genomes
2020-05-29T05:47:25,406   copying gtdbtk/tests/data/genomes/genome_2.fna -> build/lib/gtdbtk/tests/data/genomes
2020-05-29T05:47:25,531   copying gtdbtk/tests/data/genomes/genome_1.fna -> build/lib/gtdbtk/tests/data/genomes
2020-05-29T05:47:25,851   installing to build/bdist.linux-armv7l/wheel
2020-05-29T05:47:25,851   running install
2020-05-29T05:47:25,853   running install_lib
2020-05-29T05:47:25,860   creating build/bdist.linux-armv7l
2020-05-29T05:47:25,860   creating build/bdist.linux-armv7l/wheel
2020-05-29T05:47:25,865   creating build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:25,867   copying build/lib/gtdbtk/reroot_tree.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:25,875   creating build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,877   copying build/lib/gtdbtk/biolib_lite/prodigal_biolib.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,883   copying build/lib/gtdbtk/biolib_lite/execute.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,889   copying build/lib/gtdbtk/biolib_lite/logger.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,896   copying build/lib/gtdbtk/biolib_lite/common.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,904   copying build/lib/gtdbtk/biolib_lite/seq_io.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,911   copying build/lib/gtdbtk/biolib_lite/parallel.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,918   copying build/lib/gtdbtk/biolib_lite/custom_help_formatter.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,924   copying build/lib/gtdbtk/biolib_lite/taxonomy.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,933   copying build/lib/gtdbtk/biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,937   copying build/lib/gtdbtk/biolib_lite/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,942   copying build/lib/gtdbtk/biolib_lite/newick.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-05-29T05:47:25,947   copying build/lib/gtdbtk/decorate.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:25,954   copying build/lib/gtdbtk/ani_rep.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:25,960   copying build/lib/gtdbtk/infer_ranks.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:25,966   copying build/lib/gtdbtk/relative_distance.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:25,972   copying build/lib/gtdbtk/classify.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:25,988   creating build/bdist.linux-armv7l/wheel/gtdbtk/io
2020-05-29T05:47:25,991   creating build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-05-29T05:47:25,995   copying build/lib/gtdbtk/io/marker/tophit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-05-29T05:47:26,002   copying build/lib/gtdbtk/io/marker/copy_number.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-05-29T05:47:26,008   copying build/lib/gtdbtk/io/marker/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-05-29T05:47:26,014   creating build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-05-29T05:47:26,016   copying build/lib/gtdbtk/io/prodigal/tln_table_summary.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-05-29T05:47:26,022   copying build/lib/gtdbtk/io/prodigal/tln_table.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-05-29T05:47:26,027   copying build/lib/gtdbtk/io/prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-05-29T05:47:26,032   copying build/lib/gtdbtk/io/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io
2020-05-29T05:47:26,036   copying build/lib/gtdbtk/trim_msa.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,044   creating build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,046   copying build/lib/gtdbtk/external/prodigal.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,055   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam
2020-05-29T05:47:26,059   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-05-29T05:47:26,062   copying build/lib/gtdbtk/external/pypfam/Scan/PfamScan.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-05-29T05:47:26,070   copying build/lib/gtdbtk/external/pypfam/Scan/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-05-29T05:47:26,074   copying build/lib/gtdbtk/external/pypfam/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam
2020-05-29T05:47:26,080   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:26,083   copying build/lib/gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:26,091   copying build/lib/gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:26,096   copying build/lib/gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:26,101   copying build/lib/gtdbtk/external/pypfam/HMM/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:26,105   copying build/lib/gtdbtk/external/pypfam/HMM/HMMResults.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:26,111   copying build/lib/gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-05-29T05:47:26,116   copying build/lib/gtdbtk/external/hmm_aligner.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,123   copying build/lib/gtdbtk/external/tigrfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,129   copying build/lib/gtdbtk/external/fasttree.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,135   copying build/lib/gtdbtk/external/mash.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,142   copying build/lib/gtdbtk/external/pplacer.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,149   copying build/lib/gtdbtk/external/fastani.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,156   copying build/lib/gtdbtk/external/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,160   copying build/lib/gtdbtk/external/pfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-05-29T05:47:26,165   copying build/lib/gtdbtk/markers.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,172   copying build/lib/gtdbtk/misc.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,179   copying build/lib/gtdbtk/VERSION -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,187   creating build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-05-29T05:47:26,190   copying build/lib/gtdbtk/config/output.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-05-29T05:47:26,197   copying build/lib/gtdbtk/config/config.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-05-29T05:47:26,204   copying build/lib/gtdbtk/config/config_template.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-05-29T05:47:26,211   copying build/lib/gtdbtk/config/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-05-29T05:47:26,216   copying build/lib/gtdbtk/main.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,226   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests
2020-05-29T05:47:26,230   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data
2020-05-29T05:47:26,235   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-05-29T05:47:26,238   copying build/lib/gtdbtk/tests/data/genomes/genome_3.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-05-29T05:47:26,361   copying build/lib/gtdbtk/tests/data/genomes/genome_2.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-05-29T05:47:26,490   copying build/lib/gtdbtk/tests/data/genomes/genome_1.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-05-29T05:47:26,779   copying build/lib/gtdbtk/tools.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,792   copying build/lib/gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,798   copying build/lib/gtdbtk/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,804   copying build/lib/gtdbtk/__main__.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-05-29T05:47:26,811   running install_data
2020-05-29T05:47:26,818   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.2.0.data
2020-05-29T05:47:26,819   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.2.0.data/data
2020-05-29T05:47:26,822   copying LICENSE -> build/bdist.linux-armv7l/wheel/gtdbtk-1.2.0.data/data/
2020-05-29T05:47:26,830   running install_egg_info
2020-05-29T05:47:26,868   running egg_info
2020-05-29T05:47:26,869   writing gtdbtk.egg-info/PKG-INFO
2020-05-29T05:47:26,874   writing dependency_links to gtdbtk.egg-info/dependency_links.txt
2020-05-29T05:47:26,878   writing entry points to gtdbtk.egg-info/entry_points.txt
2020-05-29T05:47:26,881   writing requirements to gtdbtk.egg-info/requires.txt
2020-05-29T05:47:26,884   writing top-level names to gtdbtk.egg-info/top_level.txt
2020-05-29T05:47:26,906   reading manifest file 'gtdbtk.egg-info/SOURCES.txt'
2020-05-29T05:47:26,912   reading manifest template 'MANIFEST.in'
2020-05-29T05:47:26,914   warning: no files found matching 'genome_1.fna'
2020-05-29T05:47:26,914   warning: no files found matching 'genome_2.fna'
2020-05-29T05:47:26,915   warning: no files found matching 'genome_3.fna'
2020-05-29T05:47:26,918   warning: no previously-included files matching 'genome_*_protein.fna' found anywhere in distribution
2020-05-29T05:47:26,928   writing manifest file 'gtdbtk.egg-info/SOURCES.txt'
2020-05-29T05:47:26,932   Copying gtdbtk.egg-info to build/bdist.linux-armv7l/wheel/gtdbtk-1.2.0-py3.7.egg-info
2020-05-29T05:47:26,960   running install_scripts
2020-05-29T05:47:27,115   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2020-05-29T05:47:27,131   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.2.0.dist-info/WHEEL
2020-05-29T05:47:27,136   creating '/tmp/pip-wheel-d7ezxqfj/gtdbtk-1.2.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2020-05-29T05:47:27,143   adding 'gtdbtk/VERSION'
2020-05-29T05:47:27,146   adding 'gtdbtk/__init__.py'
2020-05-29T05:47:27,153   adding 'gtdbtk/__main__.py'
2020-05-29T05:47:27,157   adding 'gtdbtk/ani_rep.py'
2020-05-29T05:47:27,173   adding 'gtdbtk/classify.py'
2020-05-29T05:47:27,179   adding 'gtdbtk/decorate.py'
2020-05-29T05:47:27,183   adding 'gtdbtk/exceptions.py'
2020-05-29T05:47:27,187   adding 'gtdbtk/infer_ranks.py'
2020-05-29T05:47:27,193   adding 'gtdbtk/main.py'
2020-05-29T05:47:27,200   adding 'gtdbtk/markers.py'
2020-05-29T05:47:27,204   adding 'gtdbtk/misc.py'
2020-05-29T05:47:27,209   adding 'gtdbtk/relative_distance.py'
2020-05-29T05:47:27,212   adding 'gtdbtk/reroot_tree.py'
2020-05-29T05:47:27,215   adding 'gtdbtk/tools.py'
2020-05-29T05:47:27,219   adding 'gtdbtk/trim_msa.py'
2020-05-29T05:47:27,223   adding 'gtdbtk/biolib_lite/__init__.py'
2020-05-29T05:47:27,225   adding 'gtdbtk/biolib_lite/common.py'
2020-05-29T05:47:27,228   adding 'gtdbtk/biolib_lite/custom_help_formatter.py'
2020-05-29T05:47:27,231   adding 'gtdbtk/biolib_lite/exceptions.py'
2020-05-29T05:47:27,234   adding 'gtdbtk/biolib_lite/execute.py'
2020-05-29T05:47:27,237   adding 'gtdbtk/biolib_lite/logger.py'
2020-05-29T05:47:27,239   adding 'gtdbtk/biolib_lite/newick.py'
2020-05-29T05:47:27,243   adding 'gtdbtk/biolib_lite/parallel.py'
2020-05-29T05:47:27,247   adding 'gtdbtk/biolib_lite/prodigal_biolib.py'
2020-05-29T05:47:27,250   adding 'gtdbtk/biolib_lite/seq_io.py'
2020-05-29T05:47:27,256   adding 'gtdbtk/biolib_lite/taxonomy.py'
2020-05-29T05:47:27,260   adding 'gtdbtk/config/__init__.py'
2020-05-29T05:47:27,264   adding 'gtdbtk/config/config.py'
2020-05-29T05:47:27,267   adding 'gtdbtk/config/config_template.py'
2020-05-29T05:47:27,270   adding 'gtdbtk/config/output.py'
2020-05-29T05:47:27,274   adding 'gtdbtk/external/__init__.py'
2020-05-29T05:47:27,278   adding 'gtdbtk/external/fastani.py'
2020-05-29T05:47:27,281   adding 'gtdbtk/external/fasttree.py'
2020-05-29T05:47:27,285   adding 'gtdbtk/external/hmm_aligner.py'
2020-05-29T05:47:27,288   adding 'gtdbtk/external/mash.py'
2020-05-29T05:47:27,291   adding 'gtdbtk/external/pfam_search.py'
2020-05-29T05:47:27,295   adding 'gtdbtk/external/pplacer.py'
2020-05-29T05:47:27,299   adding 'gtdbtk/external/prodigal.py'
2020-05-29T05:47:27,302   adding 'gtdbtk/external/tigrfam_search.py'
2020-05-29T05:47:27,306   adding 'gtdbtk/external/pypfam/__init__.py'
2020-05-29T05:47:27,309   adding 'gtdbtk/external/pypfam/HMM/HMMMatch.py'
2020-05-29T05:47:27,312   adding 'gtdbtk/external/pypfam/HMM/HMMResults.py'
2020-05-29T05:47:27,317   adding 'gtdbtk/external/pypfam/HMM/HMMResultsIO.py'
2020-05-29T05:47:27,320   adding 'gtdbtk/external/pypfam/HMM/HMMSequence.py'
2020-05-29T05:47:27,323   adding 'gtdbtk/external/pypfam/HMM/HMMUnit.py'
2020-05-29T05:47:27,325   adding 'gtdbtk/external/pypfam/HMM/__init__.py'
2020-05-29T05:47:27,331   adding 'gtdbtk/external/pypfam/Scan/PfamScan.py'
2020-05-29T05:47:27,333   adding 'gtdbtk/external/pypfam/Scan/__init__.py'
2020-05-29T05:47:27,337   adding 'gtdbtk/io/__init__.py'
2020-05-29T05:47:27,340   adding 'gtdbtk/io/marker/__init__.py'
2020-05-29T05:47:27,344   adding 'gtdbtk/io/marker/copy_number.py'
2020-05-29T05:47:27,347   adding 'gtdbtk/io/marker/tophit.py'
2020-05-29T05:47:27,350   adding 'gtdbtk/io/prodigal/__init__.py'
2020-05-29T05:47:27,353   adding 'gtdbtk/io/prodigal/tln_table.py'
2020-05-29T05:47:27,356   adding 'gtdbtk/io/prodigal/tln_table_summary.py'
2020-05-29T05:47:29,577   adding 'gtdbtk/tests/data/genomes/genome_1.fna'
2020-05-29T05:47:30,598   adding 'gtdbtk/tests/data/genomes/genome_2.fna'
2020-05-29T05:47:31,527   adding 'gtdbtk/tests/data/genomes/genome_3.fna'
2020-05-29T05:47:31,555   adding 'gtdbtk-1.2.0.data/data/LICENSE'
2020-05-29T05:47:31,568   adding 'gtdbtk-1.2.0.dist-info/LICENSE'
2020-05-29T05:47:31,571   adding 'gtdbtk-1.2.0.dist-info/METADATA'
2020-05-29T05:47:31,573   adding 'gtdbtk-1.2.0.dist-info/WHEEL'
2020-05-29T05:47:31,575   adding 'gtdbtk-1.2.0.dist-info/entry_points.txt'
2020-05-29T05:47:31,577   adding 'gtdbtk-1.2.0.dist-info/top_level.txt'
2020-05-29T05:47:31,579   adding 'gtdbtk-1.2.0.dist-info/RECORD'
2020-05-29T05:47:31,736   removing build/bdist.linux-armv7l/wheel
2020-05-29T05:47:31,962   Building wheel for gtdbtk (setup.py): finished with status 'done'
2020-05-29T05:47:31,993   Created wheel for gtdbtk: filename=gtdbtk-1.2.0-py3-none-any.whl size=1764434 sha256=6f16eed44889ee0d388564ccd30cce43c7059cb71fea4178339085d5cda33d84
2020-05-29T05:47:31,994   Stored in directory: /tmp/pip-ephem-wheel-cache-pauh8_3f/wheels/26/a5/58/72433a41b79b30e770d4cf83e0d90d89b7516fc431eb49ad97
2020-05-29T05:47:31,997 Successfully built gtdbtk
2020-05-29T05:47:32,311 Removed build tracker: '/tmp/pip-req-tracker-fsl117m3'