2019-07-04T17:55:31 Created temporary directory: /tmp/pip-ephem-wheel-cache-zwjyk7cu
2019-07-04T17:55:31 Created temporary directory: /tmp/pip-req-tracker-_k13kxi7
2019-07-04T17:55:31 Created requirements tracker '/tmp/pip-req-tracker-_k13kxi7'
2019-07-04T17:55:31 Created temporary directory: /tmp/pip-wheel-y9csdmk3
2019-07-04T17:55:31 Collecting bcbio-nextgen==1.1.5
2019-07-04T17:55:31   1 location(s) to search for versions of bcbio-nextgen:
2019-07-04T17:55:31   * https://pypi.org/simple/bcbio-nextgen/
2019-07-04T17:55:31   Getting page https://pypi.org/simple/bcbio-nextgen/
2019-07-04T17:55:31   Analyzing links from page https://pypi.org/simple/bcbio-nextgen/
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/90/b4/bb05fa6c09806f2719dce479ec31a88ad1d221635869b16db8ec83734f7b/bcbio-nextgen-0.1.tar.gz#sha256=4f5ebc031f97f5b1dda0c121cbb0d097f373b4a75867d8eb0a0ffd77c815f270 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.1
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/9e/07/a813761539d957db2b49b65e4f9561a3dfcd5794f0a4f5024567df7cfe77/bcbio-nextgen-0.2.tar.gz#sha256=c45b1801d170fa9ba6839f39757e5bb53a988bf79358fcaba18214395a281d31 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.2
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/0e/49/246923a06b97219180d601b7b57fba2ccf7c2a203ed4fd83d95a90614a39/bcbio-nextgen-0.4a.tar.gz#sha256=a30493df08398c599b390447a722202fac3f8072c8637f7b6b4df4c693650348 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.4a
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/1b/86/07a58792badfcc88f06f80a3ff0271c1fb5ed63967db858993a2bd01a4f2/bcbio-nextgen-0.5a.tar.gz#sha256=5b0cb2e6d39d3cb3cec638ccb17942216a02554215436dbeea82de88bb703d3a (from https://pypi.org/simple/bcbio-nextgen/), version: 0.5a
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/25/1a/53dce1139fb636f098a44e752984b28a0ad3ba29846f82f4a35f912009a8/bcbio-nextgen-0.6.0.tar.gz#sha256=8c42681f2c2e3594fe82b79061852c86a1561a2792557044cf9dcd09215e23b2 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.6.0
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/a4/c0/bac1aa31690cbe10fe0dd61c9c2d3067e24f875af778f8e3b7eb71bba89f/bcbio-nextgen-0.6.1.tar.gz#sha256=735dedad8d2e0b7a9414c376dc48d1956c88a714003768ebff128c840e08590f (from https://pypi.org/simple/bcbio-nextgen/), version: 0.6.1
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/54/a8/294b8b612fbf5daf2b6bb2b0ed16acf05325e14868bd0873c1a638e829c8/bcbio-nextgen-0.6.2.tar.gz#sha256=9d30182f3c4f880f153303e8925cb36ef05b833c09a4ed601a41032084d1ab0e (from https://pypi.org/simple/bcbio-nextgen/), version: 0.6.2
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/42/52/a2c108454f73a4c4f26bdc60e9ae4f0e39dce1a5a028cad9dc9b3342f2dd/bcbio-nextgen-0.6.3.tar.gz#sha256=36126b21bd0c130425e611a294cd64216f9c6f694ce57c219d8c92704a66bdd7 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.6.3
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/cd/a7/23656a7e8496f336a87dbb1b5d0ee02ad97314dff7bb6fc710c571b10d5c/bcbio-nextgen-0.6.4.tar.gz#sha256=c0606791c99d6d9bffa1741256101080ee0f686918ab50f4462aae0c63d4e7f0 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.6.4
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/a1/47/b90385c1a709c47540bd3d89955dc7095112c9475a8ef177bd5cc89c416f/bcbio-nextgen-0.6.5.tar.gz#sha256=3365e65de83649a53f7921612fc88449b0954e47396c906632cac6d7c843bea6 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.6.5
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/a4/16/893513acd5a000c52caeb2a4e1a73bd509ca68fe7ebbd8c2640c20a94e59/bcbio-nextgen-0.7.0.tar.gz#sha256=af49bd520e7d0c20ef2a5a40dd6942864e639189cd137230c07ad523285cfe8c (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.0
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/67/33/0e73cd1eb421de225133e49611df59d74a4323c2e5eb8233dd1ba37c5fb0/bcbio-nextgen-0.7.1.tar.gz#sha256=420f2df81677a85fc04521918dda031378e4a69c741e02caf681a727b4551174 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.1
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/7d/58/141f458d7d87ece7617734b4af5384083c8eca4889f5e5cf58d8b2061d5a/bcbio-nextgen-0.7.2.tar.gz#sha256=ac8f0b98887a54611fe24078dcd8e0ec1823e902b9d84e9c7ffcd4d682dd331b (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.2
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/4e/e2/4b79494eb9009a25d3e4f7177481c673fbb13073b4dbcd49436e14a21c10/bcbio-nextgen-0.7.3.tar.gz#sha256=0b6b29928f2ce94c5d8d351f302771eea1ac677132737bafd68b9e9d9250cef2 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.3
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/e5/bd/f241e01c73ea4a559453e253e2873b762570f6508d341115828740baa072/bcbio-nextgen-0.7.4.tar.gz#sha256=078dbe25415083ca91eadb6bdd8e5af33603a9ec06723bc6f32a11ed9995d2f0 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.4
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/dc/8c/1a3069f894e8e3a96abd1ad8373b8444403ef2a8590af7da2b1297a91dcc/bcbio-nextgen-0.7.5.tar.gz#sha256=f4afd820f9f7e2457171ccb22f55cc28a37e08361695eece61397b23c5d9a74f (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.5
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/3c/00/cd089625b82d0bdbdcd1586943215bf7dc400fa969cfa0cc9d91f31f14a9/bcbio-nextgen-0.7.6.tar.gz#sha256=c0a52c5d957bc180fc5406362fed6f6361683b6f36e38d2b3e16fc10d3c81fcd (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.6
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/a1/d2/9d42dc312944f16f16ee4bc681282d4d5780d3c847a42c569e2f8515084d/bcbio-nextgen-0.7.7.tar.gz#sha256=cda5d73d24ea4a217956c886ceb7dc7bc94493c9b812f2bc76a92a0628b28785 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.7
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/59/8e/7ee38b036eb4a5aca69c87240f37f258935970c6019ec1d6976a55f3c43a/bcbio-nextgen-0.7.8.tar.gz#sha256=c5043ca4e08bd274e99284eefc2a1ea060e3bdfffa461d3322d237226c4c6cf8 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.8
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/4a/43/30a04e4310af185731103fe7cef346c7845beb1815f78c7d6bb06c2008f4/bcbio-nextgen-0.7.9.tar.gz#sha256=ae168a2aaf893b6d8b5e6e1c0c02441ccfd6d262e808278e02883449bc2e15c2 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.7.9
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/39/16/1b482d3ce7c8019170dbb57366d25d4edef5426f7afb9c41681bf1eefdd8/bcbio-nextgen-0.8.0.tar.gz#sha256=93ef5aef7b11891b8c8e422e6dbcdfecdd5c7783fc52af83e57bae128cb97070 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.0
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/0a/ab/5d08edea02995bb2ac541f93f2fde345bda1fd698db51d530e8c6ef799d4/bcbio-nextgen-0.8.1.tar.gz#sha256=64dbec604de5ae7a2c30d33633fd9a6dd49fc843100770b691d0fae00a2a440e (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.1
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/e5/dc/16102e9b8b33dee3da0baa9c8a217afd12c62e3113257f4f12e90f78345e/bcbio-nextgen-0.8.2.tar.gz#sha256=c11a49709eb5111763d20d61fb1c0b1e5eba15b7481dc5483043c70ead9d0f1d (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.2
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/89/37/ec78b367793f642c18e18e9c745f78ba8915f3c439a550f7ee98658e9c5e/bcbio-nextgen-0.8.3.tar.gz#sha256=f76f8d7560535cfcc2ed7d0c71633a1cdc5950d3f987d289f67dc8818c7bc390 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.3
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/0c/53/ccd73a90da3a6f40fc5a4445f680a746a2c312740a6333512bb545492d08/bcbio-nextgen-0.8.4.tar.gz#sha256=f850429420baa60ff4853d6cea44b50d7f2eb0e01e4f1a7c344ea1f264d1f01f (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.4
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/6b/71/e23ecfc068f31073b8e6f6124f373172b4a0ed4ea378b6035d57a66bdf78/bcbio-nextgen-0.8.5.tar.gz#sha256=533f14dc0121bbb8941a80240028712bcdaee4cefef7c0e50b8a4f53dd0b3329 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.5
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/0f/e6/a8cd04ba5d0d7c56948d6d60995ae9d25b518850f07473014c86c75bf35e/bcbio-nextgen-0.8.6.tar.gz#sha256=fa7295765a56bd3d1ed0ae4129340d8879343b9a38a27ff188da679ff47d4ed7 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.6
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/67/0e/07624aac63f5880e054358df38351cd1dbc27ce883e593e84d3ce45b05fb/bcbio-nextgen-0.8.7.tar.gz#sha256=b0e8ff39ba1d1db0fd79e18af34798a27c3278cb3f4042cfa29d680509f7f6cf (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.7
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/76/96/736cf2cd2ce04a683e93cfcbeb6fb506f0c5f778c90973ae1e7dedf3fe04/bcbio-nextgen-0.8.8.tar.gz#sha256=ad1fb039542fb806a832b3fae8ce1fea373647df41a2627eb745d2577f8084f7 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.8
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/d6/a9/1509d203cf16d94ca148df16f58541b02d0da30354c1c634b04858b6b63d/bcbio-nextgen-0.8.9.tar.gz#sha256=ac478806553b0e9364dbac5480404e7b6fa1fb6eaf3384fffbb0368c2de754e5 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.8.9
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/f5/0c/55a4d47997a5b754d4f9072f70a7e3ac9173703c542f433f038ec86cb17c/bcbio-nextgen-0.9.0.tar.gz#sha256=26f33c781b8251c948a7a72ecdcdb1b998c5c9e4f9d8da1443586e6b49fca65e (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.0
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/e5/81/769499ad121b39cd71e65e306eb07d8f3af1dc8f6ff4db513515d54a9bc2/bcbio-nextgen-0.9.1.tar.gz#sha256=662eafe88d5bf847c99b4fd1fc590f6ba78f4d0d895f01ab3e3a25a402fab7b4 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.1
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/31/86/1d2c03d9e72fa7b57d8b937d4adb134c8fee77d14533ce9d8a122f6ade9b/bcbio-nextgen-0.9.2.tar.gz#sha256=6db7c5ecf03190f2b4d52c85daa819c909a471ceb32cb1868f6d88541f7b9e65 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.2
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/d6/64/1433ac732c4aef46f372ca24ca35885d9074a4ac08f9ac6459cab0b079ea/bcbio-nextgen-0.9.3.tar.gz#sha256=d109e2077c83e327573d12f286179cd4adab7a21949435943eac497d61651bf9 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.3
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/d8/bd/96a98ff06cf63ef15e57e5dacda8b3fb82a7cc1ecbe815a661f174233110/bcbio-nextgen-0.9.4a0.tar.gz#sha256=dd7f7daa77f1c3bda4868a9fba8a8248702abac14e8b6bce1891ddf4a62bee8e (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.4a0
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/4b/78/6a058027a7221918918c828d823431d54323886e9463e0f0894fcc8aa0ae/bcbio-nextgen-0.9.4.tar.gz#sha256=924acdb2eaaae25f1af6007942121de7f18fb37edd1da4ff98e50958a12a3224 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.4
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/52/a0/391f6e8a059dfccf575f1f1e83ebf8892c0e58ba20e4dc1bb176a0106559/bcbio-nextgen-0.9.5.tar.gz#sha256=ca9dea2c4393859a91091b481fafca2dbed8075dbef2ad9d20fbaf0ca43f38d5 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.5
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/2c/51/248ee5d81d87a840ed16871a716df0743162800ffdbbde2a220e5aef3b5e/bcbio-nextgen-0.9.6.tar.gz#sha256=9d17ed30a831270723577df6837319d551fa1cf69adfaee620847ea455722e3a (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.6
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/04/ab/ea3503c78061042ccb61cce862f4cd68d2c564e8f296acf2f71f8dbcc6fc/bcbio-nextgen-0.9.7.tar.gz#sha256=8b2960e800550805bf8aca1bed1fdc901efb4b0ed4e258a12fb1aa5273f5540c (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.7
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/2c/ff/da0d27f43a045fbef606b20c311dd6003fa17964964907b88e0cafb38cfd/bcbio-nextgen-0.9.8.tar.gz#sha256=41e152b58f19d4b97e887169b0bc1520c3885ac7bc3b81fe94cf3d8d9187eda1 (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.8
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/4f/90/36f1908ef62b954102604cdfe9d4d7d490131050ae0cd294e27bac5989cc/bcbio-nextgen-0.9.9.tar.gz#sha256=ec96944259e54441af967692ae8f47c2bfacc73725d4a366eab84ee2475f48ca (from https://pypi.org/simple/bcbio-nextgen/), version: 0.9.9
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/8d/5b/80d5b73b534e485cb0254ca8e6460f7236737937a65c1b55d0dbbc9b717b/bcbio-nextgen-1.0.0.tar.gz#sha256=d2dbb5082719b2f83dd840a94ee1e329b7d3894e05a776abe7709623406c5146 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.0
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/77/ba/29c493ef6f10eff436102d19f75989d6cd970cb2e7f915f246fbaa945b14/bcbio-nextgen-1.0.1.tar.gz#sha256=8c26d8383700bf3c82a8bda0602337d59c8762c5554b62406b21af1475550636 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.1
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/3f/c0/f8e46f5cbc3b4f04f94670b157737c2a402f40a2a5cc6168d7f1dee58f9e/bcbio-nextgen-1.0.2.tar.gz#sha256=4aa35d87fb80bef9de2b8fb32dda6bd7e3ca62bb30361f0a9bbf0f4c2269d45f (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.2
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/5d/ee/ff8e669ede6d5c0f628034096224f9b664354ec59ce3f17a40808261f025/bcbio-nextgen-1.0.3.tar.gz#sha256=0c9a7ebfafeb368f45981a8a9422c19a735f8c60bce1aabb048911b6f9d67be2 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.3
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/8a/45/abe92157e562d77214a69e9a144f61dd6048e2f0426eeed6aa35f6b972fc/bcbio-nextgen-1.0.4.tar.gz#sha256=0bb483502e19fbab23a7c03d96c71de6704b5cd1ace47f1158f0bc512fc4a8c8 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.4
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/a5/3c/435e5628fcd2a7dae9d5bb039f58d75d08401ecaad3be503853357c1d55b/bcbio-nextgen-1.0.5.tar.gz#sha256=fa9fd63bbae22e9c1fa4c22135b65c1b3e77ffe652f8fafba6ab1618c5f96698 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.5
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/28/b1/86714ac61cf22aecf3edebccb1a5523b0a199e63eee71c1a28dfd08c43e2/bcbio-nextgen-1.0.6.tar.gz#sha256=e12e51520de19057c0a9e0efc214954ad34543a24ed561ff9adac3249b1de0b6 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.6
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/70/1c/4b34b2955e7f269f62ed7c1a5ab5d5ad93a70adb84bb3d80d7b7a31dd349/bcbio-nextgen-1.0.7.tar.gz#sha256=c7b8e728c74033146a59e1505d2214beb22ddd81b2a022e8798785e33b81223d (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.7
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/a6/e2/da783ca47d89b8826254b0f2b6f71434b8b93aef7519ba16cae269d51dc1/bcbio-nextgen-1.0.8.tar.gz#sha256=52d045bdc12db13fddf3dce0e101160c564672a267716bb26a5dace1c98f394d (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.8
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/98/73/648ef8f161b8a284ff0c0b3f12c7844ddbbbc1f420665821a3b472d742d6/bcbio-nextgen-1.0.9.tar.gz#sha256=a0e047cf4e8e0e3d12d8af7208818e791ec3a2ed3c681a17731802c442b1bdf4 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.0.9
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/3a/6b/6b36aeb84776855b491fc09e3c5fe5a6cfcf1473d6b5ef33d298551b434b/bcbio-nextgen-1.1.0.tar.gz#sha256=12c727aafcfdb8a034a3c2ab34f149c1d84c502a7e4558422fa0b77b46e7f533 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.0
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/5e/fc/7e35d2e7666fefe730fb1a89a88e5764fc3857193d8448518a6220949494/bcbio-nextgen-1.1.1.tar.gz#sha256=756334f29c31d5bbf99014827b0bef8d9d3776dcfba8a7a780e8436adcde2fd5 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.1
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/da/d4/7701b9b14d684bc978da35b1ec744d80d6ac6426ede4f0577b372b005179/bcbio-nextgen-1.1.2.tar.gz#sha256=623e652147865507c1564e41e3c2106a07fc1fd830b0ecf0a389c120f203d5b5 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.2
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/8c/9d/326a4e59e320f85dc0563d8f13f284cf6f9c8a309a790b83c7a4b095eb32/bcbio-nextgen-1.1.3.tar.gz#sha256=df2e944e3a60daf33e382b1d00007d5ac1f794b2f1359c8944ade51ce59dae41 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.3
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/a4/04/e2c390568c9e475e424859f9f646417e682c9d169ed396fed614b65ac549/bcbio-nextgen-1.1.4.tar.gz#sha256=0829f5d6bef9b195187ec2532d2051dffaaca403af7ef36bada15e2060fef4dc (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.4
2019-07-04T17:55:31     Found link https://files.pythonhosted.org/packages/9d/7e/452e1d1051c19c2414f7583c796dc2b165740cf1750f1b6c89226bb8f4c2/bcbio-nextgen-1.1.5.tar.gz#sha256=d02e1585df87a5fad5f4c6544337e49334c0be84690a5c37947c4dcd22d97f08 (from https://pypi.org/simple/bcbio-nextgen/), version: 1.1.5
2019-07-04T17:55:31   Using version 1.1.5 (newest of versions: 1.1.5)
2019-07-04T17:55:31   Created temporary directory: /tmp/pip-unpack-exqem38a
2019-07-04T17:55:32   Downloading https://files.pythonhosted.org/packages/9d/7e/452e1d1051c19c2414f7583c796dc2b165740cf1750f1b6c89226bb8f4c2/bcbio-nextgen-1.1.5.tar.gz (2.4MB)
2019-07-04T17:55:32   Downloading from URL https://files.pythonhosted.org/packages/9d/7e/452e1d1051c19c2414f7583c796dc2b165740cf1750f1b6c89226bb8f4c2/bcbio-nextgen-1.1.5.tar.gz#sha256=d02e1585df87a5fad5f4c6544337e49334c0be84690a5c37947c4dcd22d97f08 (from https://pypi.org/simple/bcbio-nextgen/)
2019-07-04T17:55:35   Added bcbio-nextgen==1.1.5 from https://files.pythonhosted.org/packages/9d/7e/452e1d1051c19c2414f7583c796dc2b165740cf1750f1b6c89226bb8f4c2/bcbio-nextgen-1.1.5.tar.gz#sha256=d02e1585df87a5fad5f4c6544337e49334c0be84690a5c37947c4dcd22d97f08 to build tracker '/tmp/pip-req-tracker-_k13kxi7'
2019-07-04T17:55:35     Running setup.py (path:/tmp/pip-wheel-y9csdmk3/bcbio-nextgen/setup.py) egg_info for package bcbio-nextgen
2019-07-04T17:55:35     Running command python setup.py egg_info
2019-07-04T17:55:37     fatal: Not a git repository (or any of the parent directories): .git
2019-07-04T17:55:37     running egg_info
2019-07-04T17:55:37     creating pip-egg-info/bcbio_nextgen.egg-info
2019-07-04T17:55:37     writing dependency_links to pip-egg-info/bcbio_nextgen.egg-info/dependency_links.txt
2019-07-04T17:55:37     writing pip-egg-info/bcbio_nextgen.egg-info/PKG-INFO
2019-07-04T17:55:37     writing top-level names to pip-egg-info/bcbio_nextgen.egg-info/top_level.txt
2019-07-04T17:55:37     writing manifest file 'pip-egg-info/bcbio_nextgen.egg-info/SOURCES.txt'
2019-07-04T17:55:37     reading manifest file 'pip-egg-info/bcbio_nextgen.egg-info/SOURCES.txt'
2019-07-04T17:55:37     reading manifest template 'MANIFEST.in'
2019-07-04T17:55:37     warning: no files found matching 'config/*.ini'
2019-07-04T17:55:37     writing manifest file 'pip-egg-info/bcbio_nextgen.egg-info/SOURCES.txt'
2019-07-04T17:55:38   Source in /tmp/pip-wheel-y9csdmk3/bcbio-nextgen has version 1.1.5, which satisfies requirement bcbio-nextgen==1.1.5 from https://files.pythonhosted.org/packages/9d/7e/452e1d1051c19c2414f7583c796dc2b165740cf1750f1b6c89226bb8f4c2/bcbio-nextgen-1.1.5.tar.gz#sha256=d02e1585df87a5fad5f4c6544337e49334c0be84690a5c37947c4dcd22d97f08
2019-07-04T17:55:38   Removed bcbio-nextgen==1.1.5 from https://files.pythonhosted.org/packages/9d/7e/452e1d1051c19c2414f7583c796dc2b165740cf1750f1b6c89226bb8f4c2/bcbio-nextgen-1.1.5.tar.gz#sha256=d02e1585df87a5fad5f4c6544337e49334c0be84690a5c37947c4dcd22d97f08 from build tracker '/tmp/pip-req-tracker-_k13kxi7'
2019-07-04T17:55:38 Building wheels for collected packages: bcbio-nextgen
2019-07-04T17:55:38   Created temporary directory: /tmp/pip-wheel-36i5y0kh
2019-07-04T17:55:38   Building wheel for bcbio-nextgen (setup.py): started
2019-07-04T17:55:38   Destination directory: /tmp/pip-wheel-36i5y0kh
2019-07-04T17:55:38   Running command /usr/bin/python3 -u -c 'import setuptools, tokenize;__file__='"'"'/tmp/pip-wheel-y9csdmk3/bcbio-nextgen/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-36i5y0kh
2019-07-04T17:55:39   fatal: Not a git repository (or any of the parent directories): .git
2019-07-04T17:55:40   running bdist_wheel
2019-07-04T17:55:40   running build
2019-07-04T17:55:40   running build_py
2019-07-04T17:55:40   creating build
2019-07-04T17:55:40   creating build/lib
2019-07-04T17:55:40   creating build/lib/bcbio
2019-07-04T17:55:40   copying bcbio/setpath.py -> build/lib/bcbio
2019-07-04T17:55:40   copying bcbio/install.py -> build/lib/bcbio
2019-07-04T17:55:40   copying bcbio/__init__.py -> build/lib/bcbio
2019-07-04T17:55:40   copying bcbio/utils.py -> build/lib/bcbio
2019-07-04T17:55:40   creating build/lib/tests
2019-07-04T17:55:40   creating build/lib/tests/unit
2019-07-04T17:55:40   copying tests/unit/conftest.py -> build/lib/tests/unit
2019-07-04T17:55:40   copying tests/unit/test_alignprep.py -> build/lib/tests/unit
2019-07-04T17:55:40   copying tests/unit/data.py -> build/lib/tests/unit
2019-07-04T17:55:40   copying tests/unit/__init__.py -> build/lib/tests/unit
2019-07-04T17:55:40   creating build/lib/tests/integration
2019-07-04T17:55:40   copying tests/integration/__init__.py -> build/lib/tests/integration
2019-07-04T17:55:40   copying tests/integration/test_SequencingDump.py -> build/lib/tests/integration
2019-07-04T17:55:40   copying tests/integration/test_automated_analysis.py -> build/lib/tests/integration
2019-07-04T17:55:40   copying tests/integration/test_pipeline.py -> build/lib/tests/integration
2019-07-04T17:55:40   copying tests/integration/test_S3_pipelines.py -> build/lib/tests/integration
2019-07-04T17:55:40   creating build/lib/tests/unit/upload
2019-07-04T17:55:40   copying tests/unit/upload/test_upload.py -> build/lib/tests/unit/upload
2019-07-04T17:55:40   copying tests/unit/upload/__init__.py -> build/lib/tests/unit/upload
2019-07-04T17:55:40   creating build/lib/tests/unit/distributed
2019-07-04T17:55:40   copying tests/unit/distributed/__init__.py -> build/lib/tests/unit/distributed
2019-07-04T17:55:40   copying tests/unit/distributed/test_transaction.py -> build/lib/tests/unit/distributed
2019-07-04T17:55:40   creating build/lib/tests/unit/rnaseq
2019-07-04T17:55:40   copying tests/unit/rnaseq/__init__.py -> build/lib/tests/unit/rnaseq
2019-07-04T17:55:40   copying tests/unit/rnaseq/test_ericscript.py -> build/lib/tests/unit/rnaseq
2019-07-04T17:55:40   creating build/lib/tests/unit/ngsalign
2019-07-04T17:55:40   copying tests/unit/ngsalign/__init__.py -> build/lib/tests/unit/ngsalign
2019-07-04T17:55:40   creating build/lib/tests/unit/pipeline
2019-07-04T17:55:40   copying tests/unit/pipeline/__init__.py -> build/lib/tests/unit/pipeline
2019-07-04T17:55:40   copying tests/unit/pipeline/test_rnaseq.py -> build/lib/tests/unit/pipeline
2019-07-04T17:55:40   copying tests/unit/pipeline/test_datadict.py -> build/lib/tests/unit/pipeline
2019-07-04T17:55:40   creating build/lib/tests/integration/rnaseq
2019-07-04T17:55:40   copying tests/integration/rnaseq/__init__.py -> build/lib/tests/integration/rnaseq
2019-07-04T17:55:40   copying tests/integration/rnaseq/test_ericscript.py -> build/lib/tests/integration/rnaseq
2019-07-04T17:55:40   creating build/lib/bcbio/upload
2019-07-04T17:55:40   copying bcbio/upload/shared.py -> build/lib/bcbio/upload
2019-07-04T17:55:40   copying bcbio/upload/s3.py -> build/lib/bcbio/upload
2019-07-04T17:55:40   copying bcbio/upload/irods.py -> build/lib/bcbio/upload
2019-07-04T17:55:40   copying bcbio/upload/__init__.py -> build/lib/bcbio/upload
2019-07-04T17:55:40   copying bcbio/upload/filesystem.py -> build/lib/bcbio/upload
2019-07-04T17:55:40   copying bcbio/upload/galaxy.py -> build/lib/bcbio/upload
2019-07-04T17:55:40   creating build/lib/bcbio/heterogeneity
2019-07-04T17:55:40   copying bcbio/heterogeneity/phylowgs.py -> build/lib/bcbio/heterogeneity
2019-07-04T17:55:40   copying bcbio/heterogeneity/chromhacks.py -> build/lib/bcbio/heterogeneity
2019-07-04T17:55:40   copying bcbio/heterogeneity/theta.py -> build/lib/bcbio/heterogeneity
2019-07-04T17:55:40   copying bcbio/heterogeneity/__init__.py -> build/lib/bcbio/heterogeneity
2019-07-04T17:55:40   copying bcbio/heterogeneity/loh.py -> build/lib/bcbio/heterogeneity
2019-07-04T17:55:40   copying bcbio/heterogeneity/bubbletree.py -> build/lib/bcbio/heterogeneity
2019-07-04T17:55:40   creating build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/clusterk.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/multitasks.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/clargs.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/objectstore.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/resources.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/runfn.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/ipythontasks.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/prun.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/split.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/multi.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/__init__.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/transaction.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   copying bcbio/distributed/ipython.py -> build/lib/bcbio/distributed
2019-07-04T17:55:40   creating build/lib/bcbio/graph
2019-07-04T17:55:40   copying bcbio/graph/graph.py -> build/lib/bcbio/graph
2019-07-04T17:55:40   copying bcbio/graph/__init__.py -> build/lib/bcbio/graph
2019-07-04T17:55:40   copying bcbio/graph/collectl.py -> build/lib/bcbio/graph
2019-07-04T17:55:40   creating build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/cpat.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/count.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/featureCounts.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/dexseq.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/express.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/rsem.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/qc.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/ericscript.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/singlecellexperiment.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/kallisto.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/stringtie.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/bcbiornaseq.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/rapmap.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/oncofuse.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/gtf.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/__init__.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/variation.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/cufflinks.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/pizzly.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/spikein.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/salmon.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/annotate_gtf.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/sailfish.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   copying bcbio/rnaseq/umi.py -> build/lib/bcbio/rnaseq
2019-07-04T17:55:40   creating build/lib/bcbio/hla
2019-07-04T17:55:40   copying bcbio/hla/optitype.py -> build/lib/bcbio/hla
2019-07-04T17:55:40   copying bcbio/hla/bwakit.py -> build/lib/bcbio/hla
2019-07-04T17:55:40   copying bcbio/hla/__init__.py -> build/lib/bcbio/hla
2019-07-04T17:55:40   copying bcbio/hla/groups.py -> build/lib/bcbio/hla
2019-07-04T17:55:41   creating build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/cwlutils.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/workflow.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/inspect.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/create.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/tool.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/defs.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/__init__.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/main.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   copying bcbio/cwl/hpc.py -> build/lib/bcbio/cwl
2019-07-04T17:55:41   creating build/lib/bcbio/bed
2019-07-04T17:55:41   copying bcbio/bed/__init__.py -> build/lib/bcbio/bed
2019-07-04T17:55:41   creating build/lib/bcbio/workflow
2019-07-04T17:55:41   copying bcbio/workflow/stormseq.py -> build/lib/bcbio/workflow
2019-07-04T17:55:41   copying bcbio/workflow/template.py -> build/lib/bcbio/workflow
2019-07-04T17:55:41   copying bcbio/workflow/__init__.py -> build/lib/bcbio/workflow
2019-07-04T17:55:41   copying bcbio/workflow/xprize.py -> build/lib/bcbio/workflow
2019-07-04T17:55:41   creating build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/ref.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/counts.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/trim.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/coverage.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/fastq.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/__init__.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/readstats.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/callable.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/skewer.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/cram.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   copying bcbio/bam/fasta.py -> build/lib/bcbio/bam
2019-07-04T17:55:41   creating build/lib/bcbio/srna
2019-07-04T17:55:41   copying bcbio/srna/group.py -> build/lib/bcbio/srna
2019-07-04T17:55:41   copying bcbio/srna/sample.py -> build/lib/bcbio/srna
2019-07-04T17:55:41   copying bcbio/srna/mirge.py -> build/lib/bcbio/srna
2019-07-04T17:55:41   copying bcbio/srna/mirdeep.py -> build/lib/bcbio/srna
2019-07-04T17:55:41   copying bcbio/srna/qc.py -> build/lib/bcbio/srna
2019-07-04T17:55:41   copying bcbio/srna/__init__.py -> build/lib/bcbio/srna
2019-07-04T17:55:41   copying bcbio/srna/umis.py -> build/lib/bcbio/srna
2019-07-04T17:55:41   creating build/lib/bcbio/hmmer
2019-07-04T17:55:41   copying bcbio/hmmer/__init__.py -> build/lib/bcbio/hmmer
2019-07-04T17:55:41   copying bcbio/hmmer/search.py -> build/lib/bcbio/hmmer
2019-07-04T17:55:41   creating build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/mosaik.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/bbmap.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/novoalign.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/bwa.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/bowtie.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/star.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/postalign.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/minimap2.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/tophat.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/alignprep.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/__init__.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/bowtie2.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/rtg.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/snap.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   copying bcbio/ngsalign/hisat2.py -> build/lib/bcbio/ngsalign
2019-07-04T17:55:41   creating build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/variant.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/picard.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/qualimap.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/chipseq.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/kraken.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/srna.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/coverage.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/samtools.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/multiqc.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/preseq.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/atropos.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/contamination.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/qsignature.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/__init__.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/viral.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/umi.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/fastqc.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   copying bcbio/qc/damage.py -> build/lib/bcbio/qc
2019-07-04T17:55:41   creating build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/delly.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/pindel.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/plot.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/gatkcnv.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/validate.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/shared.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/gridss.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/annotate.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/manta.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/purple.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/purecn.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/prioritize.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/wham.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/__init__.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/hydra.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/seq2c.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/cn_mops.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/lumpy.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/battenberg.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/titancna.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/metasv.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/cnvkit.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/regions.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   copying bcbio/structural/convert.py -> build/lib/bcbio/structural
2019-07-04T17:55:41   creating build/lib/bcbio/log
2019-07-04T17:55:41   copying bcbio/log/__init__.py -> build/lib/bcbio/log
2019-07-04T17:55:41   copying bcbio/log/logbook_zmqpush.py -> build/lib/bcbio/log
2019-07-04T17:55:41   creating build/lib/bcbio/illumina
2019-07-04T17:55:41   copying bcbio/illumina/demultiplex.py -> build/lib/bcbio/illumina
2019-07-04T17:55:41   copying bcbio/illumina/samplesheet.py -> build/lib/bcbio/illumina
2019-07-04T17:55:41   copying bcbio/illumina/flowcell.py -> build/lib/bcbio/illumina
2019-07-04T17:55:41   copying bcbio/illumina/__init__.py -> build/lib/bcbio/illumina
2019-07-04T17:55:41   copying bcbio/illumina/machine.py -> build/lib/bcbio/illumina
2019-07-04T17:55:41   copying bcbio/illumina/transfer.py -> build/lib/bcbio/illumina
2019-07-04T17:55:41   creating build/lib/bcbio/provenance
2019-07-04T17:55:41   copying bcbio/provenance/profile.py -> build/lib/bcbio/provenance
2019-07-04T17:55:41   copying bcbio/provenance/data.py -> build/lib/bcbio/provenance
2019-07-04T17:55:41   copying bcbio/provenance/system.py -> build/lib/bcbio/provenance
2019-07-04T17:55:41   copying bcbio/provenance/versioncheck.py -> build/lib/bcbio/provenance
2019-07-04T17:55:41   copying bcbio/provenance/__init__.py -> build/lib/bcbio/provenance
2019-07-04T17:55:41   copying bcbio/provenance/programs.py -> build/lib/bcbio/provenance
2019-07-04T17:55:41   copying bcbio/provenance/diagnostics.py -> build/lib/bcbio/provenance
2019-07-04T17:55:41   copying bcbio/provenance/do.py -> build/lib/bcbio/provenance
2019-07-04T17:55:41   creating build/lib/bcbio/server
2019-07-04T17:55:41   copying bcbio/server/__init__.py -> build/lib/bcbio/server
2019-07-04T17:55:41   copying bcbio/server/main.py -> build/lib/bcbio/server
2019-07-04T17:55:41   copying bcbio/server/run.py -> build/lib/bcbio/server
2019-07-04T17:55:41   copying bcbio/server/background.py -> build/lib/bcbio/server
2019-07-04T17:55:41   creating build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/run_info.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/sample.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/qcsummary.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/merge.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/cleanbam.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/shared.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/region.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/fastq.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/alignment.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/archive.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/rnaseq.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/genome.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/__init__.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/tools.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/main.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/variation.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/sra.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/version.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/datadict.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   copying bcbio/pipeline/config_utils.py -> build/lib/bcbio/pipeline
2019-07-04T17:55:41   creating build/lib/bcbio/picard
2019-07-04T17:55:41   copying bcbio/picard/metrics.py -> build/lib/bcbio/picard
2019-07-04T17:55:41   copying bcbio/picard/__init__.py -> build/lib/bcbio/picard
2019-07-04T17:55:41   copying bcbio/picard/utils.py -> build/lib/bcbio/picard
2019-07-04T17:55:41   creating build/lib/bcbio/variation
2019-07-04T17:55:41   copying bcbio/variation/validateplot.py -> build/lib/bcbio/variation
2019-07-04T17:55:41   copying bcbio/variation/ploidy.py -> build/lib/bcbio/variation
2019-07-04T17:55:41   copying bcbio/variation/freebayes.py -> build/lib/bcbio/variation
2019-07-04T17:55:41   copying bcbio/variation/bamprep.py -> build/lib/bcbio/variation
2019-07-04T17:55:41   copying bcbio/variation/population.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/validate.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/sentieon.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/bedutils.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/annotation.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/gatk.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/coverage.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/naming.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/split.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/vardict.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/samtools.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/varscan.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/cortex.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/deepvariant.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/multi.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/mutect.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/ensemble.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/vfilter.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/prioritize.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/mutect2.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/__init__.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/recalibrate.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/platypus.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/gatkjoint.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/joint.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/vcfanno.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/smcounter2.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/strelka2.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/germline.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/scalpel.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/pisces.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/realign.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/gatkfilter.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/effects.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/octopus.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/genotype.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/peddy.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/qsnp.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/normalize.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/damage.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   copying bcbio/variation/vcfutils.py -> build/lib/bcbio/variation
2019-07-04T17:55:42   creating build/lib/bcbio/broad
2019-07-04T17:55:42   copying bcbio/broad/metrics.py -> build/lib/bcbio/broad
2019-07-04T17:55:42   copying bcbio/broad/picardrun.py -> build/lib/bcbio/broad
2019-07-04T17:55:42   copying bcbio/broad/__init__.py -> build/lib/bcbio/broad
2019-07-04T17:55:42   creating build/lib/bcbio/chipseq
2019-07-04T17:55:42   copying bcbio/chipseq/macs2.py -> build/lib/bcbio/chipseq
2019-07-04T17:55:42   copying bcbio/chipseq/peaks.py -> build/lib/bcbio/chipseq
2019-07-04T17:55:42   copying bcbio/chipseq/__init__.py -> build/lib/bcbio/chipseq
2019-07-04T17:55:42   creating build/lib/bcbio/galaxy
2019-07-04T17:55:42   copying bcbio/galaxy/nglims.py -> build/lib/bcbio/galaxy
2019-07-04T17:55:42   copying bcbio/galaxy/api.py -> build/lib/bcbio/galaxy
2019-07-04T17:55:42   copying bcbio/galaxy/loc.py -> build/lib/bcbio/galaxy
2019-07-04T17:55:42   copying bcbio/galaxy/__init__.py -> build/lib/bcbio/galaxy
2019-07-04T17:55:42   creating build/lib/bcbio/pipeline/disambiguate
2019-07-04T17:55:42   copying bcbio/pipeline/disambiguate/__init__.py -> build/lib/bcbio/pipeline/disambiguate
2019-07-04T17:55:42   copying bcbio/pipeline/disambiguate/run.py -> build/lib/bcbio/pipeline/disambiguate
2019-07-04T17:55:42   running egg_info
2019-07-04T17:55:42   writing top-level names to bcbio_nextgen.egg-info/top_level.txt
2019-07-04T17:55:42   writing bcbio_nextgen.egg-info/PKG-INFO
2019-07-04T17:55:42   writing dependency_links to bcbio_nextgen.egg-info/dependency_links.txt
2019-07-04T17:55:42   reading manifest file 'bcbio_nextgen.egg-info/SOURCES.txt'
2019-07-04T17:55:42   reading manifest template 'MANIFEST.in'
2019-07-04T17:55:42   warning: no files found matching 'config/*.ini'
2019-07-04T17:55:42   writing manifest file 'bcbio_nextgen.egg-info/SOURCES.txt'
2019-07-04T17:55:42   creating build/lib/bcbio/data
2019-07-04T17:55:42   creating build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/10x_v2-cb1.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/10x_v2-transform.json -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/dropseq-transform.json -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-indrop-v2-cb1.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-indrop-v2-cb2.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-indrop-v2-transform.json -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-indrop-v3-cb1.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-indrop-v3-cb2.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-indrop-v3-sample_barcodes.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-indrop-v3-transform.json -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-scrb-cb1.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/harvard-scrb-transform.json -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/icell8-cb1.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/icell8-transform.json -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/qiagen_smallRNA_umi-transform.json -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/surecell-cb1.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/surecell-cb2.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/surecell-cb3.txt.gz -> build/lib/bcbio/data/umis
2019-07-04T17:55:42   copying bcbio/data/umis/surecell-transform.json -> build/lib/bcbio/data/umis
2019-07-04T17:55:43   running build_scripts
2019-07-04T17:55:43   creating build/scripts-3.5
2019-07-04T17:55:43   copying and adjusting scripts/bcbio_nextgen.py -> build/scripts-3.5
2019-07-04T17:55:43   copying and adjusting scripts/bcbio_setup_genome.py -> build/scripts-3.5
2019-07-04T17:55:43   copying and adjusting scripts/bcbio_prepare_samples.py -> build/scripts-3.5
2019-07-04T17:55:43   copying and adjusting scripts/bcbio_fastq_umi_prep.py -> build/scripts-3.5
2019-07-04T17:55:43   copying and adjusting scripts/cwltool2wdl.py -> build/scripts-3.5
2019-07-04T17:55:43   changing mode of build/scripts-3.5/bcbio_nextgen.py from 644 to 755
2019-07-04T17:55:43   changing mode of build/scripts-3.5/bcbio_setup_genome.py from 644 to 755
2019-07-04T17:55:43   changing mode of build/scripts-3.5/bcbio_prepare_samples.py from 644 to 755
2019-07-04T17:55:43   changing mode of build/scripts-3.5/bcbio_fastq_umi_prep.py from 644 to 755
2019-07-04T17:55:43   changing mode of build/scripts-3.5/cwltool2wdl.py from 644 to 755
2019-07-04T17:55:43   installing to build/bdist.linux-armv7l/wheel
2019-07-04T17:55:43   running install
2019-07-04T17:55:43   running install_lib
2019-07-04T17:55:43   creating build/bdist.linux-armv7l
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests/unit
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests/unit/upload
2019-07-04T17:55:43   copying build/lib/tests/unit/upload/test_upload.py -> build/bdist.linux-armv7l/wheel/tests/unit/upload
2019-07-04T17:55:43   copying build/lib/tests/unit/upload/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/upload
2019-07-04T17:55:43   copying build/lib/tests/unit/conftest.py -> build/bdist.linux-armv7l/wheel/tests/unit
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests/unit/distributed
2019-07-04T17:55:43   copying build/lib/tests/unit/distributed/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/distributed
2019-07-04T17:55:43   copying build/lib/tests/unit/distributed/test_transaction.py -> build/bdist.linux-armv7l/wheel/tests/unit/distributed
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests/unit/rnaseq
2019-07-04T17:55:43   copying build/lib/tests/unit/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/rnaseq
2019-07-04T17:55:43   copying build/lib/tests/unit/rnaseq/test_ericscript.py -> build/bdist.linux-armv7l/wheel/tests/unit/rnaseq
2019-07-04T17:55:43   copying build/lib/tests/unit/test_alignprep.py -> build/bdist.linux-armv7l/wheel/tests/unit
2019-07-04T17:55:43   copying build/lib/tests/unit/data.py -> build/bdist.linux-armv7l/wheel/tests/unit
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests/unit/ngsalign
2019-07-04T17:55:43   copying build/lib/tests/unit/ngsalign/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/ngsalign
2019-07-04T17:55:43   copying build/lib/tests/unit/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests/unit/pipeline
2019-07-04T17:55:43   copying build/lib/tests/unit/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/tests/unit/pipeline
2019-07-04T17:55:43   copying build/lib/tests/unit/pipeline/test_rnaseq.py -> build/bdist.linux-armv7l/wheel/tests/unit/pipeline
2019-07-04T17:55:43   copying build/lib/tests/unit/pipeline/test_datadict.py -> build/bdist.linux-armv7l/wheel/tests/unit/pipeline
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests/integration
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/tests/integration/rnaseq
2019-07-04T17:55:43   copying build/lib/tests/integration/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/tests/integration/rnaseq
2019-07-04T17:55:43   copying build/lib/tests/integration/rnaseq/test_ericscript.py -> build/bdist.linux-armv7l/wheel/tests/integration/rnaseq
2019-07-04T17:55:43   copying build/lib/tests/integration/__init__.py -> build/bdist.linux-armv7l/wheel/tests/integration
2019-07-04T17:55:43   copying build/lib/tests/integration/test_SequencingDump.py -> build/bdist.linux-armv7l/wheel/tests/integration
2019-07-04T17:55:43   copying build/lib/tests/integration/test_automated_analysis.py -> build/bdist.linux-armv7l/wheel/tests/integration
2019-07-04T17:55:43   copying build/lib/tests/integration/test_pipeline.py -> build/bdist.linux-armv7l/wheel/tests/integration
2019-07-04T17:55:43   copying build/lib/tests/integration/test_S3_pipelines.py -> build/bdist.linux-armv7l/wheel/tests/integration
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio
2019-07-04T17:55:43   copying build/lib/bcbio/setpath.py -> build/bdist.linux-armv7l/wheel/bcbio
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/upload
2019-07-04T17:55:43   copying build/lib/bcbio/upload/shared.py -> build/bdist.linux-armv7l/wheel/bcbio/upload
2019-07-04T17:55:43   copying build/lib/bcbio/upload/s3.py -> build/bdist.linux-armv7l/wheel/bcbio/upload
2019-07-04T17:55:43   copying build/lib/bcbio/upload/irods.py -> build/bdist.linux-armv7l/wheel/bcbio/upload
2019-07-04T17:55:43   copying build/lib/bcbio/upload/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/upload
2019-07-04T17:55:43   copying build/lib/bcbio/upload/filesystem.py -> build/bdist.linux-armv7l/wheel/bcbio/upload
2019-07-04T17:55:43   copying build/lib/bcbio/upload/galaxy.py -> build/bdist.linux-armv7l/wheel/bcbio/upload
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/data
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-indrop-v3-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-indrop-v2-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-scrb-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-indrop-v3-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/10x_v2-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/surecell-cb2.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-indrop-v3-sample_barcodes.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/icell8-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-scrb-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-indrop-v2-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/icell8-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/surecell-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/surecell-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-indrop-v3-cb2.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/dropseq-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/harvard-indrop-v2-cb2.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/qiagen_smallRNA_umi-transform.json -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/10x_v2-cb1.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   copying build/lib/bcbio/data/umis/surecell-cb3.txt.gz -> build/bdist.linux-armv7l/wheel/bcbio/data/umis
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/heterogeneity
2019-07-04T17:55:43   copying build/lib/bcbio/heterogeneity/phylowgs.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity
2019-07-04T17:55:43   copying build/lib/bcbio/heterogeneity/chromhacks.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity
2019-07-04T17:55:43   copying build/lib/bcbio/heterogeneity/theta.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity
2019-07-04T17:55:43   copying build/lib/bcbio/heterogeneity/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity
2019-07-04T17:55:43   copying build/lib/bcbio/heterogeneity/loh.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity
2019-07-04T17:55:43   copying build/lib/bcbio/heterogeneity/bubbletree.py -> build/bdist.linux-armv7l/wheel/bcbio/heterogeneity
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/clusterk.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/multitasks.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/clargs.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/objectstore.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/resources.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/runfn.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/ipythontasks.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/prun.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/split.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/multi.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/transaction.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   copying build/lib/bcbio/distributed/ipython.py -> build/bdist.linux-armv7l/wheel/bcbio/distributed
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/graph
2019-07-04T17:55:43   copying build/lib/bcbio/graph/graph.py -> build/bdist.linux-armv7l/wheel/bcbio/graph
2019-07-04T17:55:43   copying build/lib/bcbio/graph/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/graph
2019-07-04T17:55:43   copying build/lib/bcbio/graph/collectl.py -> build/bdist.linux-armv7l/wheel/bcbio/graph
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/cpat.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/count.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/featureCounts.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/dexseq.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/express.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/rsem.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/qc.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/ericscript.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/singlecellexperiment.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/kallisto.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/stringtie.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/bcbiornaseq.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/rapmap.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/oncofuse.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/gtf.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/variation.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/cufflinks.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/pizzly.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/spikein.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/salmon.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/annotate_gtf.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/sailfish.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   copying build/lib/bcbio/rnaseq/umi.py -> build/bdist.linux-armv7l/wheel/bcbio/rnaseq
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/hla
2019-07-04T17:55:43   copying build/lib/bcbio/hla/optitype.py -> build/bdist.linux-armv7l/wheel/bcbio/hla
2019-07-04T17:55:43   copying build/lib/bcbio/hla/bwakit.py -> build/bdist.linux-armv7l/wheel/bcbio/hla
2019-07-04T17:55:43   copying build/lib/bcbio/hla/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/hla
2019-07-04T17:55:43   copying build/lib/bcbio/hla/groups.py -> build/bdist.linux-armv7l/wheel/bcbio/hla
2019-07-04T17:55:43   creating build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:43   copying build/lib/bcbio/cwl/cwlutils.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/cwl/workflow.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/cwl/inspect.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/cwl/create.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/cwl/tool.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/cwl/defs.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/cwl/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/cwl/main.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/cwl/hpc.py -> build/bdist.linux-armv7l/wheel/bcbio/cwl
2019-07-04T17:55:44   copying build/lib/bcbio/install.py -> build/bdist.linux-armv7l/wheel/bcbio
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/bed
2019-07-04T17:55:44   copying build/lib/bcbio/bed/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/bed
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/workflow
2019-07-04T17:55:44   copying build/lib/bcbio/workflow/stormseq.py -> build/bdist.linux-armv7l/wheel/bcbio/workflow
2019-07-04T17:55:44   copying build/lib/bcbio/workflow/template.py -> build/bdist.linux-armv7l/wheel/bcbio/workflow
2019-07-04T17:55:44   copying build/lib/bcbio/workflow/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/workflow
2019-07-04T17:55:44   copying build/lib/bcbio/workflow/xprize.py -> build/bdist.linux-armv7l/wheel/bcbio/workflow
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/ref.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/counts.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/trim.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/coverage.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/fastq.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/readstats.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/callable.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/skewer.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/cram.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   copying build/lib/bcbio/bam/fasta.py -> build/bdist.linux-armv7l/wheel/bcbio/bam
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/srna
2019-07-04T17:55:44   copying build/lib/bcbio/srna/group.py -> build/bdist.linux-armv7l/wheel/bcbio/srna
2019-07-04T17:55:44   copying build/lib/bcbio/srna/sample.py -> build/bdist.linux-armv7l/wheel/bcbio/srna
2019-07-04T17:55:44   copying build/lib/bcbio/srna/mirge.py -> build/bdist.linux-armv7l/wheel/bcbio/srna
2019-07-04T17:55:44   copying build/lib/bcbio/srna/mirdeep.py -> build/bdist.linux-armv7l/wheel/bcbio/srna
2019-07-04T17:55:44   copying build/lib/bcbio/srna/qc.py -> build/bdist.linux-armv7l/wheel/bcbio/srna
2019-07-04T17:55:44   copying build/lib/bcbio/srna/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/srna
2019-07-04T17:55:44   copying build/lib/bcbio/srna/umis.py -> build/bdist.linux-armv7l/wheel/bcbio/srna
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/hmmer
2019-07-04T17:55:44   copying build/lib/bcbio/hmmer/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/hmmer
2019-07-04T17:55:44   copying build/lib/bcbio/hmmer/search.py -> build/bdist.linux-armv7l/wheel/bcbio/hmmer
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/mosaik.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/bbmap.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/novoalign.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/bwa.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/bowtie.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/star.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/postalign.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/minimap2.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/tophat.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/alignprep.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/bowtie2.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/rtg.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/snap.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   copying build/lib/bcbio/ngsalign/hisat2.py -> build/bdist.linux-armv7l/wheel/bcbio/ngsalign
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/variant.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/picard.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/qualimap.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/chipseq.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/kraken.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/srna.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/coverage.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/samtools.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/multiqc.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/preseq.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/atropos.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/contamination.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/qsignature.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/viral.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/umi.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/fastqc.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   copying build/lib/bcbio/qc/damage.py -> build/bdist.linux-armv7l/wheel/bcbio/qc
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/delly.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/pindel.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/plot.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/gatkcnv.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/validate.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/shared.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/gridss.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/annotate.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/manta.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/purple.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/purecn.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/prioritize.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/wham.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/hydra.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/seq2c.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/cn_mops.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/lumpy.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/battenberg.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/titancna.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/metasv.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/cnvkit.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/regions.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   copying build/lib/bcbio/structural/convert.py -> build/bdist.linux-armv7l/wheel/bcbio/structural
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/log
2019-07-04T17:55:44   copying build/lib/bcbio/log/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/log
2019-07-04T17:55:44   copying build/lib/bcbio/log/logbook_zmqpush.py -> build/bdist.linux-armv7l/wheel/bcbio/log
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/illumina
2019-07-04T17:55:44   copying build/lib/bcbio/illumina/demultiplex.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina
2019-07-04T17:55:44   copying build/lib/bcbio/illumina/samplesheet.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina
2019-07-04T17:55:44   copying build/lib/bcbio/illumina/flowcell.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina
2019-07-04T17:55:44   copying build/lib/bcbio/illumina/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina
2019-07-04T17:55:44   copying build/lib/bcbio/illumina/machine.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina
2019-07-04T17:55:44   copying build/lib/bcbio/illumina/transfer.py -> build/bdist.linux-armv7l/wheel/bcbio/illumina
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   copying build/lib/bcbio/provenance/profile.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   copying build/lib/bcbio/provenance/data.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   copying build/lib/bcbio/provenance/system.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   copying build/lib/bcbio/provenance/versioncheck.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   copying build/lib/bcbio/provenance/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   copying build/lib/bcbio/provenance/programs.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   copying build/lib/bcbio/provenance/diagnostics.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   copying build/lib/bcbio/provenance/do.py -> build/bdist.linux-armv7l/wheel/bcbio/provenance
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/server
2019-07-04T17:55:44   copying build/lib/bcbio/server/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/server
2019-07-04T17:55:44   copying build/lib/bcbio/server/main.py -> build/bdist.linux-armv7l/wheel/bcbio/server
2019-07-04T17:55:44   copying build/lib/bcbio/server/run.py -> build/bdist.linux-armv7l/wheel/bcbio/server
2019-07-04T17:55:44   copying build/lib/bcbio/server/background.py -> build/bdist.linux-armv7l/wheel/bcbio/server
2019-07-04T17:55:44   copying build/lib/bcbio/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/run_info.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/sample.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/qcsummary.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/merge.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/cleanbam.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/shared.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/region.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/fastq.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/alignment.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/archive.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/rnaseq.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/genome.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/tools.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/main.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/variation.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/pipeline/disambiguate
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/disambiguate/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline/disambiguate
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/disambiguate/run.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline/disambiguate
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/sra.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/version.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/datadict.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   copying build/lib/bcbio/pipeline/config_utils.py -> build/bdist.linux-armv7l/wheel/bcbio/pipeline
2019-07-04T17:55:44   creating build/bdist.linux-armv7l/wheel/bcbio/picard
2019-07-04T17:55:44   copying build/lib/bcbio/picard/metrics.py -> build/bdist.linux-armv7l/wheel/bcbio/picard
2019-07-04T17:55:44   copying build/lib/bcbio/picard/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/picard
2019-07-04T17:55:44   copying build/lib/bcbio/picard/utils.py -> build/bdist.linux-armv7l/wheel/bcbio/picard
2019-07-04T17:55:45   creating build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/validateplot.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/ploidy.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/freebayes.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/bamprep.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/population.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/validate.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/sentieon.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/bedutils.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/annotation.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/gatk.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/coverage.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/naming.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/split.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/vardict.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/samtools.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/varscan.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/cortex.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/deepvariant.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/multi.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/mutect.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/ensemble.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/vfilter.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/prioritize.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/mutect2.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/recalibrate.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/platypus.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/gatkjoint.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/joint.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/vcfanno.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/smcounter2.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/strelka2.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/germline.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/scalpel.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/pisces.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/realign.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/gatkfilter.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/effects.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/octopus.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/genotype.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/peddy.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/qsnp.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/normalize.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/damage.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/variation/vcfutils.py -> build/bdist.linux-armv7l/wheel/bcbio/variation
2019-07-04T17:55:45   copying build/lib/bcbio/utils.py -> build/bdist.linux-armv7l/wheel/bcbio
2019-07-04T17:55:45   creating build/bdist.linux-armv7l/wheel/bcbio/broad
2019-07-04T17:55:45   copying build/lib/bcbio/broad/metrics.py -> build/bdist.linux-armv7l/wheel/bcbio/broad
2019-07-04T17:55:45   copying build/lib/bcbio/broad/picardrun.py -> build/bdist.linux-armv7l/wheel/bcbio/broad
2019-07-04T17:55:45   copying build/lib/bcbio/broad/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/broad
2019-07-04T17:55:45   creating build/bdist.linux-armv7l/wheel/bcbio/chipseq
2019-07-04T17:55:45   copying build/lib/bcbio/chipseq/macs2.py -> build/bdist.linux-armv7l/wheel/bcbio/chipseq
2019-07-04T17:55:45   copying build/lib/bcbio/chipseq/peaks.py -> build/bdist.linux-armv7l/wheel/bcbio/chipseq
2019-07-04T17:55:45   copying build/lib/bcbio/chipseq/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/chipseq
2019-07-04T17:55:45   creating build/bdist.linux-armv7l/wheel/bcbio/galaxy
2019-07-04T17:55:45   copying build/lib/bcbio/galaxy/nglims.py -> build/bdist.linux-armv7l/wheel/bcbio/galaxy
2019-07-04T17:55:45   copying build/lib/bcbio/galaxy/api.py -> build/bdist.linux-armv7l/wheel/bcbio/galaxy
2019-07-04T17:55:45   copying build/lib/bcbio/galaxy/loc.py -> build/bdist.linux-armv7l/wheel/bcbio/galaxy
2019-07-04T17:55:45   copying build/lib/bcbio/galaxy/__init__.py -> build/bdist.linux-armv7l/wheel/bcbio/galaxy
2019-07-04T17:55:45   running install_egg_info
2019-07-04T17:55:45   Copying bcbio_nextgen.egg-info to build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5-py3.5.egg-info
2019-07-04T17:55:45   running install_scripts
2019-07-04T17:55:45   creating build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data
2019-07-04T17:55:45   creating build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts
2019-07-04T17:55:45   copying build/scripts-3.5/cwltool2wdl.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts
2019-07-04T17:55:45   copying build/scripts-3.5/bcbio_fastq_umi_prep.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts
2019-07-04T17:55:45   copying build/scripts-3.5/bcbio_prepare_samples.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts
2019-07-04T17:55:45   copying build/scripts-3.5/bcbio_nextgen.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts
2019-07-04T17:55:45   copying build/scripts-3.5/bcbio_setup_genome.py -> build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts
2019-07-04T17:55:45   changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts/cwltool2wdl.py to 755
2019-07-04T17:55:45   changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts/bcbio_fastq_umi_prep.py to 755
2019-07-04T17:55:45   changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts/bcbio_prepare_samples.py to 755
2019-07-04T17:55:45   changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts/bcbio_nextgen.py to 755
2019-07-04T17:55:45   changing mode of build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.data/scripts/bcbio_setup_genome.py to 755
2019-07-04T17:55:45   adding license file "LICENSE.txt" (matched pattern "LICEN[CS]E*")
2019-07-04T17:55:45   creating build/bdist.linux-armv7l/wheel/bcbio_nextgen-1.1.5.dist-info/WHEEL
2019-07-04T17:55:45   creating '/tmp/pip-wheel-36i5y0kh/bcbio_nextgen-1.1.5-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2019-07-04T17:55:45   adding 'bcbio/__init__.py'
2019-07-04T17:55:45   adding 'bcbio/install.py'
2019-07-04T17:55:45   adding 'bcbio/setpath.py'
2019-07-04T17:55:45   adding 'bcbio/utils.py'
2019-07-04T17:55:45   adding 'bcbio/bam/__init__.py'
2019-07-04T17:55:45   adding 'bcbio/bam/callable.py'
2019-07-04T17:55:45   adding 'bcbio/bam/counts.py'
2019-07-04T17:55:45   adding 'bcbio/bam/coverage.py'
2019-07-04T17:55:45   adding 'bcbio/bam/cram.py'
2019-07-04T17:55:45   adding 'bcbio/bam/fasta.py'
2019-07-04T17:55:45   adding 'bcbio/bam/fastq.py'
2019-07-04T17:55:45   adding 'bcbio/bam/readstats.py'
2019-07-04T17:55:45   adding 'bcbio/bam/ref.py'
2019-07-04T17:55:45   adding 'bcbio/bam/skewer.py'
2019-07-04T17:55:45   adding 'bcbio/bam/trim.py'
2019-07-04T17:55:45   adding 'bcbio/bed/__init__.py'
2019-07-04T17:55:45   adding 'bcbio/broad/__init__.py'
2019-07-04T17:55:45   adding 'bcbio/broad/metrics.py'
2019-07-04T17:55:45   adding 'bcbio/broad/picardrun.py'
2019-07-04T17:55:45   adding 'bcbio/chipseq/__init__.py'
2019-07-04T17:55:45   adding 'bcbio/chipseq/macs2.py'
2019-07-04T17:55:45   adding 'bcbio/chipseq/peaks.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/__init__.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/create.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/cwlutils.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/defs.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/hpc.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/inspect.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/main.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/tool.py'
2019-07-04T17:55:45   adding 'bcbio/cwl/workflow.py'
2019-07-04T17:55:46   adding 'bcbio/data/umis/10x_v2-cb1.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/10x_v2-transform.json'
2019-07-04T17:55:46   adding 'bcbio/data/umis/dropseq-transform.json'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-indrop-v2-cb1.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-indrop-v2-cb2.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-indrop-v2-transform.json'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-indrop-v3-cb1.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-indrop-v3-cb2.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-indrop-v3-sample_barcodes.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-indrop-v3-transform.json'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-scrb-cb1.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/harvard-scrb-transform.json'
2019-07-04T17:55:46   adding 'bcbio/data/umis/icell8-cb1.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/icell8-transform.json'
2019-07-04T17:55:46   adding 'bcbio/data/umis/qiagen_smallRNA_umi-transform.json'
2019-07-04T17:55:46   adding 'bcbio/data/umis/surecell-cb1.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/surecell-cb2.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/surecell-cb3.txt.gz'
2019-07-04T17:55:46   adding 'bcbio/data/umis/surecell-transform.json'
2019-07-04T17:55:46   adding 'bcbio/distributed/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/clargs.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/clusterk.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/ipython.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/ipythontasks.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/multi.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/multitasks.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/objectstore.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/prun.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/resources.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/runfn.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/split.py'
2019-07-04T17:55:46   adding 'bcbio/distributed/transaction.py'
2019-07-04T17:55:46   adding 'bcbio/galaxy/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/galaxy/api.py'
2019-07-04T17:55:46   adding 'bcbio/galaxy/loc.py'
2019-07-04T17:55:46   adding 'bcbio/galaxy/nglims.py'
2019-07-04T17:55:46   adding 'bcbio/graph/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/graph/collectl.py'
2019-07-04T17:55:46   adding 'bcbio/graph/graph.py'
2019-07-04T17:55:46   adding 'bcbio/heterogeneity/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/heterogeneity/bubbletree.py'
2019-07-04T17:55:46   adding 'bcbio/heterogeneity/chromhacks.py'
2019-07-04T17:55:46   adding 'bcbio/heterogeneity/loh.py'
2019-07-04T17:55:46   adding 'bcbio/heterogeneity/phylowgs.py'
2019-07-04T17:55:46   adding 'bcbio/heterogeneity/theta.py'
2019-07-04T17:55:46   adding 'bcbio/hla/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/hla/bwakit.py'
2019-07-04T17:55:46   adding 'bcbio/hla/groups.py'
2019-07-04T17:55:46   adding 'bcbio/hla/optitype.py'
2019-07-04T17:55:46   adding 'bcbio/hmmer/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/hmmer/search.py'
2019-07-04T17:55:46   adding 'bcbio/illumina/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/illumina/demultiplex.py'
2019-07-04T17:55:46   adding 'bcbio/illumina/flowcell.py'
2019-07-04T17:55:46   adding 'bcbio/illumina/machine.py'
2019-07-04T17:55:46   adding 'bcbio/illumina/samplesheet.py'
2019-07-04T17:55:46   adding 'bcbio/illumina/transfer.py'
2019-07-04T17:55:46   adding 'bcbio/log/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/log/logbook_zmqpush.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/alignprep.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/bbmap.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/bowtie.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/bowtie2.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/bwa.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/hisat2.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/minimap2.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/mosaik.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/novoalign.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/postalign.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/rtg.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/snap.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/star.py'
2019-07-04T17:55:46   adding 'bcbio/ngsalign/tophat.py'
2019-07-04T17:55:46   adding 'bcbio/picard/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/picard/metrics.py'
2019-07-04T17:55:46   adding 'bcbio/picard/utils.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/alignment.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/archive.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/cleanbam.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/config_utils.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/datadict.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/fastq.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/genome.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/main.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/merge.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/qcsummary.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/region.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/rnaseq.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/run_info.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/sample.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/shared.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/sra.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/tools.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/variation.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/version.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/disambiguate/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/pipeline/disambiguate/run.py'
2019-07-04T17:55:46   adding 'bcbio/provenance/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/provenance/data.py'
2019-07-04T17:55:46   adding 'bcbio/provenance/diagnostics.py'
2019-07-04T17:55:46   adding 'bcbio/provenance/do.py'
2019-07-04T17:55:46   adding 'bcbio/provenance/profile.py'
2019-07-04T17:55:46   adding 'bcbio/provenance/programs.py'
2019-07-04T17:55:46   adding 'bcbio/provenance/system.py'
2019-07-04T17:55:46   adding 'bcbio/provenance/versioncheck.py'
2019-07-04T17:55:46   adding 'bcbio/qc/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/qc/atropos.py'
2019-07-04T17:55:46   adding 'bcbio/qc/chipseq.py'
2019-07-04T17:55:46   adding 'bcbio/qc/contamination.py'
2019-07-04T17:55:46   adding 'bcbio/qc/coverage.py'
2019-07-04T17:55:46   adding 'bcbio/qc/damage.py'
2019-07-04T17:55:46   adding 'bcbio/qc/fastqc.py'
2019-07-04T17:55:46   adding 'bcbio/qc/kraken.py'
2019-07-04T17:55:46   adding 'bcbio/qc/multiqc.py'
2019-07-04T17:55:46   adding 'bcbio/qc/picard.py'
2019-07-04T17:55:46   adding 'bcbio/qc/preseq.py'
2019-07-04T17:55:46   adding 'bcbio/qc/qsignature.py'
2019-07-04T17:55:46   adding 'bcbio/qc/qualimap.py'
2019-07-04T17:55:46   adding 'bcbio/qc/samtools.py'
2019-07-04T17:55:46   adding 'bcbio/qc/srna.py'
2019-07-04T17:55:46   adding 'bcbio/qc/umi.py'
2019-07-04T17:55:46   adding 'bcbio/qc/variant.py'
2019-07-04T17:55:46   adding 'bcbio/qc/viral.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/annotate_gtf.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/bcbiornaseq.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/count.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/cpat.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/cufflinks.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/dexseq.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/ericscript.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/express.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/featureCounts.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/gtf.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/kallisto.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/oncofuse.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/pizzly.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/qc.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/rapmap.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/rsem.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/sailfish.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/salmon.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/singlecellexperiment.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/spikein.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/stringtie.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/umi.py'
2019-07-04T17:55:46   adding 'bcbio/rnaseq/variation.py'
2019-07-04T17:55:46   adding 'bcbio/server/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/server/background.py'
2019-07-04T17:55:46   adding 'bcbio/server/main.py'
2019-07-04T17:55:46   adding 'bcbio/server/run.py'
2019-07-04T17:55:46   adding 'bcbio/srna/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/srna/group.py'
2019-07-04T17:55:46   adding 'bcbio/srna/mirdeep.py'
2019-07-04T17:55:46   adding 'bcbio/srna/mirge.py'
2019-07-04T17:55:46   adding 'bcbio/srna/qc.py'
2019-07-04T17:55:46   adding 'bcbio/srna/sample.py'
2019-07-04T17:55:46   adding 'bcbio/srna/umis.py'
2019-07-04T17:55:46   adding 'bcbio/structural/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/structural/annotate.py'
2019-07-04T17:55:46   adding 'bcbio/structural/battenberg.py'
2019-07-04T17:55:46   adding 'bcbio/structural/cn_mops.py'
2019-07-04T17:55:46   adding 'bcbio/structural/cnvkit.py'
2019-07-04T17:55:46   adding 'bcbio/structural/convert.py'
2019-07-04T17:55:46   adding 'bcbio/structural/delly.py'
2019-07-04T17:55:46   adding 'bcbio/structural/gatkcnv.py'
2019-07-04T17:55:46   adding 'bcbio/structural/gridss.py'
2019-07-04T17:55:46   adding 'bcbio/structural/hydra.py'
2019-07-04T17:55:46   adding 'bcbio/structural/lumpy.py'
2019-07-04T17:55:46   adding 'bcbio/structural/manta.py'
2019-07-04T17:55:46   adding 'bcbio/structural/metasv.py'
2019-07-04T17:55:46   adding 'bcbio/structural/pindel.py'
2019-07-04T17:55:46   adding 'bcbio/structural/plot.py'
2019-07-04T17:55:46   adding 'bcbio/structural/prioritize.py'
2019-07-04T17:55:46   adding 'bcbio/structural/purecn.py'
2019-07-04T17:55:46   adding 'bcbio/structural/purple.py'
2019-07-04T17:55:46   adding 'bcbio/structural/regions.py'
2019-07-04T17:55:46   adding 'bcbio/structural/seq2c.py'
2019-07-04T17:55:46   adding 'bcbio/structural/shared.py'
2019-07-04T17:55:46   adding 'bcbio/structural/titancna.py'
2019-07-04T17:55:46   adding 'bcbio/structural/validate.py'
2019-07-04T17:55:46   adding 'bcbio/structural/wham.py'
2019-07-04T17:55:46   adding 'bcbio/upload/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/upload/filesystem.py'
2019-07-04T17:55:46   adding 'bcbio/upload/galaxy.py'
2019-07-04T17:55:46   adding 'bcbio/upload/irods.py'
2019-07-04T17:55:46   adding 'bcbio/upload/s3.py'
2019-07-04T17:55:46   adding 'bcbio/upload/shared.py'
2019-07-04T17:55:46   adding 'bcbio/variation/__init__.py'
2019-07-04T17:55:46   adding 'bcbio/variation/annotation.py'
2019-07-04T17:55:46   adding 'bcbio/variation/bamprep.py'
2019-07-04T17:55:46   adding 'bcbio/variation/bedutils.py'
2019-07-04T17:55:46   adding 'bcbio/variation/cortex.py'
2019-07-04T17:55:46   adding 'bcbio/variation/coverage.py'
2019-07-04T17:55:46   adding 'bcbio/variation/damage.py'
2019-07-04T17:55:46   adding 'bcbio/variation/deepvariant.py'
2019-07-04T17:55:46   adding 'bcbio/variation/effects.py'
2019-07-04T17:55:47   adding 'bcbio/variation/ensemble.py'
2019-07-04T17:55:47   adding 'bcbio/variation/freebayes.py'
2019-07-04T17:55:47   adding 'bcbio/variation/gatk.py'
2019-07-04T17:55:47   adding 'bcbio/variation/gatkfilter.py'
2019-07-04T17:55:47   adding 'bcbio/variation/gatkjoint.py'
2019-07-04T17:55:47   adding 'bcbio/variation/genotype.py'
2019-07-04T17:55:47   adding 'bcbio/variation/germline.py'
2019-07-04T17:55:47   adding 'bcbio/variation/joint.py'
2019-07-04T17:55:47   adding 'bcbio/variation/multi.py'
2019-07-04T17:55:47   adding 'bcbio/variation/mutect.py'
2019-07-04T17:55:47   adding 'bcbio/variation/mutect2.py'
2019-07-04T17:55:47   adding 'bcbio/variation/naming.py'
2019-07-04T17:55:47   adding 'bcbio/variation/normalize.py'
2019-07-04T17:55:47   adding 'bcbio/variation/octopus.py'
2019-07-04T17:55:47   adding 'bcbio/variation/peddy.py'
2019-07-04T17:55:47   adding 'bcbio/variation/pisces.py'
2019-07-04T17:55:47   adding 'bcbio/variation/platypus.py'
2019-07-04T17:55:47   adding 'bcbio/variation/ploidy.py'
2019-07-04T17:55:47   adding 'bcbio/variation/population.py'
2019-07-04T17:55:47   adding 'bcbio/variation/prioritize.py'
2019-07-04T17:55:47   adding 'bcbio/variation/qsnp.py'
2019-07-04T17:55:47   adding 'bcbio/variation/realign.py'
2019-07-04T17:55:47   adding 'bcbio/variation/recalibrate.py'
2019-07-04T17:55:47   adding 'bcbio/variation/samtools.py'
2019-07-04T17:55:47   adding 'bcbio/variation/scalpel.py'
2019-07-04T17:55:47   adding 'bcbio/variation/sentieon.py'
2019-07-04T17:55:47   adding 'bcbio/variation/smcounter2.py'
2019-07-04T17:55:47   adding 'bcbio/variation/split.py'
2019-07-04T17:55:47   adding 'bcbio/variation/strelka2.py'
2019-07-04T17:55:47   adding 'bcbio/variation/validate.py'
2019-07-04T17:55:47   adding 'bcbio/variation/validateplot.py'
2019-07-04T17:55:47   adding 'bcbio/variation/vardict.py'
2019-07-04T17:55:47   adding 'bcbio/variation/varscan.py'
2019-07-04T17:55:47   adding 'bcbio/variation/vcfanno.py'
2019-07-04T17:55:47   adding 'bcbio/variation/vcfutils.py'
2019-07-04T17:55:47   adding 'bcbio/variation/vfilter.py'
2019-07-04T17:55:47   adding 'bcbio/workflow/__init__.py'
2019-07-04T17:55:47   adding 'bcbio/workflow/stormseq.py'
2019-07-04T17:55:47   adding 'bcbio/workflow/template.py'
2019-07-04T17:55:47   adding 'bcbio/workflow/xprize.py'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.data/scripts/bcbio_fastq_umi_prep.py'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.data/scripts/bcbio_nextgen.py'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.data/scripts/bcbio_prepare_samples.py'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.data/scripts/bcbio_setup_genome.py'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.data/scripts/cwltool2wdl.py'
2019-07-04T17:55:47   adding 'tests/integration/__init__.py'
2019-07-04T17:55:47   adding 'tests/integration/test_S3_pipelines.py'
2019-07-04T17:55:47   adding 'tests/integration/test_SequencingDump.py'
2019-07-04T17:55:47   adding 'tests/integration/test_automated_analysis.py'
2019-07-04T17:55:47   adding 'tests/integration/test_pipeline.py'
2019-07-04T17:55:47   adding 'tests/integration/rnaseq/__init__.py'
2019-07-04T17:55:47   adding 'tests/integration/rnaseq/test_ericscript.py'
2019-07-04T17:55:47   adding 'tests/unit/__init__.py'
2019-07-04T17:55:47   adding 'tests/unit/conftest.py'
2019-07-04T17:55:47   adding 'tests/unit/data.py'
2019-07-04T17:55:47   adding 'tests/unit/test_alignprep.py'
2019-07-04T17:55:47   adding 'tests/unit/distributed/__init__.py'
2019-07-04T17:55:47   adding 'tests/unit/distributed/test_transaction.py'
2019-07-04T17:55:47   adding 'tests/unit/ngsalign/__init__.py'
2019-07-04T17:55:47   adding 'tests/unit/pipeline/__init__.py'
2019-07-04T17:55:47   adding 'tests/unit/pipeline/test_datadict.py'
2019-07-04T17:55:47   adding 'tests/unit/pipeline/test_rnaseq.py'
2019-07-04T17:55:47   adding 'tests/unit/rnaseq/__init__.py'
2019-07-04T17:55:47   adding 'tests/unit/rnaseq/test_ericscript.py'
2019-07-04T17:55:47   adding 'tests/unit/upload/__init__.py'
2019-07-04T17:55:47   adding 'tests/unit/upload/test_upload.py'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.dist-info/LICENSE.txt'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.dist-info/METADATA'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.dist-info/WHEEL'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.dist-info/top_level.txt'
2019-07-04T17:55:47   adding 'bcbio_nextgen-1.1.5.dist-info/RECORD'
2019-07-04T17:55:47   removing build/bdist.linux-armv7l/wheel
2019-07-04T17:55:47   Building wheel for bcbio-nextgen (setup.py): finished with status 'done'
2019-07-04T17:55:47   Stored in directory: /tmp/tmpfb_aeub6
2019-07-04T17:55:47 Successfully built bcbio-nextgen
2019-07-04T17:55:47 Cleaning up...
2019-07-04T17:55:47   Removing source in /tmp/pip-wheel-y9csdmk3/bcbio-nextgen
2019-07-04T17:55:48 Removed build tracker '/tmp/pip-req-tracker-_k13kxi7'