2020-04-14T05:02:58,616 Created temporary directory: /tmp/pip-ephem-wheel-cache-v6igdiq_
2020-04-14T05:02:58,620 Created temporary directory: /tmp/pip-req-tracker-4hirpimq
2020-04-14T05:02:58,621 Initialized build tracking at /tmp/pip-req-tracker-4hirpimq
2020-04-14T05:02:58,622 Created build tracker: /tmp/pip-req-tracker-4hirpimq
2020-04-14T05:02:58,622 Entered build tracker: /tmp/pip-req-tracker-4hirpimq
2020-04-14T05:02:58,623 Created temporary directory: /tmp/pip-wheel-xq43rj4w
2020-04-14T05:02:58,629 1 location(s) to search for versions of gtdbtk:
2020-04-14T05:02:58,629 * https://pypi.org/simple/gtdbtk/
2020-04-14T05:02:58,629 Fetching project page and analyzing links: https://pypi.org/simple/gtdbtk/
2020-04-14T05:02:58,630 Getting page https://pypi.org/simple/gtdbtk/
2020-04-14T05:02:58,632 Found index url https://pypi.org/simple
2020-04-14T05:02:58,636 Getting credentials from keyring for https://pypi.org/simple
2020-04-14T05:02:58,636 Getting credentials from keyring for pypi.org
2020-04-14T05:02:58,869   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
2020-04-14T05:02:58,870   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
2020-04-14T05:02:58,870   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
2020-04-14T05:02:58,871   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
2020-04-14T05:02:58,871   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
2020-04-14T05:02:58,872   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
2020-04-14T05:02:58,873   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
2020-04-14T05:02:58,873   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
2020-04-14T05:02:58,874   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
2020-04-14T05:02:58,874   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
2020-04-14T05:02:58,875   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
2020-04-14T05:02:58,875   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
2020-04-14T05:02:58,876   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
2020-04-14T05:02:58,877   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
2020-04-14T05:02:58,877   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
2020-04-14T05:02:58,878   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
2020-04-14T05:02:58,878   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
2020-04-14T05:02:58,879   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
2020-04-14T05:02:58,880   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
2020-04-14T05:02:58,881   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
2020-04-14T05:02:58,881   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
2020-04-14T05:02:58,882   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
2020-04-14T05:02:58,883   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
2020-04-14T05:02:58,884   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
2020-04-14T05:02:58,885   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
2020-04-14T05:02:58,886   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
2020-04-14T05:02:58,900 Given no hashes to check 1 links for project 'gtdbtk': discarding no candidates
2020-04-14T05:02:58,902 Using version 1.1.0 (newest of versions: 1.1.0)
2020-04-14T05:02:58,907 Collecting gtdbtk==1.1.0
2020-04-14T05:02:58,911   Created temporary directory: /tmp/pip-unpack-8pdxqsg0
2020-04-14T05:02:58,913   Getting credentials from keyring for files.pythonhosted.org
2020-04-14T05:02:59,577   Downloading gtdbtk-1.1.0.tar.gz (1.7 MB)
2020-04-14T05:03:01,174   Added gtdbtk==1.1.0 from https://files.pythonhosted.org/packages/f0/28/78411977ec02799a3a16a08ba9ea036851fd23d26126a583d7a4dbd7e129/gtdbtk-1.1.0.tar.gz#sha256=ffee0895b016c173ad043853a7d5111154f7e04194d2a2bc05a150acf9669f8a to build tracker '/tmp/pip-req-tracker-4hirpimq'
2020-04-14T05:03:01,176     Running setup.py (path:/tmp/pip-wheel-xq43rj4w/gtdbtk/setup.py) egg_info for package gtdbtk
2020-04-14T05:03:01,177     Running command python setup.py egg_info
2020-04-14T05:03:03,286     running egg_info
2020-04-14T05:03:03,291     creating /tmp/pip-wheel-xq43rj4w/gtdbtk/pip-egg-info/gtdbtk.egg-info
2020-04-14T05:03:03,293     writing /tmp/pip-wheel-xq43rj4w/gtdbtk/pip-egg-info/gtdbtk.egg-info/PKG-INFO
2020-04-14T05:03:03,304     writing dependency_links to /tmp/pip-wheel-xq43rj4w/gtdbtk/pip-egg-info/gtdbtk.egg-info/dependency_links.txt
2020-04-14T05:03:03,308     writing requirements to /tmp/pip-wheel-xq43rj4w/gtdbtk/pip-egg-info/gtdbtk.egg-info/requires.txt
2020-04-14T05:03:03,310     writing top-level names to /tmp/pip-wheel-xq43rj4w/gtdbtk/pip-egg-info/gtdbtk.egg-info/top_level.txt
2020-04-14T05:03:03,314     writing manifest file '/tmp/pip-wheel-xq43rj4w/gtdbtk/pip-egg-info/gtdbtk.egg-info/SOURCES.txt'
2020-04-14T05:03:03,611     package init file 'gtdbtk/tests/__init__.py' not found (or not a regular file)
2020-04-14T05:03:03,642     reading manifest file '/tmp/pip-wheel-xq43rj4w/gtdbtk/pip-egg-info/gtdbtk.egg-info/SOURCES.txt'
2020-04-14T05:03:03,645     reading manifest template 'MANIFEST.in'
2020-04-14T05:03:03,648     warning: no files found matching 'genome_1.fna'
2020-04-14T05:03:03,649     warning: no files found matching 'genome_2.fna'
2020-04-14T05:03:03,650     warning: no files found matching 'genome_3.fna'
2020-04-14T05:03:03,652     warning: no previously-included files matching 'genome_*_protein.fna' found anywhere in distribution
2020-04-14T05:03:03,659     writing manifest file '/tmp/pip-wheel-xq43rj4w/gtdbtk/pip-egg-info/gtdbtk.egg-info/SOURCES.txt'
2020-04-14T05:03:03,780   Source in /tmp/pip-wheel-xq43rj4w/gtdbtk has version 1.1.0, which satisfies requirement gtdbtk==1.1.0 from https://files.pythonhosted.org/packages/f0/28/78411977ec02799a3a16a08ba9ea036851fd23d26126a583d7a4dbd7e129/gtdbtk-1.1.0.tar.gz#sha256=ffee0895b016c173ad043853a7d5111154f7e04194d2a2bc05a150acf9669f8a
2020-04-14T05:03:03,782   Removed gtdbtk==1.1.0 from https://files.pythonhosted.org/packages/f0/28/78411977ec02799a3a16a08ba9ea036851fd23d26126a583d7a4dbd7e129/gtdbtk-1.1.0.tar.gz#sha256=ffee0895b016c173ad043853a7d5111154f7e04194d2a2bc05a150acf9669f8a from build tracker '/tmp/pip-req-tracker-4hirpimq'
2020-04-14T05:03:03,790 Building wheels for collected packages: gtdbtk
2020-04-14T05:03:03,799   Created temporary directory: /tmp/pip-wheel-fknuc1xq
2020-04-14T05:03:03,800   Building wheel for gtdbtk (setup.py): started
2020-04-14T05:03:03,800   Destination directory: /tmp/pip-wheel-fknuc1xq
2020-04-14T05:03:03,801   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-xq43rj4w/gtdbtk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-xq43rj4w/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-fknuc1xq
2020-04-14T05:03:05,792   running bdist_wheel
2020-04-14T05:03:05,804   running build
2020-04-14T05:03:05,805   running build_py
2020-04-14T05:03:06,079   creating build
2020-04-14T05:03:06,079   creating build/lib
2020-04-14T05:03:06,081   creating build/lib/gtdbtk
2020-04-14T05:03:06,084   copying gtdbtk/ani_rep.py -> build/lib/gtdbtk
2020-04-14T05:03:06,089   copying gtdbtk/main.py -> build/lib/gtdbtk
2020-04-14T05:03:06,096   copying gtdbtk/relative_distance.py -> build/lib/gtdbtk
2020-04-14T05:03:06,103   copying gtdbtk/misc.py -> build/lib/gtdbtk
2020-04-14T05:03:06,110   copying gtdbtk/classify.py -> build/lib/gtdbtk
2020-04-14T05:03:06,123   copying gtdbtk/trim_msa.py -> build/lib/gtdbtk
2020-04-14T05:03:06,131   copying gtdbtk/exceptions.py -> build/lib/gtdbtk
2020-04-14T05:03:06,138   copying gtdbtk/__init__.py -> build/lib/gtdbtk
2020-04-14T05:03:06,145   copying gtdbtk/reroot_tree.py -> build/lib/gtdbtk
2020-04-14T05:03:06,152   copying gtdbtk/tools.py -> build/lib/gtdbtk
2020-04-14T05:03:06,159   copying gtdbtk/markers.py -> build/lib/gtdbtk
2020-04-14T05:03:06,170   creating build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,173   copying gtdbtk/biolib_lite/common.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,180   copying gtdbtk/biolib_lite/newick.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,185   copying gtdbtk/biolib_lite/custom_help_formatter.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,196   copying gtdbtk/biolib_lite/logger.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,202   copying gtdbtk/biolib_lite/seq_io.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,208   copying gtdbtk/biolib_lite/exceptions.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,213   copying gtdbtk/biolib_lite/execute.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,219   copying gtdbtk/biolib_lite/__init__.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,223   copying gtdbtk/biolib_lite/taxonomy.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,232   copying gtdbtk/biolib_lite/parallel.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,238   copying gtdbtk/biolib_lite/prodigal_biolib.py -> build/lib/gtdbtk/biolib_lite
2020-04-14T05:03:06,247   creating build/lib/gtdbtk/config
2020-04-14T05:03:06,250   copying gtdbtk/config/output.py -> build/lib/gtdbtk/config
2020-04-14T05:03:06,255   copying gtdbtk/config/config.py -> build/lib/gtdbtk/config
2020-04-14T05:03:06,271   copying gtdbtk/config/config_template.py -> build/lib/gtdbtk/config
2020-04-14T05:03:06,278   copying gtdbtk/config/__init__.py -> build/lib/gtdbtk/config
2020-04-14T05:03:06,285   creating build/lib/gtdbtk/external
2020-04-14T05:03:06,290   copying gtdbtk/external/pfam_search.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,295   copying gtdbtk/external/tigrfam_search.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,300   copying gtdbtk/external/fastani.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,305   copying gtdbtk/external/hmm_aligner.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,312   copying gtdbtk/external/fasttree.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,318   copying gtdbtk/external/pplacer.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,328   copying gtdbtk/external/__init__.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,333   copying gtdbtk/external/prodigal.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,339   copying gtdbtk/external/mash.py -> build/lib/gtdbtk/external
2020-04-14T05:03:06,345   package init file 'gtdbtk/tests/__init__.py' not found (or not a regular file)
2020-04-14T05:03:06,349   creating build/lib/gtdbtk/external/pypfam
2020-04-14T05:03:06,351   copying gtdbtk/external/pypfam/__init__.py -> build/lib/gtdbtk/external/pypfam
2020-04-14T05:03:06,356   creating build/lib/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:06,358   copying gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:06,362   copying gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:06,368   copying gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:06,374   copying gtdbtk/external/pypfam/HMM/HMMResults.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:06,380   copying gtdbtk/external/pypfam/HMM/__init__.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:06,385   copying gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:06,391   creating build/lib/gtdbtk/external/pypfam/Scan
2020-04-14T05:03:06,393   copying gtdbtk/external/pypfam/Scan/PfamScan.py -> build/lib/gtdbtk/external/pypfam/Scan
2020-04-14T05:03:06,400   copying gtdbtk/external/pypfam/Scan/__init__.py -> build/lib/gtdbtk/external/pypfam/Scan
2020-04-14T05:03:06,404   creating build/lib/gtdbtk/io
2020-04-14T05:03:06,406   copying gtdbtk/io/__init__.py -> build/lib/gtdbtk/io
2020-04-14T05:03:06,410   creating build/lib/gtdbtk/io/marker
2020-04-14T05:03:06,413   copying gtdbtk/io/marker/copy_number.py -> build/lib/gtdbtk/io/marker
2020-04-14T05:03:06,420   copying gtdbtk/io/marker/__init__.py -> build/lib/gtdbtk/io/marker
2020-04-14T05:03:06,424   copying gtdbtk/io/marker/tophit.py -> build/lib/gtdbtk/io/marker
2020-04-14T05:03:06,432   creating build/lib/gtdbtk/io/prodigal
2020-04-14T05:03:06,434   copying gtdbtk/io/prodigal/tln_table_summary.py -> build/lib/gtdbtk/io/prodigal
2020-04-14T05:03:06,439   copying gtdbtk/io/prodigal/__init__.py -> build/lib/gtdbtk/io/prodigal
2020-04-14T05:03:06,446   copying gtdbtk/VERSION -> build/lib/gtdbtk
2020-04-14T05:03:06,451   creating build/lib/gtdbtk/tests
2020-04-14T05:03:06,452   creating build/lib/gtdbtk/tests/data
2020-04-14T05:03:06,453   creating build/lib/gtdbtk/tests/data/genomes
2020-04-14T05:03:06,456   copying gtdbtk/tests/data/genomes/genome_1.fna -> build/lib/gtdbtk/tests/data/genomes
2020-04-14T05:03:06,734   copying gtdbtk/tests/data/genomes/genome_3.fna -> build/lib/gtdbtk/tests/data/genomes
2020-04-14T05:03:06,855   copying gtdbtk/tests/data/genomes/genome_2.fna -> build/lib/gtdbtk/tests/data/genomes
2020-04-14T05:03:07,003   running build_scripts
2020-04-14T05:03:07,004   creating build/scripts-3.7
2020-04-14T05:03:07,007   copying and adjusting bin/gtdbtk -> build/scripts-3.7
2020-04-14T05:03:07,013   changing mode of build/scripts-3.7/gtdbtk from 644 to 755
2020-04-14T05:03:07,020   installing to build/bdist.linux-armv7l/wheel
2020-04-14T05:03:07,020   running install
2020-04-14T05:03:07,022   running install_lib
2020-04-14T05:03:07,030   creating build/bdist.linux-armv7l
2020-04-14T05:03:07,031   creating build/bdist.linux-armv7l/wheel
2020-04-14T05:03:07,035   creating build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,037   copying build/lib/gtdbtk/ani_rep.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,043   copying build/lib/gtdbtk/main.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,050   copying build/lib/gtdbtk/relative_distance.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,057   creating build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,060   copying build/lib/gtdbtk/external/pfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,067   copying build/lib/gtdbtk/external/tigrfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,073   copying build/lib/gtdbtk/external/fastani.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,080   copying build/lib/gtdbtk/external/hmm_aligner.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,088   copying build/lib/gtdbtk/external/fasttree.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,094   copying build/lib/gtdbtk/external/pplacer.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,101   copying build/lib/gtdbtk/external/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,106   copying build/lib/gtdbtk/external/prodigal.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,114   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam
2020-04-14T05:03:07,119   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-04-14T05:03:07,122   copying build/lib/gtdbtk/external/pypfam/Scan/PfamScan.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-04-14T05:03:07,130   copying build/lib/gtdbtk/external/pypfam/Scan/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-04-14T05:03:07,135   copying build/lib/gtdbtk/external/pypfam/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam
2020-04-14T05:03:07,141   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:07,143   copying build/lib/gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:07,150   copying build/lib/gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:07,158   copying build/lib/gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:07,163   copying build/lib/gtdbtk/external/pypfam/HMM/HMMResults.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:07,170   copying build/lib/gtdbtk/external/pypfam/HMM/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:07,175   copying build/lib/gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-14T05:03:07,181   copying build/lib/gtdbtk/external/mash.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-14T05:03:07,192   creating build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,195   copying build/lib/gtdbtk/biolib_lite/common.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,202   copying build/lib/gtdbtk/biolib_lite/newick.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,207   copying build/lib/gtdbtk/biolib_lite/custom_help_formatter.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,214   copying build/lib/gtdbtk/biolib_lite/logger.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,221   copying build/lib/gtdbtk/biolib_lite/seq_io.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,227   copying build/lib/gtdbtk/biolib_lite/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,233   copying build/lib/gtdbtk/biolib_lite/execute.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,239   copying build/lib/gtdbtk/biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,244   copying build/lib/gtdbtk/biolib_lite/taxonomy.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,252   copying build/lib/gtdbtk/biolib_lite/parallel.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,259   copying build/lib/gtdbtk/biolib_lite/prodigal_biolib.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-14T05:03:07,266   copying build/lib/gtdbtk/misc.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,274   creating build/bdist.linux-armv7l/wheel/gtdbtk/io
2020-04-14T05:03:07,278   creating build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-04-14T05:03:07,281   copying build/lib/gtdbtk/io/marker/copy_number.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-04-14T05:03:07,288   copying build/lib/gtdbtk/io/marker/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-04-14T05:03:07,292   copying build/lib/gtdbtk/io/marker/tophit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-04-14T05:03:07,299   copying build/lib/gtdbtk/io/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io
2020-04-14T05:03:07,305   creating build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-04-14T05:03:07,307   copying build/lib/gtdbtk/io/prodigal/tln_table_summary.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-04-14T05:03:07,313   copying build/lib/gtdbtk/io/prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-04-14T05:03:07,318   copying build/lib/gtdbtk/classify.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,329   copying build/lib/gtdbtk/trim_msa.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,335   copying build/lib/gtdbtk/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,340   copying build/lib/gtdbtk/VERSION -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,348   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests
2020-04-14T05:03:07,351   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data
2020-04-14T05:03:07,356   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-04-14T05:03:07,359   copying build/lib/gtdbtk/tests/data/genomes/genome_1.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-04-14T05:03:07,640   copying build/lib/gtdbtk/tests/data/genomes/genome_3.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-04-14T05:03:07,761   copying build/lib/gtdbtk/tests/data/genomes/genome_2.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-04-14T05:03:07,892   creating build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-14T05:03:07,895   copying build/lib/gtdbtk/config/output.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-14T05:03:07,901   copying build/lib/gtdbtk/config/config.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-14T05:03:07,908   copying build/lib/gtdbtk/config/config_template.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-14T05:03:07,916   copying build/lib/gtdbtk/config/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-14T05:03:07,921   copying build/lib/gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,926   copying build/lib/gtdbtk/reroot_tree.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,933   copying build/lib/gtdbtk/tools.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,940   copying build/lib/gtdbtk/markers.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-14T05:03:07,948   running install_data
2020-04-14T05:03:07,955   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.1.0.data
2020-04-14T05:03:07,955   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.1.0.data/data
2020-04-14T05:03:07,959   copying LICENSE -> build/bdist.linux-armv7l/wheel/gtdbtk-1.1.0.data/data/
2020-04-14T05:03:07,967   running install_egg_info
2020-04-14T05:03:08,012   running egg_info
2020-04-14T05:03:08,013   writing gtdbtk.egg-info/PKG-INFO
2020-04-14T05:03:08,021   writing dependency_links to gtdbtk.egg-info/dependency_links.txt
2020-04-14T05:03:08,025   writing requirements to gtdbtk.egg-info/requires.txt
2020-04-14T05:03:08,028   writing top-level names to gtdbtk.egg-info/top_level.txt
2020-04-14T05:03:08,058   reading manifest file 'gtdbtk.egg-info/SOURCES.txt'
2020-04-14T05:03:08,064   reading manifest template 'MANIFEST.in'
2020-04-14T05:03:08,065   warning: no files found matching 'genome_1.fna'
2020-04-14T05:03:08,066   warning: no files found matching 'genome_2.fna'
2020-04-14T05:03:08,066   warning: no files found matching 'genome_3.fna'
2020-04-14T05:03:08,067   warning: no previously-included files matching 'genome_*_protein.fna' found anywhere in distribution
2020-04-14T05:03:08,077   writing manifest file 'gtdbtk.egg-info/SOURCES.txt'
2020-04-14T05:03:08,080   Copying gtdbtk.egg-info to build/bdist.linux-armv7l/wheel/gtdbtk-1.1.0-py3.7.egg-info
2020-04-14T05:03:08,112   running install_scripts
2020-04-14T05:03:08,214   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.1.0.data/scripts
2020-04-14T05:03:08,216   copying build/scripts-3.7/gtdbtk -> build/bdist.linux-armv7l/wheel/gtdbtk-1.1.0.data/scripts
2020-04-14T05:03:08,223   changing mode of build/bdist.linux-armv7l/wheel/gtdbtk-1.1.0.data/scripts/gtdbtk to 755
2020-04-14T05:03:08,300   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2020-04-14T05:03:08,315   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.1.0.dist-info/WHEEL
2020-04-14T05:03:08,323   creating '/tmp/pip-wheel-fknuc1xq/gtdbtk-1.1.0-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2020-04-14T05:03:08,332   adding 'gtdbtk/VERSION'
2020-04-14T05:03:08,336   adding 'gtdbtk/__init__.py'
2020-04-14T05:03:08,339   adding 'gtdbtk/ani_rep.py'
2020-04-14T05:03:08,351   adding 'gtdbtk/classify.py'
2020-04-14T05:03:08,355   adding 'gtdbtk/exceptions.py'
2020-04-14T05:03:08,360   adding 'gtdbtk/main.py'
2020-04-14T05:03:08,366   adding 'gtdbtk/markers.py'
2020-04-14T05:03:08,369   adding 'gtdbtk/misc.py'
2020-04-14T05:03:08,374   adding 'gtdbtk/relative_distance.py'
2020-04-14T05:03:08,377   adding 'gtdbtk/reroot_tree.py'
2020-04-14T05:03:08,380   adding 'gtdbtk/tools.py'
2020-04-14T05:03:08,384   adding 'gtdbtk/trim_msa.py'
2020-04-14T05:03:08,388   adding 'gtdbtk/biolib_lite/__init__.py'
2020-04-14T05:03:08,391   adding 'gtdbtk/biolib_lite/common.py'
2020-04-14T05:03:08,394   adding 'gtdbtk/biolib_lite/custom_help_formatter.py'
2020-04-14T05:03:08,396   adding 'gtdbtk/biolib_lite/exceptions.py'
2020-04-14T05:03:08,399   adding 'gtdbtk/biolib_lite/execute.py'
2020-04-14T05:03:08,402   adding 'gtdbtk/biolib_lite/logger.py'
2020-04-14T05:03:08,405   adding 'gtdbtk/biolib_lite/newick.py'
2020-04-14T05:03:08,408   adding 'gtdbtk/biolib_lite/parallel.py'
2020-04-14T05:03:08,413   adding 'gtdbtk/biolib_lite/prodigal_biolib.py'
2020-04-14T05:03:08,416   adding 'gtdbtk/biolib_lite/seq_io.py'
2020-04-14T05:03:08,422   adding 'gtdbtk/biolib_lite/taxonomy.py'
2020-04-14T05:03:08,427   adding 'gtdbtk/config/__init__.py'
2020-04-14T05:03:08,430   adding 'gtdbtk/config/config.py'
2020-04-14T05:03:08,433   adding 'gtdbtk/config/config_template.py'
2020-04-14T05:03:08,436   adding 'gtdbtk/config/output.py'
2020-04-14T05:03:08,440   adding 'gtdbtk/external/__init__.py'
2020-04-14T05:03:08,444   adding 'gtdbtk/external/fastani.py'
2020-04-14T05:03:08,447   adding 'gtdbtk/external/fasttree.py'
2020-04-14T05:03:08,451   adding 'gtdbtk/external/hmm_aligner.py'
2020-04-14T05:03:08,454   adding 'gtdbtk/external/mash.py'
2020-04-14T05:03:08,457   adding 'gtdbtk/external/pfam_search.py'
2020-04-14T05:03:08,460   adding 'gtdbtk/external/pplacer.py'
2020-04-14T05:03:08,464   adding 'gtdbtk/external/prodigal.py'
2020-04-14T05:03:08,467   adding 'gtdbtk/external/tigrfam_search.py'
2020-04-14T05:03:08,471   adding 'gtdbtk/external/pypfam/__init__.py'
2020-04-14T05:03:08,475   adding 'gtdbtk/external/pypfam/HMM/HMMMatch.py'
2020-04-14T05:03:08,478   adding 'gtdbtk/external/pypfam/HMM/HMMResults.py'
2020-04-14T05:03:08,483   adding 'gtdbtk/external/pypfam/HMM/HMMResultsIO.py'
2020-04-14T05:03:08,485   adding 'gtdbtk/external/pypfam/HMM/HMMSequence.py'
2020-04-14T05:03:08,488   adding 'gtdbtk/external/pypfam/HMM/HMMUnit.py'
2020-04-14T05:03:08,490   adding 'gtdbtk/external/pypfam/HMM/__init__.py'
2020-04-14T05:03:08,497   adding 'gtdbtk/external/pypfam/Scan/PfamScan.py'
2020-04-14T05:03:08,499   adding 'gtdbtk/external/pypfam/Scan/__init__.py'
2020-04-14T05:03:08,503   adding 'gtdbtk/io/__init__.py'
2020-04-14T05:03:08,507   adding 'gtdbtk/io/marker/__init__.py'
2020-04-14T05:03:08,510   adding 'gtdbtk/io/marker/copy_number.py'
2020-04-14T05:03:08,513   adding 'gtdbtk/io/marker/tophit.py'
2020-04-14T05:03:08,517   adding 'gtdbtk/io/prodigal/__init__.py'
2020-04-14T05:03:08,519   adding 'gtdbtk/io/prodigal/tln_table_summary.py'
2020-04-14T05:03:10,720   adding 'gtdbtk/tests/data/genomes/genome_1.fna'
2020-04-14T05:03:11,722   adding 'gtdbtk/tests/data/genomes/genome_2.fna'
2020-04-14T05:03:12,634   adding 'gtdbtk/tests/data/genomes/genome_3.fna'
2020-04-14T05:03:12,662   adding 'gtdbtk-1.1.0.data/data/LICENSE'
2020-04-14T05:03:12,669   adding 'gtdbtk-1.1.0.data/scripts/gtdbtk'
2020-04-14T05:03:12,682   adding 'gtdbtk-1.1.0.dist-info/LICENSE'
2020-04-14T05:03:12,688   adding 'gtdbtk-1.1.0.dist-info/METADATA'
2020-04-14T05:03:12,691   adding 'gtdbtk-1.1.0.dist-info/WHEEL'
2020-04-14T05:03:12,692   adding 'gtdbtk-1.1.0.dist-info/top_level.txt'
2020-04-14T05:03:12,694   adding 'gtdbtk-1.1.0.dist-info/RECORD'
2020-04-14T05:03:12,850   removing build/bdist.linux-armv7l/wheel
2020-04-14T05:03:13,049   Building wheel for gtdbtk (setup.py): finished with status 'done'
2020-04-14T05:03:13,092   Created wheel for gtdbtk: filename=gtdbtk-1.1.0-py3-none-any.whl size=1754134 sha256=74644ddd23fa626c60834924b75ff2461cfe146825dfe8cb56ba7aa87f80065c
2020-04-14T05:03:13,093   Stored in directory: /tmp/pip-ephem-wheel-cache-v6igdiq_/wheels/7a/d0/c4/073391bf45919d728e4f6dfb6d73c3bfd29f6d2c68b96bcc72
2020-04-14T05:03:13,097 Successfully built gtdbtk
2020-04-14T05:03:13,409 Cleaning up...
2020-04-14T05:03:13,410   Removing source in /tmp/pip-wheel-xq43rj4w/gtdbtk
2020-04-14T05:03:13,569 Removed build tracker: '/tmp/pip-req-tracker-4hirpimq'