2021-06-13T20:45:29,540 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 Please upgrade your Python as Python 3.5 is no longer maintained.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.
2021-06-13T20:45:30,280 Created temporary directory: /tmp/pip-ephem-wheel-cache-_w_hnbls
2021-06-13T20:45:30,285 Created temporary directory: /tmp/pip-req-tracker-ay74c0dy
2021-06-13T20:45:30,286 Initialized build tracking at /tmp/pip-req-tracker-ay74c0dy
2021-06-13T20:45:30,287 Created build tracker: /tmp/pip-req-tracker-ay74c0dy
2021-06-13T20:45:30,287 Entered build tracker: /tmp/pip-req-tracker-ay74c0dy
2021-06-13T20:45:30,289 Created temporary directory: /tmp/pip-wheel-15ghyzyv
2021-06-13T20:45:30,363 1 location(s) to search for versions of dark-matter:
2021-06-13T20:45:30,363 * https://pypi.org/simple/dark-matter/
2021-06-13T20:45:30,364 Fetching project page and analyzing links: https://pypi.org/simple/dark-matter/
2021-06-13T20:45:30,366 Getting page https://pypi.org/simple/dark-matter/
2021-06-13T20:45:30,371 Found index url https://pypi.org/simple
2021-06-13T20:45:31,094   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
2021-06-13T20:45:31,096   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
2021-06-13T20:45:31,097   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
2021-06-13T20:45:31,098   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
2021-06-13T20:45:31,099   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
2021-06-13T20:45:31,100   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
2021-06-13T20:45:31,101   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
2021-06-13T20:45:31,102   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
2021-06-13T20:45:31,103   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
2021-06-13T20:45:31,104   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
2021-06-13T20:45:31,105   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
2021-06-13T20:45:31,105   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
2021-06-13T20:45:31,106   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
2021-06-13T20:45:31,107   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
2021-06-13T20:45:31,108   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
2021-06-13T20:45:31,109   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
2021-06-13T20:45:31,110   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
2021-06-13T20:45:31,111   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
2021-06-13T20:45:31,112   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
2021-06-13T20:45:31,113   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
2021-06-13T20:45:31,114   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
2021-06-13T20:45:31,115   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
2021-06-13T20:45:31,116   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
2021-06-13T20:45:31,117   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
2021-06-13T20:45:31,118   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
2021-06-13T20:45:31,119   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
2021-06-13T20:45:31,120   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
2021-06-13T20:45:31,121   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
2021-06-13T20:45:31,122   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
2021-06-13T20:45:31,123   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
2021-06-13T20:45:31,124   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
2021-06-13T20:45:31,125   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
2021-06-13T20:45:31,126   Found link https://files.pythonhosted.org/packages/55/52/ab50ff5d12bb5efd1171a964a4f5baa03edb0091dfa5c79af08fbbe4da16/dark-matter-1.0.61.tar.gz#sha256=09e5bdfd05c954d34fc87541f61a416169ae53daea1a22723de915a9f50ea9e4 (from https://pypi.org/simple/dark-matter/), version: 1.0.61
2021-06-13T20:45:31,127   Found link https://files.pythonhosted.org/packages/ab/de/cc9a342e642f66e60c8ff98d1786229d5cfcfb0306158f0c19ef61059303/dark-matter-1.0.62.tar.gz#sha256=6f7347e0923abd2eb2118862a03966c5204262e5d496e11900de3aed43724265 (from https://pypi.org/simple/dark-matter/), version: 1.0.62
2021-06-13T20:45:31,127   Found link https://files.pythonhosted.org/packages/cd/a5/713b8a9f25437fafe2a34291ca34f945c9e1394c2e600f73e5abd8e3282e/dark-matter-1.0.63.tar.gz#sha256=fca60020cce6b249f61f6ae5e268dbd20f71a2d257bb668c84313ca29d6873b1 (from https://pypi.org/simple/dark-matter/), version: 1.0.63
2021-06-13T20:45:31,128   Found link https://files.pythonhosted.org/packages/77/fe/320a21e0c4c116bd28487af7156a9937a90dcc44f70c4f720267e9b14291/dark-matter-1.0.64.tar.gz#sha256=d1c1764b08f3fbdf71f46a5f9acbe0deadb96d5af5b4b99d8b19e13e4abe9e3d (from https://pypi.org/simple/dark-matter/), version: 1.0.64
2021-06-13T20:45:31,129   Found link https://files.pythonhosted.org/packages/a0/08/9be54a6570a6acf6f87d5ca8ff9f91660697fc32212d0be3601785e796b9/dark-matter-1.0.65.tar.gz#sha256=1332fafc881be70d395aa69ed174c0036941f2d4f8e170f24ba6c0fa14397de6 (from https://pypi.org/simple/dark-matter/), version: 1.0.65
2021-06-13T20:45:31,131   Found link https://files.pythonhosted.org/packages/7b/61/46caedf674111789641d78a4252b26d1ea43d3d8c77f906b3abc7c638acc/dark-matter-1.0.66.tar.gz#sha256=a0ad6f3e8afe8294c1aa5011577533334d2a6cbb16eaaa9b48a451fe0a9db293 (from https://pypi.org/simple/dark-matter/), version: 1.0.66
2021-06-13T20:45:31,132   Found link https://files.pythonhosted.org/packages/97/54/fc8129e31460a4007b2d328e37efeb55a3488b7a7a34592e0c738ac27079/dark-matter-1.0.67.tar.gz#sha256=709dbe5d0c6df732587900ea0ee3a8508fd43a37d7aff3ec5387bbee7d7917cd (from https://pypi.org/simple/dark-matter/), version: 1.0.67
2021-06-13T20:45:31,133   Found link https://files.pythonhosted.org/packages/e5/33/890848c35cb392c57712943c79ffe317ce401bd2db2a616637719f8c5522/dark-matter-1.0.68.tar.gz#sha256=5426893dee726d1f3da0d38176f4489d983e698b36586b2a5d4030ccfd38ae9f (from https://pypi.org/simple/dark-matter/), version: 1.0.68
2021-06-13T20:45:31,134   Found link https://files.pythonhosted.org/packages/c2/23/5e4253583920bada6ee2f5204fbaf8a745527f8ba5c585ac8891fa959991/dark-matter-1.0.69.tar.gz#sha256=494ab515566d76d337f7b25186921029e01e84460ae1f2d81c355a9ae135a18c (from https://pypi.org/simple/dark-matter/), version: 1.0.69
2021-06-13T20:45:31,135   Found link https://files.pythonhosted.org/packages/3d/6a/1cf82dcc5f77ac300a3ee4c1fce72edad81280795e42f0da80b67b3a1838/dark-matter-1.0.70.tar.gz#sha256=f74facc816c78353ee9cdeeac334e9e03d05c38cc381588def6443125fe7ff17 (from https://pypi.org/simple/dark-matter/), version: 1.0.70
2021-06-13T20:45:31,136   Found link https://files.pythonhosted.org/packages/64/9a/ace6de00719320e68408c58f3abe036645a29901f17e3e1cd356260cb9f5/dark-matter-1.0.71.tar.gz#sha256=f0ed0a32bf00786a18d3b50596ad79ec24f01ed3fa9d56f36efec9db58a750a6 (from https://pypi.org/simple/dark-matter/), version: 1.0.71
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2021-06-13T20:45:31,139   Found link https://files.pythonhosted.org/packages/8e/dc/f8fbeb00d964a029f3e444ed65ba9ca0f69e83c4b19d93efb858ac9d67cf/dark-matter-1.0.74.tar.gz#sha256=90c2fc0dcc27bbd558041ae982768c630c602360754f3e07577c2711966c1fb7 (from https://pypi.org/simple/dark-matter/), version: 1.0.74
2021-06-13T20:45:31,140   Found link https://files.pythonhosted.org/packages/26/50/60d51f6d26ec912a10cd058c4221c4794813080bcccd2f5af993a2bfe973/dark-matter-1.0.75.tar.gz#sha256=9db8994744be84b8d67035bff720b4b8330e8682339d3bef01a857210d400c50 (from https://pypi.org/simple/dark-matter/), version: 1.0.75
2021-06-13T20:45:31,141   Found link https://files.pythonhosted.org/packages/03/bb/45b48f894b2b3f2a08e9e3c3c07ce133db94e91a363688f3ab9ce4969d80/dark-matter-1.0.76.tar.gz#sha256=940772c257a0f785f0f5efa53a7075692b5fa889a6c1d3432e17929fc30a1179 (from https://pypi.org/simple/dark-matter/), version: 1.0.76
2021-06-13T20:45:31,142   Found link https://files.pythonhosted.org/packages/5a/b2/63dea9b0ab7517190dd58b390cd9f0c007da74ad33c1ce37a74e6640e62c/dark-matter-1.0.77.tar.gz#sha256=e027b5a28158d9e74d712bdc4651580fe3c14be15a124a7a7634523e2cafd842 (from https://pypi.org/simple/dark-matter/), version: 1.0.77
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2021-06-13T20:45:31,352   Found link https://files.pythonhosted.org/packages/fe/74/37ca77e38cc0080fbe164321e7ab6be1552960f966c11c12ba6a138c1cdb/dark-matter-3.2.3.tar.gz#sha256=51d99ef9b8c7628613fed3519fac86d2575c56f4977150d0ec017a440b869692 (from https://pypi.org/simple/dark-matter/), version: 3.2.3
2021-06-13T20:45:31,353   Found link https://files.pythonhosted.org/packages/bf/8e/017b2bbd617c0e4dec88b71755855fd32a8fa54ca0c114896475378d8c10/dark-matter-3.2.4.tar.gz#sha256=1bf86c2be13ad123baff3cd4cec2443bf16ec9afca83a50da3aad256033c61e3 (from https://pypi.org/simple/dark-matter/), version: 3.2.4
2021-06-13T20:45:31,354   Found link https://files.pythonhosted.org/packages/95/55/bb9433858a72e5030fe4579502698e18fe9f21ec51f4d34a9f3f33913aed/dark-matter-3.2.5.tar.gz#sha256=1a31e2be7d17f7a47cc07b566ed2a822559fb09072efda9827666ba83d560c41 (from https://pypi.org/simple/dark-matter/), version: 3.2.5
2021-06-13T20:45:31,355   Found link https://files.pythonhosted.org/packages/31/42/f98d746754c0a92d708b8c77d5cc6156cdd264c04b850f94d4b130e573e5/dark-matter-3.2.6.tar.gz#sha256=288126f141d0ec87735c121184f06121f694e6a565df8f962aec7ec84a41058a (from https://pypi.org/simple/dark-matter/), version: 3.2.6
2021-06-13T20:45:31,356   Found link https://files.pythonhosted.org/packages/91/46/1547ccfdd762ae0eca10c8781419157a1350f009d02f1eaf0f02f4666d43/dark-matter-4.0.1.tar.gz#sha256=0bc78eb30abeb495a923f91ca67042a947c142b0bfef173c9c04168521d596bb (from https://pypi.org/simple/dark-matter/), version: 4.0.1
2021-06-13T20:45:31,509 Given no hashes to check 1 links for project 'dark-matter': discarding no candidates
2021-06-13T20:45:31,551 Collecting dark-matter==4.0.1
2021-06-13T20:45:31,555   Created temporary directory: /tmp/pip-unpack-cpm7j7e5
2021-06-13T20:45:32,049   Downloading dark-matter-4.0.1.tar.gz (332 kB)
2021-06-13T20:45:33,537   Added dark-matter==4.0.1 from https://files.pythonhosted.org/packages/91/46/1547ccfdd762ae0eca10c8781419157a1350f009d02f1eaf0f02f4666d43/dark-matter-4.0.1.tar.gz#sha256=0bc78eb30abeb495a923f91ca67042a947c142b0bfef173c9c04168521d596bb to build tracker '/tmp/pip-req-tracker-ay74c0dy'
2021-06-13T20:45:33,540     Running setup.py (path:/tmp/pip-wheel-15ghyzyv/dark-matter_d887ee63dcd54cff809b6012dff1eb67/setup.py) egg_info for package dark-matter
2021-06-13T20:45:33,543     Created temporary directory: /tmp/pip-pip-egg-info-imtlsx7a
2021-06-13T20:45:33,544     Running command python setup.py egg_info
2021-06-13T20:45:36,234     running egg_info
2021-06-13T20:45:36,240     creating /tmp/pip-pip-egg-info-imtlsx7a/dark_matter.egg-info
2021-06-13T20:45:36,245     writing /tmp/pip-pip-egg-info-imtlsx7a/dark_matter.egg-info/PKG-INFO
2021-06-13T20:45:36,250     writing dependency_links to /tmp/pip-pip-egg-info-imtlsx7a/dark_matter.egg-info/dependency_links.txt
2021-06-13T20:45:36,252     writing requirements to /tmp/pip-pip-egg-info-imtlsx7a/dark_matter.egg-info/requires.txt
2021-06-13T20:45:36,255     writing top-level names to /tmp/pip-pip-egg-info-imtlsx7a/dark_matter.egg-info/top_level.txt
2021-06-13T20:45:36,260     writing manifest file '/tmp/pip-pip-egg-info-imtlsx7a/dark_matter.egg-info/SOURCES.txt'
2021-06-13T20:45:36,706     reading manifest file '/tmp/pip-pip-egg-info-imtlsx7a/dark_matter.egg-info/SOURCES.txt'
2021-06-13T20:45:36,736     writing manifest file '/tmp/pip-pip-egg-info-imtlsx7a/dark_matter.egg-info/SOURCES.txt'
2021-06-13T20:45:36,875   Source in /tmp/pip-wheel-15ghyzyv/dark-matter_d887ee63dcd54cff809b6012dff1eb67 has version 4.0.1, which satisfies requirement dark-matter==4.0.1 from https://files.pythonhosted.org/packages/91/46/1547ccfdd762ae0eca10c8781419157a1350f009d02f1eaf0f02f4666d43/dark-matter-4.0.1.tar.gz#sha256=0bc78eb30abeb495a923f91ca67042a947c142b0bfef173c9c04168521d596bb
2021-06-13T20:45:36,877   Removed dark-matter==4.0.1 from https://files.pythonhosted.org/packages/91/46/1547ccfdd762ae0eca10c8781419157a1350f009d02f1eaf0f02f4666d43/dark-matter-4.0.1.tar.gz#sha256=0bc78eb30abeb495a923f91ca67042a947c142b0bfef173c9c04168521d596bb from build tracker '/tmp/pip-req-tracker-ay74c0dy'
2021-06-13T20:45:36,889 Created temporary directory: /tmp/pip-unpack-n03fwgcr
2021-06-13T20:45:36,891 Building wheels for collected packages: dark-matter
2021-06-13T20:45:36,903   Created temporary directory: /tmp/pip-wheel-_p64fu7l
2021-06-13T20:45:36,905   Building wheel for dark-matter (setup.py): started
2021-06-13T20:45:36,905   Destination directory: /tmp/pip-wheel-_p64fu7l
2021-06-13T20:45:36,906   Running command /usr/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-15ghyzyv/dark-matter_d887ee63dcd54cff809b6012dff1eb67/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-15ghyzyv/dark-matter_d887ee63dcd54cff809b6012dff1eb67/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-_p64fu7l
2021-06-13T20:45:39,384   running bdist_wheel
2021-06-13T20:45:39,400   running build
2021-06-13T20:45:39,401   running build_py
2021-06-13T20:45:39,749   creating build
2021-06-13T20:45:39,750   creating build/lib
2021-06-13T20:45:39,751   creating build/lib/dark
2021-06-13T20:45:39,754   copying dark/mutations.py -> build/lib/dark
2021-06-13T20:45:39,760   copying dark/ncbidb.py -> build/lib/dark
2021-06-13T20:45:39,764   copying dark/consensus.py -> build/lib/dark
2021-06-13T20:45:39,769   copying dark/analyze_reads.py -> build/lib/dark
2021-06-13T20:45:39,773   copying dark/genomes.py -> build/lib/dark
2021-06-13T20:45:39,778   copying dark/sequence.py -> build/lib/dark
2021-06-13T20:45:39,782   copying dark/proteins.py -> build/lib/dark
2021-06-13T20:45:39,793   copying dark/bowtie2.py -> build/lib/dark
2021-06-13T20:45:39,800   copying dark/distance.py -> build/lib/dark
2021-06-13T20:45:39,806   copying dark/sam.py -> build/lib/dark
2021-06-13T20:45:39,815   copying dark/features.py -> build/lib/dark
2021-06-13T20:45:39,822   copying dark/reads.py -> build/lib/dark
2021-06-13T20:45:39,835   copying dark/__init__.py -> build/lib/dark
2021-06-13T20:45:39,841   copying dark/aa.py -> build/lib/dark
2021-06-13T20:45:39,852   copying dark/hsp.py -> build/lib/dark
2021-06-13T20:45:39,860   copying dark/baseimage.py -> build/lib/dark
2021-06-13T20:45:39,866   copying dark/graphics.py -> build/lib/dark
2021-06-13T20:45:39,875   copying dark/simplify.py -> build/lib/dark
2021-06-13T20:45:39,880   copying dark/genbank.py -> build/lib/dark
2021-06-13T20:45:39,887   copying dark/fastq.py -> build/lib/dark
2021-06-13T20:45:39,894   copying dark/alignments.py -> build/lib/dark
2021-06-13T20:45:39,903   copying dark/fasta_ss.py -> build/lib/dark
2021-06-13T20:45:39,909   copying dark/fpcache.py -> build/lib/dark
2021-06-13T20:45:39,914   copying dark/utils.py -> build/lib/dark
2021-06-13T20:45:39,921   copying dark/filter.py -> build/lib/dark
2021-06-13T20:45:39,929   copying dark/taxonomy.py -> build/lib/dark
2021-06-13T20:45:39,939   copying dark/codonDistance.py -> build/lib/dark
2021-06-13T20:45:39,946   copying dark/score.py -> build/lib/dark
2021-06-13T20:45:39,952   copying dark/local_align.py -> build/lib/dark
2021-06-13T20:45:39,958   copying dark/errors.py -> build/lib/dark
2021-06-13T20:45:39,963   copying dark/dna.py -> build/lib/dark
2021-06-13T20:45:39,970   copying dark/btop.py -> build/lib/dark
2021-06-13T20:45:39,975   copying dark/dimension.py -> build/lib/dark
2021-06-13T20:45:39,980   copying dark/cigar.py -> build/lib/dark
2021-06-13T20:45:39,986   copying dark/aligners.py -> build/lib/dark
2021-06-13T20:45:39,991   copying dark/process.py -> build/lib/dark
2021-06-13T20:45:39,997   copying dark/intervals.py -> build/lib/dark
2021-06-13T20:45:40,003   copying dark/entrez.py -> build/lib/dark
2021-06-13T20:45:40,009   copying dark/orfs.py -> build/lib/dark
2021-06-13T20:45:40,016   copying dark/colors.py -> build/lib/dark
2021-06-13T20:45:40,023   copying dark/database.py -> build/lib/dark
2021-06-13T20:45:40,029   copying dark/html.py -> build/lib/dark
2021-06-13T20:45:40,036   copying dark/fasta.py -> build/lib/dark
2021-06-13T20:45:40,043   copying dark/ipynb.py -> build/lib/dark
2021-06-13T20:45:40,048   copying dark/titles.py -> build/lib/dark
2021-06-13T20:45:40,057   copying dark/summarize.py -> build/lib/dark
2021-06-13T20:45:40,067   creating build/lib/dark/blast
2021-06-13T20:45:40,071   copying dark/blast/conversion.py -> build/lib/dark/blast
2021-06-13T20:45:40,078   copying dark/blast/__init__.py -> build/lib/dark/blast
2021-06-13T20:45:40,082   copying dark/blast/records.py -> build/lib/dark/blast
2021-06-13T20:45:40,087   copying dark/blast/hsp.py -> build/lib/dark/blast
2021-06-13T20:45:40,095   copying dark/blast/params.py -> build/lib/dark/blast
2021-06-13T20:45:40,102   copying dark/blast/alignments.py -> build/lib/dark/blast
2021-06-13T20:45:40,110   copying dark/blast/score.py -> build/lib/dark/blast
2021-06-13T20:45:40,116   copying dark/blast/hacks.py -> build/lib/dark/blast
2021-06-13T20:45:40,122   creating build/lib/dark/diamond
2021-06-13T20:45:40,125   copying dark/diamond/sam.py -> build/lib/dark/diamond
2021-06-13T20:45:40,132   copying dark/diamond/conversion.py -> build/lib/dark/diamond
2021-06-13T20:45:40,139   copying dark/diamond/__init__.py -> build/lib/dark/diamond
2021-06-13T20:45:40,144   copying dark/diamond/hsp.py -> build/lib/dark/diamond
2021-06-13T20:45:40,150   copying dark/diamond/alignments.py -> build/lib/dark/diamond
2021-06-13T20:45:40,156   copying dark/diamond/run.py -> build/lib/dark/diamond
2021-06-13T20:45:40,162   creating build/lib/dark/civ
2021-06-13T20:45:40,165   copying dark/civ/proteins.py -> build/lib/dark/civ
2021-06-13T20:45:40,181   copying dark/civ/__init__.py -> build/lib/dark/civ
2021-06-13T20:45:40,187   copying dark/civ/graphics.py -> build/lib/dark/civ
2021-06-13T20:45:40,196   copying dark/civ/html.py -> build/lib/dark/civ
2021-06-13T20:45:40,214   running build_scripts
2021-06-13T20:45:40,215   creating build/scripts-3.5
2021-06-13T20:45:40,219   copying and adjusting bin/aa-info.py -> build/scripts-3.5
2021-06-13T20:45:40,224   copying and adjusting bin/aa-to-dna.py -> build/scripts-3.5
2021-06-13T20:45:40,228   copying and adjusting bin/aa-to-properties.py -> build/scripts-3.5
2021-06-13T20:45:40,233   copying and adjusting bin/adaptor-distances.py -> build/scripts-3.5
2021-06-13T20:45:40,237   copying and adjusting bin/alignment-panel-civ.py -> build/scripts-3.5
2021-06-13T20:45:40,244   copying and adjusting bin/alignments-per-read.py -> build/scripts-3.5
2021-06-13T20:45:40,249   copying and adjusting bin/bit-score-to-e-value.py -> build/scripts-3.5
2021-06-13T20:45:40,253   copying and adjusting bin/cat-json-blast-records.py -> build/scripts-3.5
2021-06-13T20:45:40,257   copying and adjusting bin/check-fasta-json-blast-consistency.py -> build/scripts-3.5
2021-06-13T20:45:40,262   copying and adjusting bin/codon-distance.py -> build/scripts-3.5
2021-06-13T20:45:40,266   copying and adjusting bin/compare-consensuses.py -> build/scripts-3.5
2021-06-13T20:45:40,272   copying and adjusting bin/compare-sequences.py -> build/scripts-3.5
2021-06-13T20:45:40,277   copying and adjusting bin/convert-blast-xml-to-json.py -> build/scripts-3.5
2021-06-13T20:45:40,281   copying and adjusting bin/convert-diamond-to-json.py -> build/scripts-3.5
2021-06-13T20:45:40,286   copying and adjusting bin/convert-diamond-to-sam.py -> build/scripts-3.5
2021-06-13T20:45:40,291   copying bin/convert-sam-to-fastq.sh -> build/scripts-3.5
2021-06-13T20:45:40,297   copying and adjusting bin/create-newick-relabeling-output.py -> build/scripts-3.5
2021-06-13T20:45:40,302   copying and adjusting bin/dark-matter-version.py -> build/scripts-3.5
2021-06-13T20:45:40,306   copying and adjusting bin/describe-protein-database.py -> build/scripts-3.5
2021-06-13T20:45:40,310   copying and adjusting bin/dna-to-aa.py -> build/scripts-3.5
2021-06-13T20:45:40,316   copying bin/download-genbank.sh -> build/scripts-3.5
2021-06-13T20:45:40,321   copying and adjusting bin/e-value-to-bit-score.py -> build/scripts-3.5
2021-06-13T20:45:40,325   copying and adjusting bin/extract-ORFs.py -> build/scripts-3.5
2021-06-13T20:45:40,329   copying and adjusting bin/fasta-base-indices.py -> build/scripts-3.5
2021-06-13T20:45:40,333   copying and adjusting bin/fasta-count.py -> build/scripts-3.5
2021-06-13T20:45:40,336   copying bin/fasta-diff.sh -> build/scripts-3.5
2021-06-13T20:45:40,341   copying and adjusting bin/fasta-identity-table.py -> build/scripts-3.5
2021-06-13T20:45:40,349   copying and adjusting bin/fasta-ids.py -> build/scripts-3.5
2021-06-13T20:45:40,352   copying and adjusting bin/fasta-join.py -> build/scripts-3.5
2021-06-13T20:45:40,355   copying and adjusting bin/fasta-lengths.py -> build/scripts-3.5
2021-06-13T20:45:40,358   copying and adjusting bin/fasta-sequences.py -> build/scripts-3.5
2021-06-13T20:45:40,362   copying and adjusting bin/fasta-sort.py -> build/scripts-3.5
2021-06-13T20:45:40,365   copying and adjusting bin/fasta-split-by-id.py -> build/scripts-3.5
2021-06-13T20:45:40,369   copying and adjusting bin/fasta-subset.py -> build/scripts-3.5
2021-06-13T20:45:40,372   copying and adjusting bin/fasta-subtraction.py -> build/scripts-3.5
2021-06-13T20:45:40,375   copying and adjusting bin/fasta-to-phylip.py -> build/scripts-3.5
2021-06-13T20:45:40,379   copying and adjusting bin/fasta-variable-sites.py -> build/scripts-3.5
2021-06-13T20:45:40,383   copying and adjusting bin/filter-fasta-by-complexity.py -> build/scripts-3.5
2021-06-13T20:45:40,387   copying and adjusting bin/filter-fasta-by-taxonomy.py -> build/scripts-3.5
2021-06-13T20:45:40,391   copying and adjusting bin/filter-fasta.py -> build/scripts-3.5
2021-06-13T20:45:40,395   copying and adjusting bin/filter-hits-to-fasta.py -> build/scripts-3.5
2021-06-13T20:45:40,399   copying and adjusting bin/filter-reads-alignments.py -> build/scripts-3.5
2021-06-13T20:45:40,404   copying and adjusting bin/filter-sam.py -> build/scripts-3.5
2021-06-13T20:45:40,408   copying and adjusting bin/find-hits.py -> build/scripts-3.5
2021-06-13T20:45:40,412   copying and adjusting bin/format-fasta.py -> build/scripts-3.5
2021-06-13T20:45:40,415   copying and adjusting bin/genome-protein-summary.py -> build/scripts-3.5
2021-06-13T20:45:40,421   copying and adjusting bin/get-features.py -> build/scripts-3.5
2021-06-13T20:45:40,426   copying and adjusting bin/get-hosts.py -> build/scripts-3.5
2021-06-13T20:45:40,431   copying and adjusting bin/get-reads.py -> build/scripts-3.5
2021-06-13T20:45:40,436   copying and adjusting bin/get-taxonomy.py -> build/scripts-3.5
2021-06-13T20:45:40,441   copying and adjusting bin/graph-evalues.py -> build/scripts-3.5
2021-06-13T20:45:40,444   copying and adjusting bin/local-align.py -> build/scripts-3.5
2021-06-13T20:45:40,447   copying and adjusting bin/make-consensus.py -> build/scripts-3.5
2021-06-13T20:45:40,453   copying and adjusting bin/make-fasta-database.py -> build/scripts-3.5
2021-06-13T20:45:40,456   copying and adjusting bin/make-protein-database.py -> build/scripts-3.5
2021-06-13T20:45:40,461   copying and adjusting bin/ncbi-fetch-id.py -> build/scripts-3.5
2021-06-13T20:45:40,464   copying and adjusting bin/newick-to-ascii.py -> build/scripts-3.5
2021-06-13T20:45:40,468   copying and adjusting bin/noninteractive-alignment-panel.py -> build/scripts-3.5
2021-06-13T20:45:40,475   copying and adjusting bin/parse-genbank-flat-file.py -> build/scripts-3.5
2021-06-13T20:45:40,478   copying and adjusting bin/position-summary.py -> build/scripts-3.5
2021-06-13T20:45:40,482   copying bin/pre-commit.sh -> build/scripts-3.5
2021-06-13T20:45:40,487   copying and adjusting bin/print-blast-xml-for-derek.py -> build/scripts-3.5
2021-06-13T20:45:40,490   copying and adjusting bin/print-blast-xml.py -> build/scripts-3.5
2021-06-13T20:45:40,493   copying and adjusting bin/print-read-lengths.py -> build/scripts-3.5
2021-06-13T20:45:40,497   copying and adjusting bin/proteins-to-pathogens.py -> build/scripts-3.5
2021-06-13T20:45:40,502   copying and adjusting bin/proteins-to-pathogens-civ.py -> build/scripts-3.5
2021-06-13T20:45:40,508   copying and adjusting bin/randomize-fasta.py -> build/scripts-3.5
2021-06-13T20:45:40,511   copying and adjusting bin/read-blast-json.py -> build/scripts-3.5
2021-06-13T20:45:40,514   copying and adjusting bin/read-blast-xml.py -> build/scripts-3.5
2021-06-13T20:45:40,517   copying and adjusting bin/relabel-newick-tree.py -> build/scripts-3.5
2021-06-13T20:45:40,521   copying and adjusting bin/run-bwa.py -> build/scripts-3.5
2021-06-13T20:45:40,525   copying and adjusting bin/run-bowtie2.py -> build/scripts-3.5
2021-06-13T20:45:40,531   copying and adjusting bin/sam-coverage.py -> build/scripts-3.5
2021-06-13T20:45:40,535   copying and adjusting bin/sam-coverage-depth.py -> build/scripts-3.5
2021-06-13T20:45:40,540   copying and adjusting bin/sam-to-fasta-alignment.py -> build/scripts-3.5
2021-06-13T20:45:40,543   copying and adjusting bin/sam-reference-read-counts.py -> build/scripts-3.5
2021-06-13T20:45:40,547   copying and adjusting bin/sam-references.py -> build/scripts-3.5
2021-06-13T20:45:40,551   copying and adjusting bin/sff-to-fastq.py -> build/scripts-3.5
2021-06-13T20:45:40,554   copying and adjusting bin/split-fasta-by-adaptors.py -> build/scripts-3.5
2021-06-13T20:45:40,559   copying and adjusting bin/subset-protein-database.py -> build/scripts-3.5
2021-06-13T20:45:40,562   copying and adjusting bin/summarize-fasta-bases.py -> build/scripts-3.5
2021-06-13T20:45:40,567   copying and adjusting bin/summarize-reads.py -> build/scripts-3.5
2021-06-13T20:45:40,570   copying and adjusting bin/translate.py -> build/scripts-3.5
2021-06-13T20:45:40,573   copying and adjusting bin/trim-primers.py -> build/scripts-3.5
2021-06-13T20:45:40,577   copying and adjusting bin/trim-reads.py -> build/scripts-3.5
2021-06-13T20:45:40,580   copying and adjusting bin/write-htcondor-job-spec.py -> build/scripts-3.5
2021-06-13T20:45:40,586   changing mode of build/scripts-3.5/aa-info.py from 644 to 755
2021-06-13T20:45:40,587   changing mode of build/scripts-3.5/aa-to-dna.py from 644 to 755
2021-06-13T20:45:40,589   changing mode of build/scripts-3.5/aa-to-properties.py from 644 to 755
2021-06-13T20:45:40,590   changing mode of build/scripts-3.5/adaptor-distances.py from 644 to 755
2021-06-13T20:45:40,592   changing mode of build/scripts-3.5/alignment-panel-civ.py from 644 to 755
2021-06-13T20:45:40,593   changing mode of build/scripts-3.5/alignments-per-read.py from 644 to 755
2021-06-13T20:45:40,594   changing mode of build/scripts-3.5/bit-score-to-e-value.py from 644 to 755
2021-06-13T20:45:40,595   changing mode of build/scripts-3.5/cat-json-blast-records.py from 644 to 755
2021-06-13T20:45:40,597   changing mode of build/scripts-3.5/check-fasta-json-blast-consistency.py from 644 to 755
2021-06-13T20:45:40,598   changing mode of build/scripts-3.5/codon-distance.py from 644 to 755
2021-06-13T20:45:40,600   changing mode of build/scripts-3.5/compare-consensuses.py from 644 to 755
2021-06-13T20:45:40,601   changing mode of build/scripts-3.5/compare-sequences.py from 644 to 755
2021-06-13T20:45:40,602   changing mode of build/scripts-3.5/convert-blast-xml-to-json.py from 644 to 755
2021-06-13T20:45:40,603   changing mode of build/scripts-3.5/convert-diamond-to-json.py from 644 to 755
2021-06-13T20:45:40,604   changing mode of build/scripts-3.5/convert-diamond-to-sam.py from 644 to 755
2021-06-13T20:45:40,605   changing mode of build/scripts-3.5/create-newick-relabeling-output.py from 644 to 755
2021-06-13T20:45:40,605   changing mode of build/scripts-3.5/dark-matter-version.py from 644 to 755
2021-06-13T20:45:40,606   changing mode of build/scripts-3.5/describe-protein-database.py from 644 to 755
2021-06-13T20:45:40,607   changing mode of build/scripts-3.5/dna-to-aa.py from 644 to 755
2021-06-13T20:45:40,608   changing mode of build/scripts-3.5/e-value-to-bit-score.py from 644 to 755
2021-06-13T20:45:40,608   changing mode of build/scripts-3.5/extract-ORFs.py from 644 to 755
2021-06-13T20:45:40,609   changing mode of build/scripts-3.5/fasta-base-indices.py from 644 to 755
2021-06-13T20:45:40,610   changing mode of build/scripts-3.5/fasta-count.py from 644 to 755
2021-06-13T20:45:40,610   changing mode of build/scripts-3.5/fasta-identity-table.py from 644 to 755
2021-06-13T20:45:40,611   changing mode of build/scripts-3.5/fasta-ids.py from 644 to 755
2021-06-13T20:45:40,612   changing mode of build/scripts-3.5/fasta-join.py from 644 to 755
2021-06-13T20:45:40,613   changing mode of build/scripts-3.5/fasta-lengths.py from 644 to 755
2021-06-13T20:45:40,613   changing mode of build/scripts-3.5/fasta-sequences.py from 644 to 755
2021-06-13T20:45:40,614   changing mode of build/scripts-3.5/fasta-sort.py from 644 to 755
2021-06-13T20:45:40,615   changing mode of build/scripts-3.5/fasta-split-by-id.py from 644 to 755
2021-06-13T20:45:40,616   changing mode of build/scripts-3.5/fasta-subset.py from 644 to 755
2021-06-13T20:45:40,616   changing mode of build/scripts-3.5/fasta-subtraction.py from 644 to 755
2021-06-13T20:45:40,617   changing mode of build/scripts-3.5/fasta-to-phylip.py from 644 to 755
2021-06-13T20:45:40,618   changing mode of build/scripts-3.5/fasta-variable-sites.py from 644 to 755
2021-06-13T20:45:40,618   changing mode of build/scripts-3.5/filter-fasta-by-complexity.py from 644 to 755
2021-06-13T20:45:40,619   changing mode of build/scripts-3.5/filter-fasta-by-taxonomy.py from 644 to 755
2021-06-13T20:45:40,620   changing mode of build/scripts-3.5/filter-fasta.py from 644 to 755
2021-06-13T20:45:40,621   changing mode of build/scripts-3.5/filter-hits-to-fasta.py from 644 to 755
2021-06-13T20:45:40,621   changing mode of build/scripts-3.5/filter-reads-alignments.py from 644 to 755
2021-06-13T20:45:40,622   changing mode of build/scripts-3.5/filter-sam.py from 644 to 755
2021-06-13T20:45:40,623   changing mode of build/scripts-3.5/find-hits.py from 644 to 755
2021-06-13T20:45:40,624   changing mode of build/scripts-3.5/format-fasta.py from 644 to 755
2021-06-13T20:45:40,624   changing mode of build/scripts-3.5/genome-protein-summary.py from 644 to 755
2021-06-13T20:45:40,625   changing mode of build/scripts-3.5/get-features.py from 644 to 755
2021-06-13T20:45:40,626   changing mode of build/scripts-3.5/get-hosts.py from 644 to 755
2021-06-13T20:45:40,627   changing mode of build/scripts-3.5/get-reads.py from 644 to 755
2021-06-13T20:45:40,627   changing mode of build/scripts-3.5/get-taxonomy.py from 644 to 755
2021-06-13T20:45:40,628   changing mode of build/scripts-3.5/graph-evalues.py from 644 to 755
2021-06-13T20:45:40,629   changing mode of build/scripts-3.5/local-align.py from 644 to 755
2021-06-13T20:45:40,629   changing mode of build/scripts-3.5/make-consensus.py from 644 to 755
2021-06-13T20:45:40,630   changing mode of build/scripts-3.5/make-fasta-database.py from 644 to 755
2021-06-13T20:45:40,631   changing mode of build/scripts-3.5/make-protein-database.py from 644 to 755
2021-06-13T20:45:40,632   changing mode of build/scripts-3.5/ncbi-fetch-id.py from 644 to 755
2021-06-13T20:45:40,632   changing mode of build/scripts-3.5/newick-to-ascii.py from 644 to 755
2021-06-13T20:45:40,633   changing mode of build/scripts-3.5/noninteractive-alignment-panel.py from 644 to 755
2021-06-13T20:45:40,634   changing mode of build/scripts-3.5/parse-genbank-flat-file.py from 644 to 755
2021-06-13T20:45:40,635   changing mode of build/scripts-3.5/position-summary.py from 644 to 755
2021-06-13T20:45:40,635   changing mode of build/scripts-3.5/print-blast-xml-for-derek.py from 644 to 755
2021-06-13T20:45:40,636   changing mode of build/scripts-3.5/print-blast-xml.py from 644 to 755
2021-06-13T20:45:40,637   changing mode of build/scripts-3.5/print-read-lengths.py from 644 to 755
2021-06-13T20:45:40,638   changing mode of build/scripts-3.5/proteins-to-pathogens.py from 644 to 755
2021-06-13T20:45:40,638   changing mode of build/scripts-3.5/proteins-to-pathogens-civ.py from 644 to 755
2021-06-13T20:45:40,639   changing mode of build/scripts-3.5/randomize-fasta.py from 644 to 755
2021-06-13T20:45:40,640   changing mode of build/scripts-3.5/read-blast-json.py from 644 to 755
2021-06-13T20:45:40,641   changing mode of build/scripts-3.5/read-blast-xml.py from 644 to 755
2021-06-13T20:45:40,641   changing mode of build/scripts-3.5/relabel-newick-tree.py from 644 to 755
2021-06-13T20:45:40,642   changing mode of build/scripts-3.5/run-bwa.py from 644 to 755
2021-06-13T20:45:40,643   changing mode of build/scripts-3.5/run-bowtie2.py from 644 to 755
2021-06-13T20:45:40,644   changing mode of build/scripts-3.5/sam-coverage.py from 644 to 755
2021-06-13T20:45:40,644   changing mode of build/scripts-3.5/sam-coverage-depth.py from 644 to 755
2021-06-13T20:45:40,645   changing mode of build/scripts-3.5/sam-to-fasta-alignment.py from 644 to 755
2021-06-13T20:45:40,646   changing mode of build/scripts-3.5/sam-reference-read-counts.py from 644 to 755
2021-06-13T20:45:40,646   changing mode of build/scripts-3.5/sam-references.py from 644 to 755
2021-06-13T20:45:40,647   changing mode of build/scripts-3.5/sff-to-fastq.py from 644 to 755
2021-06-13T20:45:40,648   changing mode of build/scripts-3.5/split-fasta-by-adaptors.py from 644 to 755
2021-06-13T20:45:40,649   changing mode of build/scripts-3.5/subset-protein-database.py from 644 to 755
2021-06-13T20:45:40,649   changing mode of build/scripts-3.5/summarize-fasta-bases.py from 644 to 755
2021-06-13T20:45:40,650   changing mode of build/scripts-3.5/summarize-reads.py from 644 to 755
2021-06-13T20:45:40,651   changing mode of build/scripts-3.5/translate.py from 644 to 755
2021-06-13T20:45:40,652   changing mode of build/scripts-3.5/trim-primers.py from 644 to 755
2021-06-13T20:45:40,652   changing mode of build/scripts-3.5/trim-reads.py from 644 to 755
2021-06-13T20:45:40,653   changing mode of build/scripts-3.5/write-htcondor-job-spec.py from 644 to 755
2021-06-13T20:45:40,658   installing to build/bdist.linux-armv7l/wheel
2021-06-13T20:45:40,658   running install
2021-06-13T20:45:40,660   running install_lib
2021-06-13T20:45:40,669   creating build/bdist.linux-armv7l
2021-06-13T20:45:40,670   creating build/bdist.linux-armv7l/wheel
2021-06-13T20:45:40,676   creating build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,678   copying build/lib/dark/mutations.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,684   copying build/lib/dark/ncbidb.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,689   copying build/lib/dark/consensus.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,694   copying build/lib/dark/analyze_reads.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,698   copying build/lib/dark/genomes.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,704   copying build/lib/dark/sequence.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,710   copying build/lib/dark/proteins.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,720   copying build/lib/dark/bowtie2.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,727   copying build/lib/dark/distance.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,733   creating build/bdist.linux-armv7l/wheel/dark/diamond
2021-06-13T20:45:40,735   copying build/lib/dark/diamond/sam.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-06-13T20:45:40,742   copying build/lib/dark/diamond/conversion.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-06-13T20:45:40,749   copying build/lib/dark/diamond/__init__.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-06-13T20:45:40,752   copying build/lib/dark/diamond/hsp.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-06-13T20:45:40,758   copying build/lib/dark/diamond/alignments.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-06-13T20:45:40,763   copying build/lib/dark/diamond/run.py -> build/bdist.linux-armv7l/wheel/dark/diamond
2021-06-13T20:45:40,767   copying build/lib/dark/sam.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,775   copying build/lib/dark/features.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,781   copying build/lib/dark/reads.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,793   copying build/lib/dark/__init__.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,798   copying build/lib/dark/aa.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,808   copying build/lib/dark/hsp.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,814   copying build/lib/dark/baseimage.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,818   copying build/lib/dark/graphics.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,827   copying build/lib/dark/simplify.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,833   copying build/lib/dark/genbank.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,840   copying build/lib/dark/fastq.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,845   copying build/lib/dark/alignments.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,852   copying build/lib/dark/fasta_ss.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,857   copying build/lib/dark/fpcache.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,861   copying build/lib/dark/utils.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,867   copying build/lib/dark/filter.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,875   copying build/lib/dark/taxonomy.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,883   copying build/lib/dark/codonDistance.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,889   copying build/lib/dark/score.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,895   copying build/lib/dark/local_align.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,903   copying build/lib/dark/errors.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,908   copying build/lib/dark/dna.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,914   copying build/lib/dark/btop.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,919   copying build/lib/dark/dimension.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,925   creating build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,927   copying build/lib/dark/blast/conversion.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,935   copying build/lib/dark/blast/__init__.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,940   copying build/lib/dark/blast/records.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,945   copying build/lib/dark/blast/hsp.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,951   copying build/lib/dark/blast/params.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,956   copying build/lib/dark/blast/alignments.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,962   copying build/lib/dark/blast/score.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,966   copying build/lib/dark/blast/hacks.py -> build/bdist.linux-armv7l/wheel/dark/blast
2021-06-13T20:45:40,971   copying build/lib/dark/cigar.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:40,979   creating build/bdist.linux-armv7l/wheel/dark/civ
2021-06-13T20:45:40,981   copying build/lib/dark/civ/proteins.py -> build/bdist.linux-armv7l/wheel/dark/civ
2021-06-13T20:45:41,366   copying build/lib/dark/civ/__init__.py -> build/bdist.linux-armv7l/wheel/dark/civ
2021-06-13T20:45:41,373   copying build/lib/dark/civ/graphics.py -> build/bdist.linux-armv7l/wheel/dark/civ
2021-06-13T20:45:41,383   copying build/lib/dark/civ/html.py -> build/bdist.linux-armv7l/wheel/dark/civ
2021-06-13T20:45:41,390   copying build/lib/dark/aligners.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,396   copying build/lib/dark/process.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,403   copying build/lib/dark/intervals.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,410   copying build/lib/dark/entrez.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,414   copying build/lib/dark/orfs.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,419   copying build/lib/dark/colors.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,424   copying build/lib/dark/database.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,428   copying build/lib/dark/html.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,436   copying build/lib/dark/fasta.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,445   copying build/lib/dark/ipynb.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,452   copying build/lib/dark/titles.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,461   copying build/lib/dark/summarize.py -> build/bdist.linux-armv7l/wheel/dark
2021-06-13T20:45:41,466   running install_egg_info
2021-06-13T20:45:41,512   running egg_info
2021-06-13T20:45:41,515   writing top-level names to dark_matter.egg-info/top_level.txt
2021-06-13T20:45:41,518   writing dark_matter.egg-info/PKG-INFO
2021-06-13T20:45:41,523   writing dependency_links to dark_matter.egg-info/dependency_links.txt
2021-06-13T20:45:41,527   writing requirements to dark_matter.egg-info/requires.txt
2021-06-13T20:45:41,584   reading manifest file 'dark_matter.egg-info/SOURCES.txt'
2021-06-13T20:45:41,625   writing manifest file 'dark_matter.egg-info/SOURCES.txt'
2021-06-13T20:45:41,630   Copying dark_matter.egg-info to build/bdist.linux-armv7l/wheel/dark_matter-4.0.1-py3.5.egg-info
2021-06-13T20:45:41,657   running install_scripts
2021-06-13T20:45:41,802   creating build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data
2021-06-13T20:45:41,803   creating build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,806   copying build/scripts-3.5/convert-diamond-to-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,810   copying build/scripts-3.5/graph-evalues.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,815   copying build/scripts-3.5/aa-to-dna.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,819   copying build/scripts-3.5/pre-commit.sh -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,824   copying build/scripts-3.5/filter-fasta-by-taxonomy.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,831   copying build/scripts-3.5/filter-fasta-by-complexity.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,837   copying build/scripts-3.5/randomize-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,843   copying build/scripts-3.5/sam-coverage-depth.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,848   copying build/scripts-3.5/fasta-split-by-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,853   copying build/scripts-3.5/sam-to-fasta-alignment.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,857   copying build/scripts-3.5/fasta-ids.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,861   copying build/scripts-3.5/alignment-panel-civ.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,867   copying build/scripts-3.5/translate.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,871   copying build/scripts-3.5/position-summary.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,876   copying build/scripts-3.5/fasta-lengths.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,880   copying build/scripts-3.5/e-value-to-bit-score.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,884   copying build/scripts-3.5/parse-genbank-flat-file.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,890   copying build/scripts-3.5/fasta-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,895   copying build/scripts-3.5/convert-diamond-to-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:41,903   copying build/scripts-3.5/newick-to-ascii.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
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2021-06-13T20:45:42,258   copying build/scripts-3.5/get-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:42,264   copying build/scripts-3.5/sff-to-fastq.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:42,268   copying build/scripts-3.5/convert-blast-xml-to-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:42,272   copying build/scripts-3.5/fasta-subtraction.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:42,278   copying build/scripts-3.5/check-fasta-json-blast-consistency.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:42,284   copying build/scripts-3.5/describe-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:42,289   copying build/scripts-3.5/fasta-base-indices.py -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:42,296   copying build/scripts-3.5/fasta-diff.sh -> build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts
2021-06-13T20:45:42,300   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/convert-diamond-to-json.py to 755
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2021-06-13T20:45:42,349   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/read-blast-json.py to 755
2021-06-13T20:45:42,350   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/filter-hits-to-fasta.py to 755
2021-06-13T20:45:42,351   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/codon-distance.py to 755
2021-06-13T20:45:42,352   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/aa-to-properties.py to 755
2021-06-13T20:45:42,352   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/dna-to-aa.py to 755
2021-06-13T20:45:42,353   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/bit-score-to-e-value.py to 755
2021-06-13T20:45:42,354   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/fasta-sort.py to 755
2021-06-13T20:45:42,355   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/fasta-subset.py to 755
2021-06-13T20:45:42,355   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/fasta-variable-sites.py to 755
2021-06-13T20:45:42,356   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/sam-references.py to 755
2021-06-13T20:45:42,357   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/fasta-join.py to 755
2021-06-13T20:45:42,358   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/get-taxonomy.py to 755
2021-06-13T20:45:42,358   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/get-reads.py to 755
2021-06-13T20:45:42,359   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/sff-to-fastq.py to 755
2021-06-13T20:45:42,360   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/convert-blast-xml-to-json.py to 755
2021-06-13T20:45:42,361   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/fasta-subtraction.py to 755
2021-06-13T20:45:42,362   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/check-fasta-json-blast-consistency.py to 755
2021-06-13T20:45:42,362   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/describe-protein-database.py to 755
2021-06-13T20:45:42,363   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/fasta-base-indices.py to 755
2021-06-13T20:45:42,364   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.data/scripts/fasta-diff.sh to 755
2021-06-13T20:45:42,460   creating build/bdist.linux-armv7l/wheel/dark_matter-4.0.1.dist-info/WHEEL
2021-06-13T20:45:43,439   Building wheel for dark-matter (setup.py): finished with status 'done'
2021-06-13T20:45:43,449   Created wheel for dark-matter: filename=dark_matter-4.0.1-py3-none-any.whl size=316932 sha256=27c33e73ea85e4692ba8059df142cd74ce73b0d014a2fed5f6b3f7b91c8076f4
2021-06-13T20:45:43,450   Stored in directory: /tmp/pip-ephem-wheel-cache-_w_hnbls/wheels/fb/49/ec/e91cc6a3134baeb7c61c6fc1b772e147074793b612f77c14aa
2021-06-13T20:45:43,482 Successfully built dark-matter
2021-06-13T20:45:43,542 Removed build tracker: '/tmp/pip-req-tracker-ay74c0dy'