2021-02-02T16:37:07,360 DEPRECATION: Python 3.5 reached the end of its life on September 13th, 2020. Please upgrade your Python as Python 3.5 is no longer maintained. pip 21.0 will drop support for Python 3.5 in January 2021. pip 21.0 will remove support for this functionality.
2021-02-02T16:37:08,053 Created temporary directory: /tmp/pip-ephem-wheel-cache-yol_k8z1
2021-02-02T16:37:08,058 Created temporary directory: /tmp/pip-req-tracker-_4mx0kjg
2021-02-02T16:37:08,059 Initialized build tracking at /tmp/pip-req-tracker-_4mx0kjg
2021-02-02T16:37:08,059 Created build tracker: /tmp/pip-req-tracker-_4mx0kjg
2021-02-02T16:37:08,060 Entered build tracker: /tmp/pip-req-tracker-_4mx0kjg
2021-02-02T16:37:08,061 Created temporary directory: /tmp/pip-wheel-s1atjcb0
2021-02-02T16:37:08,134 1 location(s) to search for versions of dark-matter:
2021-02-02T16:37:08,134 * https://pypi.org/simple/dark-matter/
2021-02-02T16:37:08,135 Fetching project page and analyzing links: https://pypi.org/simple/dark-matter/
2021-02-02T16:37:08,137 Getting page https://pypi.org/simple/dark-matter/
2021-02-02T16:37:08,142 Found index url https://pypi.org/simple
2021-02-02T16:37:08,829   Found link https://files.pythonhosted.org/packages/7a/5d/5704534d2e83673ec3c8534b39fe1a3f071291761d421803f6b2f04ca6b3/dark-matter-1.0.0.tar.gz#sha256=e915679610d0e94ca32b047d9ef8db6bb16aca43edbba1f7ea13d8f9a00b77d7 (from https://pypi.org/simple/dark-matter/), version: 1.0.0
2021-02-02T16:37:08,830   Found link https://files.pythonhosted.org/packages/4a/50/cc5fbbe75b550d6819af04e15ffc633d99b636f2e2d3c22ca4fc09ba2380/dark-matter-1.0.11.tar.gz#sha256=4157ac389269821b5c3a2de3b32922bf437df79e858f2ae8c7293479d393c90b (from https://pypi.org/simple/dark-matter/), version: 1.0.11
2021-02-02T16:37:08,831   Found link https://files.pythonhosted.org/packages/12/38/d44b5b2e9c08c507a583accb8ee246ce0f98a57c553d06e0199943d0dbf4/dark-matter-1.0.12.tar.gz#sha256=4cde134f526e38562547db4df9069bf9ae04564c92fdfc58cb17593934944861 (from https://pypi.org/simple/dark-matter/), version: 1.0.12
2021-02-02T16:37:08,832   Found link https://files.pythonhosted.org/packages/42/69/f0d13d1e43ec50d1ca85b70c27cc5333f85186668700544a7661c4d6d374/dark-matter-1.0.13.tar.gz#sha256=4b061448407711cab985c60762244028d74b32a322d7329a63138e4080d110d9 (from https://pypi.org/simple/dark-matter/), version: 1.0.13
2021-02-02T16:37:08,833   Found link https://files.pythonhosted.org/packages/30/5a/9c56b0639b13c2c78cad8ac304e9c5d834eed0cab07d0dcd780b7be47249/dark-matter-1.0.16.tar.gz#sha256=c0c11585b9a71c47aa248794779111a9ab30c48e32e17540f95347d98ce116a6 (from https://pypi.org/simple/dark-matter/), version: 1.0.16
2021-02-02T16:37:08,834   Found link https://files.pythonhosted.org/packages/26/8d/eb629def26e051253c4070e70dfc7c8258d513b2685fe4e92bb975b6e613/dark-matter-1.0.19.tar.gz#sha256=4944ba9c898e0b956b6a8c0b8e78e5aa91579ac469885c61e70d71e89f92883d (from https://pypi.org/simple/dark-matter/), version: 1.0.19
2021-02-02T16:37:08,835   Found link https://files.pythonhosted.org/packages/6d/6f/755f4b72e91ce15571d5884761d34627eba8dc173005bc8d41a2e4d2ec81/dark-matter-1.0.27.tar.gz#sha256=70b765fdc0932137cb1ee2b9183018261c218fd27c87a3f3ab5fabb93a9d0e3c (from https://pypi.org/simple/dark-matter/), version: 1.0.27
2021-02-02T16:37:08,836   Found link https://files.pythonhosted.org/packages/c1/41/a8cb27f9a68dd388473a594c0a5cb162fb1518d16197c357ec3617e9631c/dark-matter-1.0.32.tar.gz#sha256=405b6a4a51ac4c1660435c882fb548d1e6ad1a889779b3893bddf5f876732eef (from https://pypi.org/simple/dark-matter/), version: 1.0.32
2021-02-02T16:37:08,837   Found link https://files.pythonhosted.org/packages/26/f5/ea2b1d090cd00bb769d4e07cc4b697373c58dac65a52cf442a4f60a833ba/dark-matter-1.0.34.tar.gz#sha256=8fe1d83a0b0476164c5a4ca8197890e1936ed0d66a689870a71676a14f671539 (from https://pypi.org/simple/dark-matter/), version: 1.0.34
2021-02-02T16:37:08,837   Found link https://files.pythonhosted.org/packages/1d/a3/954c4ab15080556dbb33a1c2053ce9028b51cb160099978332b9252b5f93/dark-matter-1.0.36.tar.gz#sha256=9f639deedd5d4e4da0276c9a6780288c5d78e95b0c5b69d08b312ed10cc10d25 (from https://pypi.org/simple/dark-matter/), version: 1.0.36
2021-02-02T16:37:08,838   Found link https://files.pythonhosted.org/packages/fd/f7/352dcf1f8fb13001175a73acb52fff4bc20760300f87459d7e1e967823a1/dark-matter-1.0.38.tar.gz#sha256=b506f4177d9334da17c7fdd2054944851b96c3872be6d00cd5ece2de2ddc7d82 (from https://pypi.org/simple/dark-matter/), version: 1.0.38
2021-02-02T16:37:08,839   Found link https://files.pythonhosted.org/packages/17/94/5d0c424a52cc3d16793cef2a6b38a8a3542c4bda072c49d61efd18a1ec60/dark-matter-1.0.40.tar.gz#sha256=6e38036fc94ef7817c18d607b937b916ef1caafe40fe072d4748306b2e646a1f (from https://pypi.org/simple/dark-matter/), version: 1.0.40
2021-02-02T16:37:08,840   Found link https://files.pythonhosted.org/packages/4c/d7/9fa11fcb1f9923e3e980f1b493791ca3fbe6920a68a939971fb1eb333d05/dark-matter-1.0.41.tar.gz#sha256=e6e0364aa69a1fef4621e7d016839a3dffbcddff5d575ba4ee7f4af5cebd754d (from https://pypi.org/simple/dark-matter/), version: 1.0.41
2021-02-02T16:37:08,841   Found link https://files.pythonhosted.org/packages/1b/bb/9a2bffcc74c3bb8c2f45106443174a74dbe3424e45eb483ba7bf72da1fe2/dark-matter-1.0.42.tar.gz#sha256=2540312ed60fed3f5a52b5ec60409e712c8a562569baa132be6ab0c53edbec83 (from https://pypi.org/simple/dark-matter/), version: 1.0.42
2021-02-02T16:37:08,842   Found link https://files.pythonhosted.org/packages/e2/dd/cb0a17ce78d39d3b6d6dc93f54c49069b722569042312f7044143a67af30/dark-matter-1.0.43.tar.gz#sha256=17548e06b695864df72afb4e6664261333612b991373745f4e68f99ed48ace5f (from https://pypi.org/simple/dark-matter/), version: 1.0.43
2021-02-02T16:37:08,843   Found link https://files.pythonhosted.org/packages/88/ee/c6e7d4142ee1baca46ff0d7f295b7d5a4059648c815de4223f873f17a448/dark-matter-1.0.44.tar.gz#sha256=468d2be2ad00ddcdfafe52f09a6a8971b40964e816fdb95de2772d32879d3fc5 (from https://pypi.org/simple/dark-matter/), version: 1.0.44
2021-02-02T16:37:08,844   Found link https://files.pythonhosted.org/packages/7e/71/19001567a982f1ea235095e6f2042990e0666c343bfd985b2c2b8a6a6edc/dark-matter-1.0.45.tar.gz#sha256=b60e397a82b3183fae2cdee32ac92f43f4533bcb5a7683d5fc3e58dd6ceee4fd (from https://pypi.org/simple/dark-matter/), version: 1.0.45
2021-02-02T16:37:08,845   Found link https://files.pythonhosted.org/packages/9b/71/0395a4c77fc9443e4b1c8d6d3787d527c2d06ecf56c75db9779bb602d594/dark-matter-1.0.46.tar.gz#sha256=66aaa9872db60c407b047f5e997c8155fe0626df9222b251a6f65b15ca4d3423 (from https://pypi.org/simple/dark-matter/), version: 1.0.46
2021-02-02T16:37:08,846   Found link https://files.pythonhosted.org/packages/85/3b/b68351e5280d2f65b26ca3e225a5a0385d921a6d25cef62563eeaec42343/dark-matter-1.0.47.tar.gz#sha256=b51c372b06fe94fcc93f8795aa5d2b2a547108934cc5c429e89972cdea153baf (from https://pypi.org/simple/dark-matter/), version: 1.0.47
2021-02-02T16:37:08,847   Found link https://files.pythonhosted.org/packages/fb/4c/6e27c41b817fc86240a956472978b226008da91e8c2b2b5dd991091c3a2d/dark-matter-1.0.48.tar.gz#sha256=e9ca7aad5b5631658d2ab154108568faa6196f7cea8dfaef1881d0013a3c59bd (from https://pypi.org/simple/dark-matter/), version: 1.0.48
2021-02-02T16:37:08,848   Found link https://files.pythonhosted.org/packages/07/65/1253b1fcd6c75fbbc19eee09982ec62023742959583d6687c666befffb71/dark-matter-1.0.49.tar.gz#sha256=7fe2af86f08e9e2416869c8fa571fc79b5a6965d4e2e9624536984a6ede94d5e (from https://pypi.org/simple/dark-matter/), version: 1.0.49
2021-02-02T16:37:08,849   Found link https://files.pythonhosted.org/packages/ac/93/e94fa7a2455aa54ebc294bb5bd93c11aca3c461073aee1fab28b4ee380ae/dark-matter-1.0.50.tar.gz#sha256=cd9ce5690ff46e8a27b17505dc500d0dc065bb403d6aa731615fbcfa0e9ecb50 (from https://pypi.org/simple/dark-matter/), version: 1.0.50
2021-02-02T16:37:08,850   Found link https://files.pythonhosted.org/packages/b9/ce/7d74daae572ebb32ffdbd439440361f5bf39eb9f9d0f55654878cbd7cbb2/dark-matter-1.0.51.tar.gz#sha256=ca7762302eb529ec15dbc0bba35397dc018cb3b43b371b02495ba1caa8fc6fe2 (from https://pypi.org/simple/dark-matter/), version: 1.0.51
2021-02-02T16:37:08,851   Found link https://files.pythonhosted.org/packages/cd/fb/8ff473df5992d3cdfc57151ff5595561c42fff343fcc01c76f3b95cd1eb9/dark-matter-1.0.52.tar.gz#sha256=7c5cadd1c74c4c85d55ec808f2ecd1a86abf726b7f3dc4b8755a32dc81a57094 (from https://pypi.org/simple/dark-matter/), version: 1.0.52
2021-02-02T16:37:08,851   Found link https://files.pythonhosted.org/packages/d4/a7/8e4a7fc079ce3324a605902fb7fe865ab846ba3376408987680cc68703c7/dark-matter-1.0.53.tar.gz#sha256=c06386be8fc1f85e76fc6f7c6b8ea6597503a9c238e5368e0975f18ea9fe3f6a (from https://pypi.org/simple/dark-matter/), version: 1.0.53
2021-02-02T16:37:08,852   Found link https://files.pythonhosted.org/packages/a8/50/55d45de9c1903904647e651a955b56dff452d61f9e095a5004a149ab2eca/dark-matter-1.0.54.tar.gz#sha256=cb4fefda8208eb0d40c4b172c30286b4be960018e89c89aacb94f177cbd0a77a (from https://pypi.org/simple/dark-matter/), version: 1.0.54
2021-02-02T16:37:08,853   Found link https://files.pythonhosted.org/packages/47/41/cc272f599662d184f754abc67ee763ac9da02c5d9ef5d1155effe67d132f/dark-matter-1.0.55.tar.gz#sha256=d1b4537860411417b98b32252f8a363623c263464c32d994cd442de74e36d4d9 (from https://pypi.org/simple/dark-matter/), version: 1.0.55
2021-02-02T16:37:08,854   Found link https://files.pythonhosted.org/packages/d3/d8/250e7506219460c7da81f6f51bf93cce13d21b461392dcbfa1311e504a95/dark-matter-1.0.56.tar.gz#sha256=d5cbddab4a2b8cc948329f46660259c2bb30b866446ddfc12e8c6b8ddc9822ff (from https://pypi.org/simple/dark-matter/), version: 1.0.56
2021-02-02T16:37:08,855   Found link https://files.pythonhosted.org/packages/81/c7/3bf4ec17c4f0e02ca7741f7ede49d58680f12b48a4a7350031ffe8b38ba1/dark-matter-1.0.57.tar.gz#sha256=3d33c771486b56c8a4dd10fb70f91e4c0ce1d279d05cbdf6dac92cceffb35809 (from https://pypi.org/simple/dark-matter/), version: 1.0.57
2021-02-02T16:37:08,856   Found link https://files.pythonhosted.org/packages/f1/d5/6e02cb418664b484f16ea42b60a86add44acf56dda4875001528957c27b2/dark-matter-1.0.58.tar.gz#sha256=6a9e75658cacc7ae7e9926d0debd5605e15e5761452455e4f65c96b3cd947c6b (from https://pypi.org/simple/dark-matter/), version: 1.0.58
2021-02-02T16:37:08,857   Found link https://files.pythonhosted.org/packages/5a/d3/a69ed2feeac3afcb852a8bcce6cadd5b541cd78de3756f0519a62ca29371/dark-matter-1.0.59.tar.gz#sha256=1f0c71e01cce5ca62b1599c974ff24b8b211349f880c365ecbdce369c6877280 (from https://pypi.org/simple/dark-matter/), version: 1.0.59
2021-02-02T16:37:08,858   Found link https://files.pythonhosted.org/packages/68/70/96bd4a89d1c5f40e05d734be94ae1571be35c0b4c4e19e22c0be893c9e1c/dark-matter-1.0.60.tar.gz#sha256=933a4cc3f34ed03198cacedaab9cc0915402bfff0ad238a0f879c7b246243f02 (from https://pypi.org/simple/dark-matter/), version: 1.0.60
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2021-02-02T16:37:09,056   Found link https://files.pythonhosted.org/packages/63/f5/c113abaa137fabb548cbce7de51585a391ccbef68fdb50bac8b113c7881e/dark-matter-3.1.74.tar.gz#sha256=68d96ddda46298d92677dd83f4be92cf0f4d7bff45017ec362d4a7b954281bc0 (from https://pypi.org/simple/dark-matter/), version: 3.1.74
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2021-02-02T16:37:09,069   Found link https://files.pythonhosted.org/packages/d1/29/20a1d35035fece08efda70f18f4fea4913d179edd497a811516589b6f6c0/dark-matter-3.1.84.tar.gz#sha256=8202263762607e3312781054ed326f82c0b8348bae1b9b803f21b07ea1ce15fd (from https://pypi.org/simple/dark-matter/), version: 3.1.84
2021-02-02T16:37:09,070   Found link https://files.pythonhosted.org/packages/13/d4/262226886768170d06cdc7b41b143e9151aaf6651725b48a949f9920305f/dark-matter-3.1.85.tar.gz#sha256=ef2ba3420eec01ff6aa91d30ac7a7e19e3abc53b270fb66c060540b4fbdb703a (from https://pypi.org/simple/dark-matter/), version: 3.1.85
2021-02-02T16:37:09,071   Found link https://files.pythonhosted.org/packages/b1/83/5f937593c1325857d5820729d1571331c1384af1b2c750848f0ddf25f32c/dark-matter-3.1.86.tar.gz#sha256=0c94c6ee0b76e1aa9e2d2820ba54ae865cd72fc99d32c89ac0cffb85b66dee90 (from https://pypi.org/simple/dark-matter/), version: 3.1.86
2021-02-02T16:37:09,072   Found link https://files.pythonhosted.org/packages/da/f4/36e03445ef41eab619e83e9b305085541a1fe3afe4080c7bbfd910538b73/dark-matter-3.1.87.tar.gz#sha256=fdc7c53b959e42dbc15e8be69e686459637121e160f922afc4f6ea724dce2e6a (from https://pypi.org/simple/dark-matter/), version: 3.1.87
2021-02-02T16:37:09,073   Found link https://files.pythonhosted.org/packages/c0/00/7fae5de4b38e001949cf2f5604456f361a4e4b16dccac360cad9c618774e/dark-matter-3.1.88.tar.gz#sha256=ee3972366f54ac8e8a8e6d82bb5eb3c8858e6991b839180cec0cd3726e2d2764 (from https://pypi.org/simple/dark-matter/), version: 3.1.88
2021-02-02T16:37:09,218 Given no hashes to check 1 links for project 'dark-matter': discarding no candidates
2021-02-02T16:37:09,256 Collecting dark-matter==3.1.88
2021-02-02T16:37:09,260   Created temporary directory: /tmp/pip-unpack-_t8jk219
2021-02-02T16:37:09,567   Downloading dark-matter-3.1.88.tar.gz (330 kB)
2021-02-02T16:37:10,978   Added dark-matter==3.1.88 from https://files.pythonhosted.org/packages/c0/00/7fae5de4b38e001949cf2f5604456f361a4e4b16dccac360cad9c618774e/dark-matter-3.1.88.tar.gz#sha256=ee3972366f54ac8e8a8e6d82bb5eb3c8858e6991b839180cec0cd3726e2d2764 to build tracker '/tmp/pip-req-tracker-_4mx0kjg'
2021-02-02T16:37:10,980     Running setup.py (path:/tmp/pip-wheel-s1atjcb0/dark-matter_f83cb942ec1943f9bb6d1711415b2ee9/setup.py) egg_info for package dark-matter
2021-02-02T16:37:10,982     Created temporary directory: /tmp/pip-pip-egg-info-063ht1ko
2021-02-02T16:37:10,982     Running command python setup.py egg_info
2021-02-02T16:37:13,286     running egg_info
2021-02-02T16:37:13,292     creating /tmp/pip-pip-egg-info-063ht1ko/dark_matter.egg-info
2021-02-02T16:37:13,295     writing top-level names to /tmp/pip-pip-egg-info-063ht1ko/dark_matter.egg-info/top_level.txt
2021-02-02T16:37:13,299     writing requirements to /tmp/pip-pip-egg-info-063ht1ko/dark_matter.egg-info/requires.txt
2021-02-02T16:37:13,302     writing /tmp/pip-pip-egg-info-063ht1ko/dark_matter.egg-info/PKG-INFO
2021-02-02T16:37:13,306     writing dependency_links to /tmp/pip-pip-egg-info-063ht1ko/dark_matter.egg-info/dependency_links.txt
2021-02-02T16:37:13,311     writing manifest file '/tmp/pip-pip-egg-info-063ht1ko/dark_matter.egg-info/SOURCES.txt'
2021-02-02T16:37:13,746     reading manifest file '/tmp/pip-pip-egg-info-063ht1ko/dark_matter.egg-info/SOURCES.txt'
2021-02-02T16:37:13,779     writing manifest file '/tmp/pip-pip-egg-info-063ht1ko/dark_matter.egg-info/SOURCES.txt'
2021-02-02T16:37:13,915   Source in /tmp/pip-wheel-s1atjcb0/dark-matter_f83cb942ec1943f9bb6d1711415b2ee9 has version 3.1.88, which satisfies requirement dark-matter==3.1.88 from https://files.pythonhosted.org/packages/c0/00/7fae5de4b38e001949cf2f5604456f361a4e4b16dccac360cad9c618774e/dark-matter-3.1.88.tar.gz#sha256=ee3972366f54ac8e8a8e6d82bb5eb3c8858e6991b839180cec0cd3726e2d2764
2021-02-02T16:37:13,916   Removed dark-matter==3.1.88 from https://files.pythonhosted.org/packages/c0/00/7fae5de4b38e001949cf2f5604456f361a4e4b16dccac360cad9c618774e/dark-matter-3.1.88.tar.gz#sha256=ee3972366f54ac8e8a8e6d82bb5eb3c8858e6991b839180cec0cd3726e2d2764 from build tracker '/tmp/pip-req-tracker-_4mx0kjg'
2021-02-02T16:37:13,925 Created temporary directory: /tmp/pip-unpack-t3byo3pn
2021-02-02T16:37:13,926 Building wheels for collected packages: dark-matter
2021-02-02T16:37:13,935   Created temporary directory: /tmp/pip-wheel-a9mqi_7r
2021-02-02T16:37:13,936   Building wheel for dark-matter (setup.py): started
2021-02-02T16:37:13,937   Destination directory: /tmp/pip-wheel-a9mqi_7r
2021-02-02T16:37:13,937   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-s1atjcb0/dark-matter_f83cb942ec1943f9bb6d1711415b2ee9/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-s1atjcb0/dark-matter_f83cb942ec1943f9bb6d1711415b2ee9/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-a9mqi_7r
2021-02-02T16:37:16,223   running bdist_wheel
2021-02-02T16:37:16,240   running build
2021-02-02T16:37:16,241   running build_py
2021-02-02T16:37:16,583   creating build
2021-02-02T16:37:16,585   creating build/lib
2021-02-02T16:37:16,587   creating build/lib/dark
2021-02-02T16:37:16,590   copying dark/intervals.py -> build/lib/dark
2021-02-02T16:37:16,596   copying dark/sam.py -> build/lib/dark
2021-02-02T16:37:16,604   copying dark/taxonomy.py -> build/lib/dark
2021-02-02T16:37:16,612   copying dark/process.py -> build/lib/dark
2021-02-02T16:37:16,617   copying dark/cigar.py -> build/lib/dark
2021-02-02T16:37:16,623   copying dark/entrez.py -> build/lib/dark
2021-02-02T16:37:16,630   copying dark/dna.py -> build/lib/dark
2021-02-02T16:37:16,638   copying dark/reads.py -> build/lib/dark
2021-02-02T16:37:16,650   copying dark/summarize.py -> build/lib/dark
2021-02-02T16:37:16,655   copying dark/aa.py -> build/lib/dark
2021-02-02T16:37:16,665   copying dark/alignments.py -> build/lib/dark
2021-02-02T16:37:16,674   copying dark/proteins.py -> build/lib/dark
2021-02-02T16:37:16,685   copying dark/html.py -> build/lib/dark
2021-02-02T16:37:16,691   copying dark/baseimage.py -> build/lib/dark
2021-02-02T16:37:16,696   copying dark/fasta.py -> build/lib/dark
2021-02-02T16:37:16,704   copying dark/ncbidb.py -> build/lib/dark
2021-02-02T16:37:16,711   copying dark/consensus.py -> build/lib/dark
2021-02-02T16:37:16,719   copying dark/utils.py -> build/lib/dark
2021-02-02T16:37:16,726   copying dark/fasta_ss.py -> build/lib/dark
2021-02-02T16:37:16,731   copying dark/analyze_reads.py -> build/lib/dark
2021-02-02T16:37:16,736   copying dark/features.py -> build/lib/dark
2021-02-02T16:37:16,743   copying dark/genomes.py -> build/lib/dark
2021-02-02T16:37:16,751   copying dark/dimension.py -> build/lib/dark
2021-02-02T16:37:16,758   copying dark/local_align.py -> build/lib/dark
2021-02-02T16:37:16,766   copying dark/bowtie2.py -> build/lib/dark
2021-02-02T16:37:16,773   copying dark/titles.py -> build/lib/dark
2021-02-02T16:37:16,780   copying dark/database.py -> build/lib/dark
2021-02-02T16:37:16,786   copying dark/colors.py -> build/lib/dark
2021-02-02T16:37:16,794   copying dark/genbank.py -> build/lib/dark
2021-02-02T16:37:16,801   copying dark/graphics.py -> build/lib/dark
2021-02-02T16:37:16,810   copying dark/codonDistance.py -> build/lib/dark
2021-02-02T16:37:16,816   copying dark/fastq.py -> build/lib/dark
2021-02-02T16:37:16,821   copying dark/filter.py -> build/lib/dark
2021-02-02T16:37:16,829   copying dark/hsp.py -> build/lib/dark
2021-02-02T16:37:16,835   copying dark/mutations.py -> build/lib/dark
2021-02-02T16:37:16,843   copying dark/sequence.py -> build/lib/dark
2021-02-02T16:37:16,847   copying dark/ipynb.py -> build/lib/dark
2021-02-02T16:37:16,852   copying dark/simplify.py -> build/lib/dark
2021-02-02T16:37:16,856   copying dark/distance.py -> build/lib/dark
2021-02-02T16:37:16,860   copying dark/orfs.py -> build/lib/dark
2021-02-02T16:37:16,865   copying dark/score.py -> build/lib/dark
2021-02-02T16:37:16,870   copying dark/errors.py -> build/lib/dark
2021-02-02T16:37:16,876   copying dark/fpcache.py -> build/lib/dark
2021-02-02T16:37:16,881   copying dark/btop.py -> build/lib/dark
2021-02-02T16:37:16,887   copying dark/aligners.py -> build/lib/dark
2021-02-02T16:37:16,891   copying dark/__init__.py -> build/lib/dark
2021-02-02T16:37:16,896   creating build/lib/dark/blast
2021-02-02T16:37:16,898   copying dark/blast/alignments.py -> build/lib/dark/blast
2021-02-02T16:37:16,904   copying dark/blast/params.py -> build/lib/dark/blast
2021-02-02T16:37:16,909   copying dark/blast/conversion.py -> build/lib/dark/blast
2021-02-02T16:37:16,917   copying dark/blast/records.py -> build/lib/dark/blast
2021-02-02T16:37:16,922   copying dark/blast/hacks.py -> build/lib/dark/blast
2021-02-02T16:37:16,926   copying dark/blast/hsp.py -> build/lib/dark/blast
2021-02-02T16:37:16,931   copying dark/blast/score.py -> build/lib/dark/blast
2021-02-02T16:37:16,935   copying dark/blast/__init__.py -> build/lib/dark/blast
2021-02-02T16:37:16,940   creating build/lib/dark/diamond
2021-02-02T16:37:16,942   copying dark/diamond/sam.py -> build/lib/dark/diamond
2021-02-02T16:37:16,950   copying dark/diamond/alignments.py -> build/lib/dark/diamond
2021-02-02T16:37:16,956   copying dark/diamond/conversion.py -> build/lib/dark/diamond
2021-02-02T16:37:16,964   copying dark/diamond/run.py -> build/lib/dark/diamond
2021-02-02T16:37:16,970   copying dark/diamond/hsp.py -> build/lib/dark/diamond
2021-02-02T16:37:16,976   copying dark/diamond/__init__.py -> build/lib/dark/diamond
2021-02-02T16:37:16,982   creating build/lib/dark/civ
2021-02-02T16:37:16,985   copying dark/civ/proteins.py -> build/lib/dark/civ
2021-02-02T16:37:16,999   copying dark/civ/html.py -> build/lib/dark/civ
2021-02-02T16:37:17,004   copying dark/civ/graphics.py -> build/lib/dark/civ
2021-02-02T16:37:17,012   copying dark/civ/__init__.py -> build/lib/dark/civ
2021-02-02T16:37:17,033   running build_scripts
2021-02-02T16:37:17,034   creating build/scripts-3.5
2021-02-02T16:37:17,037   copying and adjusting bin/aa-info.py -> build/scripts-3.5
2021-02-02T16:37:17,041   copying and adjusting bin/aa-to-dna.py -> build/scripts-3.5
2021-02-02T16:37:17,044   copying and adjusting bin/aa-to-properties.py -> build/scripts-3.5
2021-02-02T16:37:17,047   copying and adjusting bin/adaptor-distances.py -> build/scripts-3.5
2021-02-02T16:37:17,051   copying and adjusting bin/alignment-panel-civ.py -> build/scripts-3.5
2021-02-02T16:37:17,057   copying and adjusting bin/alignments-per-read.py -> build/scripts-3.5
2021-02-02T16:37:17,060   copying and adjusting bin/bit-score-to-e-value.py -> build/scripts-3.5
2021-02-02T16:37:17,063   copying and adjusting bin/cat-json-blast-records.py -> build/scripts-3.5
2021-02-02T16:37:17,066   copying and adjusting bin/check-fasta-json-blast-consistency.py -> build/scripts-3.5
2021-02-02T16:37:17,071   copying and adjusting bin/codon-distance.py -> build/scripts-3.5
2021-02-02T16:37:17,076   copying and adjusting bin/compare-consensuses.py -> build/scripts-3.5
2021-02-02T16:37:17,082   copying and adjusting bin/compare-sequences.py -> build/scripts-3.5
2021-02-02T16:37:17,089   copying and adjusting bin/convert-blast-xml-to-json.py -> build/scripts-3.5
2021-02-02T16:37:17,092   copying and adjusting bin/convert-diamond-to-json.py -> build/scripts-3.5
2021-02-02T16:37:17,095   copying and adjusting bin/convert-diamond-to-sam.py -> build/scripts-3.5
2021-02-02T16:37:17,100   copying bin/convert-sam-to-fastq.sh -> build/scripts-3.5
2021-02-02T16:37:17,105   copying and adjusting bin/create-newick-relabeling-output.py -> build/scripts-3.5
2021-02-02T16:37:17,109   copying and adjusting bin/dark-matter-version.py -> build/scripts-3.5
2021-02-02T16:37:17,113   copying and adjusting bin/describe-protein-database.py -> build/scripts-3.5
2021-02-02T16:37:17,117   copying and adjusting bin/dna-to-aa.py -> build/scripts-3.5
2021-02-02T16:37:17,122   copying bin/download-genbank.sh -> build/scripts-3.5
2021-02-02T16:37:17,129   copying and adjusting bin/e-value-to-bit-score.py -> build/scripts-3.5
2021-02-02T16:37:17,133   copying and adjusting bin/extract-ORFs.py -> build/scripts-3.5
2021-02-02T16:37:17,137   copying and adjusting bin/fasta-base-indices.py -> build/scripts-3.5
2021-02-02T16:37:17,141   copying and adjusting bin/fasta-count.py -> build/scripts-3.5
2021-02-02T16:37:17,146   copying bin/fasta-diff.sh -> build/scripts-3.5
2021-02-02T16:37:17,153   copying and adjusting bin/fasta-identity-table.py -> build/scripts-3.5
2021-02-02T16:37:17,163   copying and adjusting bin/fasta-ids.py -> build/scripts-3.5
2021-02-02T16:37:17,167   copying and adjusting bin/fasta-join.py -> build/scripts-3.5
2021-02-02T16:37:17,171   copying and adjusting bin/fasta-lengths.py -> build/scripts-3.5
2021-02-02T16:37:17,174   copying and adjusting bin/fasta-sequences.py -> build/scripts-3.5
2021-02-02T16:37:17,177   copying and adjusting bin/fasta-sort.py -> build/scripts-3.5
2021-02-02T16:37:17,181   copying and adjusting bin/fasta-split-by-id.py -> build/scripts-3.5
2021-02-02T16:37:17,184   copying and adjusting bin/fasta-subset.py -> build/scripts-3.5
2021-02-02T16:37:17,188   copying and adjusting bin/fasta-subtraction.py -> build/scripts-3.5
2021-02-02T16:37:17,192   copying and adjusting bin/fasta-to-phylip.py -> build/scripts-3.5
2021-02-02T16:37:17,197   copying and adjusting bin/fasta-variable-sites.py -> build/scripts-3.5
2021-02-02T16:37:17,203   copying and adjusting bin/filter-fasta-by-complexity.py -> build/scripts-3.5
2021-02-02T16:37:17,208   copying and adjusting bin/filter-fasta-by-taxonomy.py -> build/scripts-3.5
2021-02-02T16:37:17,213   copying and adjusting bin/filter-fasta.py -> build/scripts-3.5
2021-02-02T16:37:17,216   copying and adjusting bin/filter-hits-to-fasta.py -> build/scripts-3.5
2021-02-02T16:37:17,221   copying and adjusting bin/filter-reads-alignments.py -> build/scripts-3.5
2021-02-02T16:37:17,226   copying and adjusting bin/filter-sam.py -> build/scripts-3.5
2021-02-02T16:37:17,231   copying and adjusting bin/find-hits.py -> build/scripts-3.5
2021-02-02T16:37:17,235   copying and adjusting bin/format-fasta.py -> build/scripts-3.5
2021-02-02T16:37:17,240   copying and adjusting bin/genome-protein-summary.py -> build/scripts-3.5
2021-02-02T16:37:17,247   copying and adjusting bin/get-features.py -> build/scripts-3.5
2021-02-02T16:37:17,251   copying and adjusting bin/get-hosts.py -> build/scripts-3.5
2021-02-02T16:37:17,255   copying and adjusting bin/get-reads.py -> build/scripts-3.5
2021-02-02T16:37:17,259   copying and adjusting bin/get-taxonomy.py -> build/scripts-3.5
2021-02-02T16:37:17,263   copying and adjusting bin/graph-evalues.py -> build/scripts-3.5
2021-02-02T16:37:17,266   copying and adjusting bin/local-align.py -> build/scripts-3.5
2021-02-02T16:37:17,270   copying and adjusting bin/make-consensus.py -> build/scripts-3.5
2021-02-02T16:37:17,277   copying and adjusting bin/make-fasta-database.py -> build/scripts-3.5
2021-02-02T16:37:17,282   copying and adjusting bin/make-protein-database.py -> build/scripts-3.5
2021-02-02T16:37:17,289   copying and adjusting bin/ncbi-fetch-id.py -> build/scripts-3.5
2021-02-02T16:37:17,293   copying and adjusting bin/newick-to-ascii.py -> build/scripts-3.5
2021-02-02T16:37:17,296   copying and adjusting bin/noninteractive-alignment-panel.py -> build/scripts-3.5
2021-02-02T16:37:17,303   copying and adjusting bin/parse-genbank-flat-file.py -> build/scripts-3.5
2021-02-02T16:37:17,307   copying and adjusting bin/position-summary.py -> build/scripts-3.5
2021-02-02T16:37:17,312   copying bin/pre-commit.sh -> build/scripts-3.5
2021-02-02T16:37:17,319   copying and adjusting bin/print-blast-xml-for-derek.py -> build/scripts-3.5
2021-02-02T16:37:17,323   copying and adjusting bin/print-blast-xml.py -> build/scripts-3.5
2021-02-02T16:37:17,327   copying and adjusting bin/print-read-lengths.py -> build/scripts-3.5
2021-02-02T16:37:17,331   copying and adjusting bin/proteins-to-pathogens.py -> build/scripts-3.5
2021-02-02T16:37:17,337   copying and adjusting bin/proteins-to-pathogens-civ.py -> build/scripts-3.5
2021-02-02T16:37:17,342   copying and adjusting bin/randomize-fasta.py -> build/scripts-3.5
2021-02-02T16:37:17,345   copying and adjusting bin/read-blast-json.py -> build/scripts-3.5
2021-02-02T16:37:17,349   copying and adjusting bin/read-blast-xml.py -> build/scripts-3.5
2021-02-02T16:37:17,352   copying and adjusting bin/relabel-newick-tree.py -> build/scripts-3.5
2021-02-02T16:37:17,357   copying and adjusting bin/run-bwa.py -> build/scripts-3.5
2021-02-02T16:37:17,362   copying and adjusting bin/run-bowtie2.py -> build/scripts-3.5
2021-02-02T16:37:17,371   copying and adjusting bin/sam-coverage.py -> build/scripts-3.5
2021-02-02T16:37:17,374   copying and adjusting bin/sam-coverage-depth.py -> build/scripts-3.5
2021-02-02T16:37:17,379   copying and adjusting bin/sam-to-fasta-alignment.py -> build/scripts-3.5
2021-02-02T16:37:17,383   copying and adjusting bin/sam-reference-read-counts.py -> build/scripts-3.5
2021-02-02T16:37:17,386   copying and adjusting bin/sam-references.py -> build/scripts-3.5
2021-02-02T16:37:17,389   copying and adjusting bin/sff-to-fastq.py -> build/scripts-3.5
2021-02-02T16:37:17,393   copying and adjusting bin/split-fasta-by-adaptors.py -> build/scripts-3.5
2021-02-02T16:37:17,399   copying and adjusting bin/subset-protein-database.py -> build/scripts-3.5
2021-02-02T16:37:17,404   copying and adjusting bin/summarize-fasta-bases.py -> build/scripts-3.5
2021-02-02T16:37:17,409   copying and adjusting bin/summarize-reads.py -> build/scripts-3.5
2021-02-02T16:37:17,413   copying and adjusting bin/translate.py -> build/scripts-3.5
2021-02-02T16:37:17,416   copying and adjusting bin/trim-primers.py -> build/scripts-3.5
2021-02-02T16:37:17,419   copying and adjusting bin/trim-reads.py -> build/scripts-3.5
2021-02-02T16:37:17,423   copying and adjusting bin/write-htcondor-job-spec.py -> build/scripts-3.5
2021-02-02T16:37:17,426   changing mode of build/scripts-3.5/aa-info.py from 644 to 755
2021-02-02T16:37:17,427   changing mode of build/scripts-3.5/aa-to-dna.py from 644 to 755
2021-02-02T16:37:17,428   changing mode of build/scripts-3.5/aa-to-properties.py from 644 to 755
2021-02-02T16:37:17,429   changing mode of build/scripts-3.5/adaptor-distances.py from 644 to 755
2021-02-02T16:37:17,429   changing mode of build/scripts-3.5/alignment-panel-civ.py from 644 to 755
2021-02-02T16:37:17,430   changing mode of build/scripts-3.5/alignments-per-read.py from 644 to 755
2021-02-02T16:37:17,431   changing mode of build/scripts-3.5/bit-score-to-e-value.py from 644 to 755
2021-02-02T16:37:17,431   changing mode of build/scripts-3.5/cat-json-blast-records.py from 644 to 755
2021-02-02T16:37:17,432   changing mode of build/scripts-3.5/check-fasta-json-blast-consistency.py from 644 to 755
2021-02-02T16:37:17,433   changing mode of build/scripts-3.5/codon-distance.py from 644 to 755
2021-02-02T16:37:17,434   changing mode of build/scripts-3.5/compare-consensuses.py from 644 to 755
2021-02-02T16:37:17,435   changing mode of build/scripts-3.5/compare-sequences.py from 644 to 755
2021-02-02T16:37:17,436   changing mode of build/scripts-3.5/convert-blast-xml-to-json.py from 644 to 755
2021-02-02T16:37:17,437   changing mode of build/scripts-3.5/convert-diamond-to-json.py from 644 to 755
2021-02-02T16:37:17,438   changing mode of build/scripts-3.5/convert-diamond-to-sam.py from 644 to 755
2021-02-02T16:37:17,440   changing mode of build/scripts-3.5/create-newick-relabeling-output.py from 644 to 755
2021-02-02T16:37:17,441   changing mode of build/scripts-3.5/dark-matter-version.py from 644 to 755
2021-02-02T16:37:17,442   changing mode of build/scripts-3.5/describe-protein-database.py from 644 to 755
2021-02-02T16:37:17,443   changing mode of build/scripts-3.5/dna-to-aa.py from 644 to 755
2021-02-02T16:37:17,444   changing mode of build/scripts-3.5/e-value-to-bit-score.py from 644 to 755
2021-02-02T16:37:17,445   changing mode of build/scripts-3.5/extract-ORFs.py from 644 to 755
2021-02-02T16:37:17,447   changing mode of build/scripts-3.5/fasta-base-indices.py from 644 to 755
2021-02-02T16:37:17,448   changing mode of build/scripts-3.5/fasta-count.py from 644 to 755
2021-02-02T16:37:17,449   changing mode of build/scripts-3.5/fasta-identity-table.py from 644 to 755
2021-02-02T16:37:17,450   changing mode of build/scripts-3.5/fasta-ids.py from 644 to 755
2021-02-02T16:37:17,451   changing mode of build/scripts-3.5/fasta-join.py from 644 to 755
2021-02-02T16:37:17,453   changing mode of build/scripts-3.5/fasta-lengths.py from 644 to 755
2021-02-02T16:37:17,454   changing mode of build/scripts-3.5/fasta-sequences.py from 644 to 755
2021-02-02T16:37:17,455   changing mode of build/scripts-3.5/fasta-sort.py from 644 to 755
2021-02-02T16:37:17,456   changing mode of build/scripts-3.5/fasta-split-by-id.py from 644 to 755
2021-02-02T16:37:17,456   changing mode of build/scripts-3.5/fasta-subset.py from 644 to 755
2021-02-02T16:37:17,457   changing mode of build/scripts-3.5/fasta-subtraction.py from 644 to 755
2021-02-02T16:37:17,458   changing mode of build/scripts-3.5/fasta-to-phylip.py from 644 to 755
2021-02-02T16:37:17,458   changing mode of build/scripts-3.5/fasta-variable-sites.py from 644 to 755
2021-02-02T16:37:17,459   changing mode of build/scripts-3.5/filter-fasta-by-complexity.py from 644 to 755
2021-02-02T16:37:17,460   changing mode of build/scripts-3.5/filter-fasta-by-taxonomy.py from 644 to 755
2021-02-02T16:37:17,461   changing mode of build/scripts-3.5/filter-fasta.py from 644 to 755
2021-02-02T16:37:17,461   changing mode of build/scripts-3.5/filter-hits-to-fasta.py from 644 to 755
2021-02-02T16:37:17,462   changing mode of build/scripts-3.5/filter-reads-alignments.py from 644 to 755
2021-02-02T16:37:17,463   changing mode of build/scripts-3.5/filter-sam.py from 644 to 755
2021-02-02T16:37:17,463   changing mode of build/scripts-3.5/find-hits.py from 644 to 755
2021-02-02T16:37:17,464   changing mode of build/scripts-3.5/format-fasta.py from 644 to 755
2021-02-02T16:37:17,464   changing mode of build/scripts-3.5/genome-protein-summary.py from 644 to 755
2021-02-02T16:37:17,465   changing mode of build/scripts-3.5/get-features.py from 644 to 755
2021-02-02T16:37:17,466   changing mode of build/scripts-3.5/get-hosts.py from 644 to 755
2021-02-02T16:37:17,466   changing mode of build/scripts-3.5/get-reads.py from 644 to 755
2021-02-02T16:37:17,467   changing mode of build/scripts-3.5/get-taxonomy.py from 644 to 755
2021-02-02T16:37:17,468   changing mode of build/scripts-3.5/graph-evalues.py from 644 to 755
2021-02-02T16:37:17,468   changing mode of build/scripts-3.5/local-align.py from 644 to 755
2021-02-02T16:37:17,469   changing mode of build/scripts-3.5/make-consensus.py from 644 to 755
2021-02-02T16:37:17,470   changing mode of build/scripts-3.5/make-fasta-database.py from 644 to 755
2021-02-02T16:37:17,470   changing mode of build/scripts-3.5/make-protein-database.py from 644 to 755
2021-02-02T16:37:17,471   changing mode of build/scripts-3.5/ncbi-fetch-id.py from 644 to 755
2021-02-02T16:37:17,472   changing mode of build/scripts-3.5/newick-to-ascii.py from 644 to 755
2021-02-02T16:37:17,472   changing mode of build/scripts-3.5/noninteractive-alignment-panel.py from 644 to 755
2021-02-02T16:37:17,473   changing mode of build/scripts-3.5/parse-genbank-flat-file.py from 644 to 755
2021-02-02T16:37:17,474   changing mode of build/scripts-3.5/position-summary.py from 644 to 755
2021-02-02T16:37:17,474   changing mode of build/scripts-3.5/print-blast-xml-for-derek.py from 644 to 755
2021-02-02T16:37:17,475   changing mode of build/scripts-3.5/print-blast-xml.py from 644 to 755
2021-02-02T16:37:17,476   changing mode of build/scripts-3.5/print-read-lengths.py from 644 to 755
2021-02-02T16:37:17,476   changing mode of build/scripts-3.5/proteins-to-pathogens.py from 644 to 755
2021-02-02T16:37:17,477   changing mode of build/scripts-3.5/proteins-to-pathogens-civ.py from 644 to 755
2021-02-02T16:37:17,478   changing mode of build/scripts-3.5/randomize-fasta.py from 644 to 755
2021-02-02T16:37:17,478   changing mode of build/scripts-3.5/read-blast-json.py from 644 to 755
2021-02-02T16:37:17,479   changing mode of build/scripts-3.5/read-blast-xml.py from 644 to 755
2021-02-02T16:37:17,480   changing mode of build/scripts-3.5/relabel-newick-tree.py from 644 to 755
2021-02-02T16:37:17,480   changing mode of build/scripts-3.5/run-bwa.py from 644 to 755
2021-02-02T16:37:17,481   changing mode of build/scripts-3.5/run-bowtie2.py from 644 to 755
2021-02-02T16:37:17,482   changing mode of build/scripts-3.5/sam-coverage.py from 644 to 755
2021-02-02T16:37:17,482   changing mode of build/scripts-3.5/sam-coverage-depth.py from 644 to 755
2021-02-02T16:37:17,483   changing mode of build/scripts-3.5/sam-to-fasta-alignment.py from 644 to 755
2021-02-02T16:37:17,484   changing mode of build/scripts-3.5/sam-reference-read-counts.py from 644 to 755
2021-02-02T16:37:17,484   changing mode of build/scripts-3.5/sam-references.py from 644 to 755
2021-02-02T16:37:17,485   changing mode of build/scripts-3.5/sff-to-fastq.py from 644 to 755
2021-02-02T16:37:17,486   changing mode of build/scripts-3.5/split-fasta-by-adaptors.py from 644 to 755
2021-02-02T16:37:17,486   changing mode of build/scripts-3.5/subset-protein-database.py from 644 to 755
2021-02-02T16:37:17,487   changing mode of build/scripts-3.5/summarize-fasta-bases.py from 644 to 755
2021-02-02T16:37:17,487   changing mode of build/scripts-3.5/summarize-reads.py from 644 to 755
2021-02-02T16:37:17,488   changing mode of build/scripts-3.5/translate.py from 644 to 755
2021-02-02T16:37:17,489   changing mode of build/scripts-3.5/trim-primers.py from 644 to 755
2021-02-02T16:37:17,490   changing mode of build/scripts-3.5/trim-reads.py from 644 to 755
2021-02-02T16:37:17,490   changing mode of build/scripts-3.5/write-htcondor-job-spec.py from 644 to 755
2021-02-02T16:37:17,493   installing to build/bdist.linux-armv7l/wheel
2021-02-02T16:37:17,494   running install
2021-02-02T16:37:17,496   running install_lib
2021-02-02T16:37:17,504   creating build/bdist.linux-armv7l
2021-02-02T16:37:17,504   creating build/bdist.linux-armv7l/wheel
2021-02-02T16:37:17,510   creating build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,513   copying build/lib/dark/intervals.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,519   copying build/lib/dark/sam.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,529   copying build/lib/dark/taxonomy.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,539   copying build/lib/dark/process.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,545   copying build/lib/dark/cigar.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,551   copying build/lib/dark/entrez.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,556   copying build/lib/dark/dna.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,566   creating build/bdist.linux-armv7l/wheel/dark/diamond
2021-02-02T16:37:17,568   copying build/lib/dark/diamond/sam.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-02-02T16:37:17,577   copying build/lib/dark/diamond/alignments.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-02-02T16:37:17,582   copying build/lib/dark/diamond/conversion.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-02-02T16:37:17,588   copying build/lib/dark/diamond/run.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-02-02T16:37:17,593   copying build/lib/dark/diamond/hsp.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-02-02T16:37:17,599   copying build/lib/dark/diamond/__init__.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-02-02T16:37:17,604   copying build/lib/dark/reads.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,616   copying build/lib/dark/summarize.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,621   copying build/lib/dark/aa.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,629   copying build/lib/dark/alignments.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,637   creating build/bdist.linux-armv7l/wheel/dark/civ
2021-02-02T16:37:17,640   copying build/lib/dark/civ/proteins.py -> build/bdist.linux-armv7l/wheel/dark/civ
2021-02-02T16:37:17,657   copying build/lib/dark/civ/html.py -> build/bdist.linux-armv7l/wheel/dark/civ
2021-02-02T16:37:17,663   copying build/lib/dark/civ/graphics.py -> build/bdist.linux-armv7l/wheel/dark/civ
2021-02-02T16:37:17,672   copying build/lib/dark/civ/__init__.py -> build/bdist.linux-armv7l/wheel/dark/civ
2021-02-02T16:37:17,677   copying build/lib/dark/proteins.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,689   creating build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,691   copying build/lib/dark/blast/alignments.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,699   copying build/lib/dark/blast/params.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,705   copying build/lib/dark/blast/conversion.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,712   copying build/lib/dark/blast/records.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,718   copying build/lib/dark/blast/hacks.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,723   copying build/lib/dark/blast/hsp.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,730   copying build/lib/dark/blast/score.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,736   copying build/lib/dark/blast/__init__.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-02-02T16:37:17,740   copying build/lib/dark/html.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,748   copying build/lib/dark/baseimage.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,753   copying build/lib/dark/fasta.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,761   copying build/lib/dark/ncbidb.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,767   copying build/lib/dark/consensus.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,773   copying build/lib/dark/utils.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,780   copying build/lib/dark/fasta_ss.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,786   copying build/lib/dark/analyze_reads.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,792   copying build/lib/dark/features.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,799   copying build/lib/dark/genomes.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,806   copying build/lib/dark/dimension.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,812   copying build/lib/dark/local_align.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,820   copying build/lib/dark/bowtie2.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,827   copying build/lib/dark/titles.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,835   copying build/lib/dark/database.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,841   copying build/lib/dark/colors.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,847   copying build/lib/dark/genbank.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,853   copying build/lib/dark/graphics.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,864   copying build/lib/dark/codonDistance.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,870   copying build/lib/dark/fastq.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,875   copying build/lib/dark/filter.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,883   copying build/lib/dark/hsp.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,888   copying build/lib/dark/mutations.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,895   copying build/lib/dark/sequence.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,899   copying build/lib/dark/ipynb.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,904   copying build/lib/dark/simplify.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,910   copying build/lib/dark/distance.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,916   copying build/lib/dark/orfs.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,922   copying build/lib/dark/score.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,926   copying build/lib/dark/errors.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,931   copying build/lib/dark/fpcache.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,935   copying build/lib/dark/btop.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,940   copying build/lib/dark/aligners.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,945   copying build/lib/dark/__init__.py -> build/bdist.linux-armv7l/wheel/dark
2021-02-02T16:37:17,950   running install_egg_info
2021-02-02T16:37:18,003   running egg_info
2021-02-02T16:37:18,005   writing top-level names to dark_matter.egg-info/top_level.txt
2021-02-02T16:37:18,007   writing requirements to dark_matter.egg-info/requires.txt
2021-02-02T16:37:18,010   writing dependency_links to dark_matter.egg-info/dependency_links.txt
2021-02-02T16:37:18,012   writing dark_matter.egg-info/PKG-INFO
2021-02-02T16:37:18,073   reading manifest file 'dark_matter.egg-info/SOURCES.txt'
2021-02-02T16:37:18,114   writing manifest file 'dark_matter.egg-info/SOURCES.txt'
2021-02-02T16:37:18,118   Copying dark_matter.egg-info to build/bdist.linux-armv7l/wheel/dark_matter-3.1.88-py3.5.egg-info
2021-02-02T16:37:18,144   running install_scripts
2021-02-02T16:37:18,285   creating build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data
2021-02-02T16:37:18,286   creating build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,289   copying build/scripts-3.5/compare-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,295   copying build/scripts-3.5/convert-diamond-to-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,300   copying build/scripts-3.5/bit-score-to-e-value.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,306   copying build/scripts-3.5/aa-to-dna.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,312   copying build/scripts-3.5/filter-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,318   copying build/scripts-3.5/run-bowtie2.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,326   copying build/scripts-3.5/sff-to-fastq.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,331   copying build/scripts-3.5/parse-genbank-flat-file.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,337   copying build/scripts-3.5/get-features.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,342   copying build/scripts-3.5/e-value-to-bit-score.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,348   copying build/scripts-3.5/genome-protein-summary.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,355   copying build/scripts-3.5/fasta-base-indices.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,361   copying build/scripts-3.5/sam-to-fasta-alignment.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,367   copying build/scripts-3.5/fasta-variable-sites.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,373   copying build/scripts-3.5/summarize-fasta-bases.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,379   copying build/scripts-3.5/ncbi-fetch-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,385   copying build/scripts-3.5/sam-coverage.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,390   copying build/scripts-3.5/codon-distance.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,396   copying build/scripts-3.5/cat-json-blast-records.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,402   copying build/scripts-3.5/sam-coverage-depth.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,408   copying build/scripts-3.5/extract-ORFs.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,415   copying build/scripts-3.5/print-read-lengths.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,420   copying build/scripts-3.5/read-blast-xml.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,426   copying build/scripts-3.5/filter-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,432   copying build/scripts-3.5/adaptor-distances.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,438   copying build/scripts-3.5/filter-hits-to-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,444   copying build/scripts-3.5/noninteractive-alignment-panel.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,452   copying build/scripts-3.5/randomize-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,457   copying build/scripts-3.5/make-consensus.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,463   copying build/scripts-3.5/fasta-count.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,467   copying build/scripts-3.5/run-bwa.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,472   copying build/scripts-3.5/describe-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,476   copying build/scripts-3.5/summarize-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,480   copying build/scripts-3.5/trim-primers.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,485   copying build/scripts-3.5/filter-fasta-by-complexity.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,491   copying build/scripts-3.5/get-hosts.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,496   copying build/scripts-3.5/fasta-identity-table.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,504   copying build/scripts-3.5/format-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
2021-02-02T16:37:18,508   copying build/scripts-3.5/alignments-per-read.py -> build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts
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2021-02-02T16:37:18,809   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.data/scripts/aa-info.py to 755
2021-02-02T16:37:18,902   creating build/bdist.linux-armv7l/wheel/dark_matter-3.1.88.dist-info/WHEEL
2021-02-02T16:37:19,870   Building wheel for dark-matter (setup.py): finished with status 'done'
2021-02-02T16:37:19,879   Created wheel for dark-matter: filename=dark_matter-3.1.88-py3-none-any.whl size=316358 sha256=7bcc82ff72a007c9cb8ddb3ebfae1df9f1639d2270bd184373fec2d8bdbb9834
2021-02-02T16:37:19,880   Stored in directory: /tmp/pip-ephem-wheel-cache-yol_k8z1/wheels/e6/32/9c/11190d0a70a6bb0d2bab520669d114bf8997f8aabf2363b03c
2021-02-02T16:37:19,913 Successfully built dark-matter
2021-02-02T16:37:19,972 Removed build tracker: '/tmp/pip-req-tracker-_4mx0kjg'