2020-04-22T07:37:50,133 Created temporary directory: /tmp/pip-ephem-wheel-cache-eav_yvte
2020-04-22T07:37:50,138 Created temporary directory: /tmp/pip-req-tracker-jp4v4qqo
2020-04-22T07:37:50,138 Initialized build tracking at /tmp/pip-req-tracker-jp4v4qqo
2020-04-22T07:37:50,139 Created build tracker: /tmp/pip-req-tracker-jp4v4qqo
2020-04-22T07:37:50,139 Entered build tracker: /tmp/pip-req-tracker-jp4v4qqo
2020-04-22T07:37:50,140 Created temporary directory: /tmp/pip-wheel-nx8548hc
2020-04-22T07:37:50,146 1 location(s) to search for versions of gtdbtk:
2020-04-22T07:37:50,146 * https://pypi.org/simple/gtdbtk/
2020-04-22T07:37:50,146 Fetching project page and analyzing links: https://pypi.org/simple/gtdbtk/
2020-04-22T07:37:50,147 Getting page https://pypi.org/simple/gtdbtk/
2020-04-22T07:37:50,150 Found index url https://pypi.org/simple
2020-04-22T07:37:50,153 Getting credentials from keyring for https://pypi.org/simple
2020-04-22T07:37:50,154 Getting credentials from keyring for pypi.org
2020-04-22T07:37:50,388   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
2020-04-22T07:37:50,388   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
2020-04-22T07:37:50,389   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
2020-04-22T07:37:50,390   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
2020-04-22T07:37:50,390   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
2020-04-22T07:37:50,391   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
2020-04-22T07:37:50,391   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
2020-04-22T07:37:50,392   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
2020-04-22T07:37:50,392   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
2020-04-22T07:37:50,393   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
2020-04-22T07:37:50,394   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
2020-04-22T07:37:50,394   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
2020-04-22T07:37:50,395   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
2020-04-22T07:37:50,395   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
2020-04-22T07:37:50,396   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
2020-04-22T07:37:50,396   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
2020-04-22T07:37:50,398   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
2020-04-22T07:37:50,398   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
2020-04-22T07:37:50,399   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
2020-04-22T07:37:50,399   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
2020-04-22T07:37:50,400   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
2020-04-22T07:37:50,400   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
2020-04-22T07:37:50,401   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
2020-04-22T07:37:50,402   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
2020-04-22T07:37:50,403   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
2020-04-22T07:37:50,404   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
2020-04-22T07:37:50,405   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
2020-04-22T07:37:50,420 Given no hashes to check 1 links for project 'gtdbtk': discarding no candidates
2020-04-22T07:37:50,422 Using version 1.1.1 (newest of versions: 1.1.1)
2020-04-22T07:37:50,427 Collecting gtdbtk==1.1.1
2020-04-22T07:37:50,431   Created temporary directory: /tmp/pip-unpack-eob6kvzz
2020-04-22T07:37:50,433   Getting credentials from keyring for files.pythonhosted.org
2020-04-22T07:37:50,676   Downloading gtdbtk-1.1.1.tar.gz (1.6 MB)
2020-04-22T07:37:52,295   Added gtdbtk==1.1.1 from https://files.pythonhosted.org/packages/68/d0/bcdb38880ed7e0d0ae563c62b1f192b1d77a35a0d00b193f9e5a01817454/gtdbtk-1.1.1.tar.gz#sha256=b1ee2e8c0a75132b8061b454676f9dd68acfeaf6ee71fab48db005b6eed57263 to build tracker '/tmp/pip-req-tracker-jp4v4qqo'
2020-04-22T07:37:52,298     Running setup.py (path:/tmp/pip-wheel-nx8548hc/gtdbtk/setup.py) egg_info for package gtdbtk
2020-04-22T07:37:52,300     Running command python setup.py egg_info
2020-04-22T07:37:54,412     running egg_info
2020-04-22T07:37:54,417     creating /tmp/pip-wheel-nx8548hc/gtdbtk/pip-egg-info/gtdbtk.egg-info
2020-04-22T07:37:54,419     writing /tmp/pip-wheel-nx8548hc/gtdbtk/pip-egg-info/gtdbtk.egg-info/PKG-INFO
2020-04-22T07:37:54,425     writing dependency_links to /tmp/pip-wheel-nx8548hc/gtdbtk/pip-egg-info/gtdbtk.egg-info/dependency_links.txt
2020-04-22T07:37:54,429     writing requirements to /tmp/pip-wheel-nx8548hc/gtdbtk/pip-egg-info/gtdbtk.egg-info/requires.txt
2020-04-22T07:37:54,431     writing top-level names to /tmp/pip-wheel-nx8548hc/gtdbtk/pip-egg-info/gtdbtk.egg-info/top_level.txt
2020-04-22T07:37:54,435     writing manifest file '/tmp/pip-wheel-nx8548hc/gtdbtk/pip-egg-info/gtdbtk.egg-info/SOURCES.txt'
2020-04-22T07:37:54,742     package init file 'gtdbtk/tests/__init__.py' not found (or not a regular file)
2020-04-22T07:37:54,773     reading manifest file '/tmp/pip-wheel-nx8548hc/gtdbtk/pip-egg-info/gtdbtk.egg-info/SOURCES.txt'
2020-04-22T07:37:54,776     reading manifest template 'MANIFEST.in'
2020-04-22T07:37:54,779     warning: no files found matching 'genome_1.fna'
2020-04-22T07:37:54,779     warning: no files found matching 'genome_2.fna'
2020-04-22T07:37:54,780     warning: no files found matching 'genome_3.fna'
2020-04-22T07:37:54,782     warning: no previously-included files matching 'genome_*_protein.fna' found anywhere in distribution
2020-04-22T07:37:54,789     writing manifest file '/tmp/pip-wheel-nx8548hc/gtdbtk/pip-egg-info/gtdbtk.egg-info/SOURCES.txt'
2020-04-22T07:37:54,908   Source in /tmp/pip-wheel-nx8548hc/gtdbtk has version 1.1.1, which satisfies requirement gtdbtk==1.1.1 from https://files.pythonhosted.org/packages/68/d0/bcdb38880ed7e0d0ae563c62b1f192b1d77a35a0d00b193f9e5a01817454/gtdbtk-1.1.1.tar.gz#sha256=b1ee2e8c0a75132b8061b454676f9dd68acfeaf6ee71fab48db005b6eed57263
2020-04-22T07:37:54,910   Removed gtdbtk==1.1.1 from https://files.pythonhosted.org/packages/68/d0/bcdb38880ed7e0d0ae563c62b1f192b1d77a35a0d00b193f9e5a01817454/gtdbtk-1.1.1.tar.gz#sha256=b1ee2e8c0a75132b8061b454676f9dd68acfeaf6ee71fab48db005b6eed57263 from build tracker '/tmp/pip-req-tracker-jp4v4qqo'
2020-04-22T07:37:54,914 Building wheels for collected packages: gtdbtk
2020-04-22T07:37:54,924   Created temporary directory: /tmp/pip-wheel-r30q1unt
2020-04-22T07:37:54,924   Building wheel for gtdbtk (setup.py): started
2020-04-22T07:37:54,925   Destination directory: /tmp/pip-wheel-r30q1unt
2020-04-22T07:37:54,925   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-nx8548hc/gtdbtk/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-nx8548hc/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-r30q1unt
2020-04-22T07:37:57,053   running bdist_wheel
2020-04-22T07:37:57,782   running build
2020-04-22T07:37:57,783   running build_py
2020-04-22T07:37:58,053   creating build
2020-04-22T07:37:58,053   creating build/lib
2020-04-22T07:37:58,055   creating build/lib/gtdbtk
2020-04-22T07:37:58,058   copying gtdbtk/ani_rep.py -> build/lib/gtdbtk
2020-04-22T07:37:58,064   copying gtdbtk/main.py -> build/lib/gtdbtk
2020-04-22T07:37:58,072   copying gtdbtk/relative_distance.py -> build/lib/gtdbtk
2020-04-22T07:37:58,080   copying gtdbtk/misc.py -> build/lib/gtdbtk
2020-04-22T07:37:58,087   copying gtdbtk/classify.py -> build/lib/gtdbtk
2020-04-22T07:37:58,100   copying gtdbtk/trim_msa.py -> build/lib/gtdbtk
2020-04-22T07:37:58,108   copying gtdbtk/exceptions.py -> build/lib/gtdbtk
2020-04-22T07:37:58,114   copying gtdbtk/__init__.py -> build/lib/gtdbtk
2020-04-22T07:37:58,119   copying gtdbtk/reroot_tree.py -> build/lib/gtdbtk
2020-04-22T07:37:58,126   copying gtdbtk/tools.py -> build/lib/gtdbtk
2020-04-22T07:37:58,133   copying gtdbtk/markers.py -> build/lib/gtdbtk
2020-04-22T07:37:58,145   creating build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,148   copying gtdbtk/biolib_lite/common.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,153   copying gtdbtk/biolib_lite/newick.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,158   copying gtdbtk/biolib_lite/custom_help_formatter.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,163   copying gtdbtk/biolib_lite/logger.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,169   copying gtdbtk/biolib_lite/seq_io.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,176   copying gtdbtk/biolib_lite/exceptions.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,182   copying gtdbtk/biolib_lite/execute.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,188   copying gtdbtk/biolib_lite/__init__.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,193   copying gtdbtk/biolib_lite/taxonomy.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,202   copying gtdbtk/biolib_lite/parallel.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,209   copying gtdbtk/biolib_lite/prodigal_biolib.py -> build/lib/gtdbtk/biolib_lite
2020-04-22T07:37:58,218   creating build/lib/gtdbtk/config
2020-04-22T07:37:58,221   copying gtdbtk/config/output.py -> build/lib/gtdbtk/config
2020-04-22T07:37:58,227   copying gtdbtk/config/config.py -> build/lib/gtdbtk/config
2020-04-22T07:37:58,234   copying gtdbtk/config/config_template.py -> build/lib/gtdbtk/config
2020-04-22T07:37:58,241   copying gtdbtk/config/__init__.py -> build/lib/gtdbtk/config
2020-04-22T07:37:58,248   creating build/lib/gtdbtk/external
2020-04-22T07:37:58,251   copying gtdbtk/external/pfam_search.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,256   copying gtdbtk/external/tigrfam_search.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,261   copying gtdbtk/external/fastani.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,267   copying gtdbtk/external/hmm_aligner.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,272   copying gtdbtk/external/fasttree.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,278   copying gtdbtk/external/pplacer.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,285   copying gtdbtk/external/__init__.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,289   copying gtdbtk/external/prodigal.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,296   copying gtdbtk/external/mash.py -> build/lib/gtdbtk/external
2020-04-22T07:37:58,301   package init file 'gtdbtk/tests/__init__.py' not found (or not a regular file)
2020-04-22T07:37:58,305   creating build/lib/gtdbtk/external/pypfam
2020-04-22T07:37:58,308   copying gtdbtk/external/pypfam/__init__.py -> build/lib/gtdbtk/external/pypfam
2020-04-22T07:37:58,315   creating build/lib/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:58,318   copying gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:58,324   copying gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:58,332   copying gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:58,336   copying gtdbtk/external/pypfam/HMM/HMMResults.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:58,341   copying gtdbtk/external/pypfam/HMM/__init__.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:58,344   copying gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/lib/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:58,349   creating build/lib/gtdbtk/external/pypfam/Scan
2020-04-22T07:37:58,351   copying gtdbtk/external/pypfam/Scan/PfamScan.py -> build/lib/gtdbtk/external/pypfam/Scan
2020-04-22T07:37:58,359   copying gtdbtk/external/pypfam/Scan/__init__.py -> build/lib/gtdbtk/external/pypfam/Scan
2020-04-22T07:37:58,364   creating build/lib/gtdbtk/io
2020-04-22T07:37:58,367   copying gtdbtk/io/__init__.py -> build/lib/gtdbtk/io
2020-04-22T07:37:58,374   creating build/lib/gtdbtk/io/marker
2020-04-22T07:37:58,376   copying gtdbtk/io/marker/copy_number.py -> build/lib/gtdbtk/io/marker
2020-04-22T07:37:58,381   copying gtdbtk/io/marker/__init__.py -> build/lib/gtdbtk/io/marker
2020-04-22T07:37:58,384   copying gtdbtk/io/marker/tophit.py -> build/lib/gtdbtk/io/marker
2020-04-22T07:37:58,391   creating build/lib/gtdbtk/io/prodigal
2020-04-22T07:37:58,393   copying gtdbtk/io/prodigal/tln_table_summary.py -> build/lib/gtdbtk/io/prodigal
2020-04-22T07:37:58,399   copying gtdbtk/io/prodigal/__init__.py -> build/lib/gtdbtk/io/prodigal
2020-04-22T07:37:58,411   copying gtdbtk/VERSION -> build/lib/gtdbtk
2020-04-22T07:37:58,417   creating build/lib/gtdbtk/tests
2020-04-22T07:37:58,418   creating build/lib/gtdbtk/tests/data
2020-04-22T07:37:58,420   creating build/lib/gtdbtk/tests/data/genomes
2020-04-22T07:37:58,423   copying gtdbtk/tests/data/genomes/genome_1.fna -> build/lib/gtdbtk/tests/data/genomes
2020-04-22T07:37:58,701   copying gtdbtk/tests/data/genomes/genome_3.fna -> build/lib/gtdbtk/tests/data/genomes
2020-04-22T07:37:58,823   copying gtdbtk/tests/data/genomes/genome_2.fna -> build/lib/gtdbtk/tests/data/genomes
2020-04-22T07:37:58,977   running build_scripts
2020-04-22T07:37:58,979   creating build/scripts-3.7
2020-04-22T07:37:58,981   copying and adjusting bin/gtdbtk -> build/scripts-3.7
2020-04-22T07:37:58,989   changing mode of build/scripts-3.7/gtdbtk from 644 to 755
2020-04-22T07:37:58,993   installing to build/bdist.linux-armv7l/wheel
2020-04-22T07:37:58,994   running install
2020-04-22T07:37:58,995   running install_lib
2020-04-22T07:37:59,009   creating build/bdist.linux-armv7l
2020-04-22T07:37:59,011   creating build/bdist.linux-armv7l/wheel
2020-04-22T07:37:59,016   creating build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,019   copying build/lib/gtdbtk/ani_rep.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,026   copying build/lib/gtdbtk/main.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,035   copying build/lib/gtdbtk/relative_distance.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,044   creating build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,047   copying build/lib/gtdbtk/external/pfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,054   copying build/lib/gtdbtk/external/tigrfam_search.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,061   copying build/lib/gtdbtk/external/fastani.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,069   copying build/lib/gtdbtk/external/hmm_aligner.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,076   copying build/lib/gtdbtk/external/fasttree.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,086   copying build/lib/gtdbtk/external/pplacer.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,093   copying build/lib/gtdbtk/external/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,098   copying build/lib/gtdbtk/external/prodigal.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,107   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam
2020-04-22T07:37:59,111   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-04-22T07:37:59,114   copying build/lib/gtdbtk/external/pypfam/Scan/PfamScan.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-04-22T07:37:59,123   copying build/lib/gtdbtk/external/pypfam/Scan/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/Scan
2020-04-22T07:37:59,128   copying build/lib/gtdbtk/external/pypfam/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam
2020-04-22T07:37:59,134   creating build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:59,137   copying build/lib/gtdbtk/external/pypfam/HMM/HMMUnit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:59,143   copying build/lib/gtdbtk/external/pypfam/HMM/HMMResultsIO.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:59,152   copying build/lib/gtdbtk/external/pypfam/HMM/HMMMatch.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:59,158   copying build/lib/gtdbtk/external/pypfam/HMM/HMMResults.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:59,165   copying build/lib/gtdbtk/external/pypfam/HMM/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:59,169   copying build/lib/gtdbtk/external/pypfam/HMM/HMMSequence.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external/pypfam/HMM
2020-04-22T07:37:59,175   copying build/lib/gtdbtk/external/mash.py -> build/bdist.linux-armv7l/wheel/gtdbtk/external
2020-04-22T07:37:59,184   creating build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,187   copying build/lib/gtdbtk/biolib_lite/common.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,194   copying build/lib/gtdbtk/biolib_lite/newick.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,200   copying build/lib/gtdbtk/biolib_lite/custom_help_formatter.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,207   copying build/lib/gtdbtk/biolib_lite/logger.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,214   copying build/lib/gtdbtk/biolib_lite/seq_io.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,221   copying build/lib/gtdbtk/biolib_lite/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,227   copying build/lib/gtdbtk/biolib_lite/execute.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,234   copying build/lib/gtdbtk/biolib_lite/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,239   copying build/lib/gtdbtk/biolib_lite/taxonomy.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,249   copying build/lib/gtdbtk/biolib_lite/parallel.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,256   copying build/lib/gtdbtk/biolib_lite/prodigal_biolib.py -> build/bdist.linux-armv7l/wheel/gtdbtk/biolib_lite
2020-04-22T07:37:59,264   copying build/lib/gtdbtk/misc.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,272   creating build/bdist.linux-armv7l/wheel/gtdbtk/io
2020-04-22T07:37:59,276   creating build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-04-22T07:37:59,279   copying build/lib/gtdbtk/io/marker/copy_number.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-04-22T07:37:59,287   copying build/lib/gtdbtk/io/marker/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-04-22T07:37:59,292   copying build/lib/gtdbtk/io/marker/tophit.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/marker
2020-04-22T07:37:59,299   copying build/lib/gtdbtk/io/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io
2020-04-22T07:37:59,305   creating build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-04-22T07:37:59,308   copying build/lib/gtdbtk/io/prodigal/tln_table_summary.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-04-22T07:37:59,314   copying build/lib/gtdbtk/io/prodigal/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/io/prodigal
2020-04-22T07:37:59,319   copying build/lib/gtdbtk/classify.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,333   copying build/lib/gtdbtk/trim_msa.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,341   copying build/lib/gtdbtk/exceptions.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,348   copying build/lib/gtdbtk/VERSION -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,357   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests
2020-04-22T07:37:59,361   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data
2020-04-22T07:37:59,366   creating build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-04-22T07:37:59,369   copying build/lib/gtdbtk/tests/data/genomes/genome_1.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-04-22T07:37:59,657   copying build/lib/gtdbtk/tests/data/genomes/genome_3.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-04-22T07:37:59,780   copying build/lib/gtdbtk/tests/data/genomes/genome_2.fna -> build/bdist.linux-armv7l/wheel/gtdbtk/tests/data/genomes
2020-04-22T07:37:59,907   creating build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-22T07:37:59,911   copying build/lib/gtdbtk/config/output.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-22T07:37:59,919   copying build/lib/gtdbtk/config/config.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-22T07:37:59,926   copying build/lib/gtdbtk/config/config_template.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-22T07:37:59,933   copying build/lib/gtdbtk/config/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk/config
2020-04-22T07:37:59,937   copying build/lib/gtdbtk/__init__.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,943   copying build/lib/gtdbtk/reroot_tree.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,951   copying build/lib/gtdbtk/tools.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,960   copying build/lib/gtdbtk/markers.py -> build/bdist.linux-armv7l/wheel/gtdbtk
2020-04-22T07:37:59,973   running install_data
2020-04-22T07:37:59,981   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.1.1.data
2020-04-22T07:37:59,983   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.1.1.data/data
2020-04-22T07:37:59,988   copying LICENSE -> build/bdist.linux-armv7l/wheel/gtdbtk-1.1.1.data/data/
2020-04-22T07:37:59,996   running install_egg_info
2020-04-22T07:38:00,044   running egg_info
2020-04-22T07:38:00,045   writing gtdbtk.egg-info/PKG-INFO
2020-04-22T07:38:00,050   writing dependency_links to gtdbtk.egg-info/dependency_links.txt
2020-04-22T07:38:00,054   writing requirements to gtdbtk.egg-info/requires.txt
2020-04-22T07:38:00,057   writing top-level names to gtdbtk.egg-info/top_level.txt
2020-04-22T07:38:00,079   reading manifest file 'gtdbtk.egg-info/SOURCES.txt'
2020-04-22T07:38:00,085   reading manifest template 'MANIFEST.in'
2020-04-22T07:38:00,086   warning: no files found matching 'genome_1.fna'
2020-04-22T07:38:00,086   warning: no files found matching 'genome_2.fna'
2020-04-22T07:38:00,087   warning: no files found matching 'genome_3.fna'
2020-04-22T07:38:00,088   warning: no previously-included files matching 'genome_*_protein.fna' found anywhere in distribution
2020-04-22T07:38:00,097   writing manifest file 'gtdbtk.egg-info/SOURCES.txt'
2020-04-22T07:38:00,101   Copying gtdbtk.egg-info to build/bdist.linux-armv7l/wheel/gtdbtk-1.1.1-py3.7.egg-info
2020-04-22T07:38:00,127   running install_scripts
2020-04-22T07:38:00,239   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.1.1.data/scripts
2020-04-22T07:38:00,241   copying build/scripts-3.7/gtdbtk -> build/bdist.linux-armv7l/wheel/gtdbtk-1.1.1.data/scripts
2020-04-22T07:38:00,249   changing mode of build/bdist.linux-armv7l/wheel/gtdbtk-1.1.1.data/scripts/gtdbtk to 755
2020-04-22T07:38:00,292   adding license file "LICENSE" (matched pattern "LICEN[CS]E*")
2020-04-22T07:38:00,307   creating build/bdist.linux-armv7l/wheel/gtdbtk-1.1.1.dist-info/WHEEL
2020-04-22T07:38:00,313   creating '/tmp/pip-wheel-r30q1unt/gtdbtk-1.1.1-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2020-04-22T07:38:00,319   adding 'gtdbtk/VERSION'
2020-04-22T07:38:00,322   adding 'gtdbtk/__init__.py'
2020-04-22T07:38:00,324   adding 'gtdbtk/ani_rep.py'
2020-04-22T07:38:00,337   adding 'gtdbtk/classify.py'
2020-04-22T07:38:00,341   adding 'gtdbtk/exceptions.py'
2020-04-22T07:38:00,346   adding 'gtdbtk/main.py'
2020-04-22T07:38:00,354   adding 'gtdbtk/markers.py'
2020-04-22T07:38:00,357   adding 'gtdbtk/misc.py'
2020-04-22T07:38:00,364   adding 'gtdbtk/relative_distance.py'
2020-04-22T07:38:00,367   adding 'gtdbtk/reroot_tree.py'
2020-04-22T07:38:00,371   adding 'gtdbtk/tools.py'
2020-04-22T07:38:00,374   adding 'gtdbtk/trim_msa.py'
2020-04-22T07:38:00,379   adding 'gtdbtk/biolib_lite/__init__.py'
2020-04-22T07:38:00,381   adding 'gtdbtk/biolib_lite/common.py'
2020-04-22T07:38:00,384   adding 'gtdbtk/biolib_lite/custom_help_formatter.py'
2020-04-22T07:38:00,387   adding 'gtdbtk/biolib_lite/exceptions.py'
2020-04-22T07:38:00,390   adding 'gtdbtk/biolib_lite/execute.py'
2020-04-22T07:38:00,393   adding 'gtdbtk/biolib_lite/logger.py'
2020-04-22T07:38:00,396   adding 'gtdbtk/biolib_lite/newick.py'
2020-04-22T07:38:00,399   adding 'gtdbtk/biolib_lite/parallel.py'
2020-04-22T07:38:00,404   adding 'gtdbtk/biolib_lite/prodigal_biolib.py'
2020-04-22T07:38:00,407   adding 'gtdbtk/biolib_lite/seq_io.py'
2020-04-22T07:38:00,414   adding 'gtdbtk/biolib_lite/taxonomy.py'
2020-04-22T07:38:00,418   adding 'gtdbtk/config/__init__.py'
2020-04-22T07:38:00,421   adding 'gtdbtk/config/config.py'
2020-04-22T07:38:00,425   adding 'gtdbtk/config/config_template.py'
2020-04-22T07:38:00,428   adding 'gtdbtk/config/output.py'
2020-04-22T07:38:00,432   adding 'gtdbtk/external/__init__.py'
2020-04-22T07:38:00,435   adding 'gtdbtk/external/fastani.py'
2020-04-22T07:38:00,439   adding 'gtdbtk/external/fasttree.py'
2020-04-22T07:38:00,443   adding 'gtdbtk/external/hmm_aligner.py'
2020-04-22T07:38:00,446   adding 'gtdbtk/external/mash.py'
2020-04-22T07:38:00,450   adding 'gtdbtk/external/pfam_search.py'
2020-04-22T07:38:00,453   adding 'gtdbtk/external/pplacer.py'
2020-04-22T07:38:00,457   adding 'gtdbtk/external/prodigal.py'
2020-04-22T07:38:00,460   adding 'gtdbtk/external/tigrfam_search.py'
2020-04-22T07:38:00,464   adding 'gtdbtk/external/pypfam/__init__.py'
2020-04-22T07:38:00,468   adding 'gtdbtk/external/pypfam/HMM/HMMMatch.py'
2020-04-22T07:38:00,471   adding 'gtdbtk/external/pypfam/HMM/HMMResults.py'
2020-04-22T07:38:00,476   adding 'gtdbtk/external/pypfam/HMM/HMMResultsIO.py'
2020-04-22T07:38:00,479   adding 'gtdbtk/external/pypfam/HMM/HMMSequence.py'
2020-04-22T07:38:00,482   adding 'gtdbtk/external/pypfam/HMM/HMMUnit.py'
2020-04-22T07:38:00,484   adding 'gtdbtk/external/pypfam/HMM/__init__.py'
2020-04-22T07:38:00,490   adding 'gtdbtk/external/pypfam/Scan/PfamScan.py'
2020-04-22T07:38:00,493   adding 'gtdbtk/external/pypfam/Scan/__init__.py'
2020-04-22T07:38:00,497   adding 'gtdbtk/io/__init__.py'
2020-04-22T07:38:00,500   adding 'gtdbtk/io/marker/__init__.py'
2020-04-22T07:38:00,504   adding 'gtdbtk/io/marker/copy_number.py'
2020-04-22T07:38:00,507   adding 'gtdbtk/io/marker/tophit.py'
2020-04-22T07:38:00,511   adding 'gtdbtk/io/prodigal/__init__.py'
2020-04-22T07:38:00,514   adding 'gtdbtk/io/prodigal/tln_table_summary.py'
2020-04-22T07:38:02,757   adding 'gtdbtk/tests/data/genomes/genome_1.fna'
2020-04-22T07:38:03,765   adding 'gtdbtk/tests/data/genomes/genome_2.fna'
2020-04-22T07:38:04,680   adding 'gtdbtk/tests/data/genomes/genome_3.fna'
2020-04-22T07:38:04,710   adding 'gtdbtk-1.1.1.data/data/LICENSE'
2020-04-22T07:38:04,717   adding 'gtdbtk-1.1.1.data/scripts/gtdbtk'
2020-04-22T07:38:04,730   adding 'gtdbtk-1.1.1.dist-info/LICENSE'
2020-04-22T07:38:04,734   adding 'gtdbtk-1.1.1.dist-info/METADATA'
2020-04-22T07:38:04,736   adding 'gtdbtk-1.1.1.dist-info/WHEEL'
2020-04-22T07:38:04,738   adding 'gtdbtk-1.1.1.dist-info/top_level.txt'
2020-04-22T07:38:04,740   adding 'gtdbtk-1.1.1.dist-info/RECORD'
2020-04-22T07:38:04,895   removing build/bdist.linux-armv7l/wheel
2020-04-22T07:38:05,133   Building wheel for gtdbtk (setup.py): finished with status 'done'
2020-04-22T07:38:05,166   Created wheel for gtdbtk: filename=gtdbtk-1.1.1-py3-none-any.whl size=1747871 sha256=6015c83a790205e33f5f1a6b18e6dc3f59ed21785e21e2335e333d2a0c2b6149
2020-04-22T07:38:05,166   Stored in directory: /tmp/pip-ephem-wheel-cache-eav_yvte/wheels/8f/bc/e0/0d929e83fddf780a6a7fbca35f3940b132d7764949a3fefbdf
2020-04-22T07:38:05,170 Successfully built gtdbtk
2020-04-22T07:38:05,478 Cleaning up...
2020-04-22T07:38:05,479   Removing source in /tmp/pip-wheel-nx8548hc/gtdbtk
2020-04-22T07:38:05,639 Removed build tracker: '/tmp/pip-req-tracker-jp4v4qqo'