2020-09-20T12:57:10,746 Created temporary directory: /tmp/pip-ephem-wheel-cache-auwt3fvy 2020-09-20T12:57:10,748 Created temporary directory: /tmp/pip-req-tracker-gnby2sky 2020-09-20T12:57:10,749 Initialized build tracking at /tmp/pip-req-tracker-gnby2sky 2020-09-20T12:57:10,749 Created build tracker: /tmp/pip-req-tracker-gnby2sky 2020-09-20T12:57:10,749 Entered build tracker: /tmp/pip-req-tracker-gnby2sky 2020-09-20T12:57:10,750 Created temporary directory: /tmp/pip-wheel-2tq3a4ej 2020-09-20T12:57:10,759 1 location(s) to search for versions of cgat: 2020-09-20T12:57:10,759 * https://pypi.org/simple/cgat/ 2020-09-20T12:57:10,759 Fetching project page and analyzing links: https://pypi.org/simple/cgat/ 2020-09-20T12:57:10,760 Getting page https://pypi.org/simple/cgat/ 2020-09-20T12:57:10,761 Found index url https://pypi.org/simple 2020-09-20T12:57:10,859 Found link https://files.pythonhosted.org/packages/82/a0/23011460a9548932524dd5b17d18b02e1803b5b638b78503f2b9319837a7/CGAT-0.1.tar.gz#sha256=ddfa2dd7c465607ff3a26a15c79d3172be5dfd0a5ddbee46436073a00afc8962 (from https://pypi.org/simple/cgat/), version: 0.1 2020-09-20T12:57:10,860 Found link https://files.pythonhosted.org/packages/90/20/9ecc442d1b6d352d72480376b3713a29875b9dbaf0d72bb820e4bfc9bf28/CGAT-0.1.1.tar.gz#sha256=c4f19fd4b02050245b3902edf55a65de971015fb26e4e6361ab6ed35b8baa729 (from https://pypi.org/simple/cgat/), version: 0.1.1 2020-09-20T12:57:10,860 Found link https://files.pythonhosted.org/packages/e4/fe/5858c1d7f331982f24326b8220a0c54564c069435cce5bde568ceb9b4373/CGAT-0.1.3.tar.gz#sha256=7a0056da88f6fa57c108af63632e95e06804bdc6041b42c85de48c84daa8f7f9 (from https://pypi.org/simple/cgat/), version: 0.1.3 2020-09-20T12:57:10,860 Found link https://files.pythonhosted.org/packages/96/85/e31f136aab7e0803f82c62e1a9f0dd5d17d873ea3892ec1e4dfc759f7f51/CGAT-0.1.4.tar.gz#sha256=cfa92f36d599510fda0abb3728e96ef6643593d4c91fcc6094cad894684de633 (from https://pypi.org/simple/cgat/), version: 0.1.4 2020-09-20T12:57:10,861 Found link https://files.pythonhosted.org/packages/ba/e8/1ef67c7be3f57254b74c41b89e6b79112ed7360226d891d15fcc95b95cfd/CGAT-0.1.5.tar.gz#sha256=8db06f98b11ea48d3b91db991f5786e5c60ef6e3130418e755bcf6bb75e590a7 (from https://pypi.org/simple/cgat/), version: 0.1.5 2020-09-20T12:57:10,861 Found link https://files.pythonhosted.org/packages/13/ca/99f09c68029bc1cd011c8c946a74fd9b970a40a26bc54eb279bd0f0045c2/CGAT-0.1.6.tar.gz#sha256=33dc3014a113efcdd2adfee5f558603099463c3d4f8df79ede06f4217af78674 (from https://pypi.org/simple/cgat/), version: 0.1.6 2020-09-20T12:57:10,861 Found link https://files.pythonhosted.org/packages/94/b0/2d158572aa0ec70826ac5805d5fd5a42631dcb8f2ea0d6150dfc41794212/CGAT-0.1.7.tar.gz#sha256=f3e24fe22d5341bfc57b720ecc4808076962b0af53fab0aae98b7915aec97607 (from https://pypi.org/simple/cgat/), version: 0.1.7 2020-09-20T12:57:10,861 Found link https://files.pythonhosted.org/packages/c9/96/19787a37483d45b902ce2378bce0ee6ca1c538b253fb0eb28b5b23b7d7a5/CGAT-0.1.8.tar.gz#sha256=f5ec266e005ce9f9dae0a3d32149b5b3f6aa6b4e65658761393f3a1bcfd10fd8 (from https://pypi.org/simple/cgat/), version: 0.1.8 2020-09-20T12:57:10,862 Found link https://files.pythonhosted.org/packages/f2/d1/ca23c8156b4ae13b7b82e02b56055a9cf7a6d3eb38f28c39898da8a5784c/CGAT-0.1.9.tar.gz#sha256=a49f4d00c5337e0d99bc50bd184b4fd45db01103a832135ad9df107cfa76cf41 (from https://pypi.org/simple/cgat/), version: 0.1.9 2020-09-20T12:57:10,862 Found link https://files.pythonhosted.org/packages/c5/97/065fec28bcca210fadaa3be6f1b149922d69bff46ed56debf746355b2372/CGAT-0.2.0.tar.gz#sha256=56d2adb9a15b963c74a5a2b40d751f0b45bf4a3d4ffb3f062172b0830866be9f (from https://pypi.org/simple/cgat/), version: 0.2.0 2020-09-20T12:57:10,862 Found link https://files.pythonhosted.org/packages/2e/e8/3fe3d5cfb0348a9e13f87f253265a6906f4d41391137506f46c0019af93c/CGAT-0.2.1.tar.gz#sha256=de026223daa30fbfc6f4e72b2842e29ea54d99c5524a0116117a6b9873de0234 (from https://pypi.org/simple/cgat/), version: 0.2.1 2020-09-20T12:57:10,863 Found link https://files.pythonhosted.org/packages/d7/dd/870a8ff2404e9786faa3dd3ca8d6ae65d58dc7a6e4470cbd6d08c1646d84/CGAT-0.2.2.tar.gz#sha256=331ec1f5913a3ddb76bc41b72a9fc336739526f74f329f85853e8fcc6e4b0ac1 (from https://pypi.org/simple/cgat/), version: 0.2.2 2020-09-20T12:57:10,863 Found link https://files.pythonhosted.org/packages/f2/f3/b80f5dad0f604ca68840639f5ac64147768b044b8f0797d7bc1fb8d69ba7/CGAT-0.2.3.tar.gz#sha256=75ba018ad71a9776cfb83bedfd6c66d39c5f019cddb97f307c0be9af08aba95e (from https://pypi.org/simple/cgat/), version: 0.2.3 2020-09-20T12:57:10,863 Found link https://files.pythonhosted.org/packages/05/d5/d8deed8eebc26c37a4e463345a137ab5e0d4fa0ac9dc92617bc12f495f43/CGAT-0.2.4.tar.gz#sha256=a15f68579358d6506afa94690876041b37fbe4e64887a140b793de8720231003 (from https://pypi.org/simple/cgat/), version: 0.2.4 2020-09-20T12:57:10,864 Found link https://files.pythonhosted.org/packages/89/75/6a2b039d71228269b1aa918bc640646cb55ad6d047a497c55dc11778ae42/CGAT-0.2.5.tar.gz#sha256=eeb990c0b7423b57e4e11e5deb891076be73e7d19d2725dbc53b17271f9cd683 (from https://pypi.org/simple/cgat/), version: 0.2.5 2020-09-20T12:57:10,864 Found link https://files.pythonhosted.org/packages/fe/86/be2a14843dc272abe33dd0de754e8ba142fc07c3cfe11410be7230d27078/CGAT-0.2.6.tar.gz#sha256=a7f1ffe13981fe95ecface2ae86c80a48914799713e674512b6355be8c7f8b0b (from https://pypi.org/simple/cgat/), version: 0.2.6 2020-09-20T12:57:10,864 Found link https://files.pythonhosted.org/packages/a3/ff/e5f2175450e1a362b941d96afd139a4c66ad884765cfe7d7bb7d9a735a95/CGAT-0.2.7.tar.gz#sha256=6976ab4b2888583ab9516f3e68f91f7ccd2a5a3c3614d71042fd22e3389a4aa6 (from https://pypi.org/simple/cgat/), version: 0.2.7 2020-09-20T12:57:10,865 Found link https://files.pythonhosted.org/packages/ba/39/a13ca9d92ef0caf2852617fff6ebdb8e83697bb1a2e61fb9dc4608f5e4f9/CGAT-0.3.0.tar.gz#sha256=4ea98ae7a35d7422712a89784efde70f393bbdce24902770a7cbb4dc3313e6ee (from https://pypi.org/simple/cgat/), version: 0.3.0 2020-09-20T12:57:10,865 Found link https://files.pythonhosted.org/packages/4a/4e/775ffc1bf3c9a7e13ffd22ce69cb9d61826c69855f0523225977f9884bdc/CGAT-0.3.1.tar.gz#sha256=16a9d03f6fae3f1fe1481eb3d388da4353178bdd996e1b9c01e6b030eabdd69f (from https://pypi.org/simple/cgat/), version: 0.3.1 2020-09-20T12:57:10,865 Found link https://files.pythonhosted.org/packages/88/19/c19e9e16c3b8e19f05381c780f3583eae2982c91c163ee8e2aa3311eec7e/CGAT-0.3.2.tar.gz#sha256=986fcada180d943df1ba4666c173c1b7e7b209bdbf9755571c2b946617a53386 (from https://pypi.org/simple/cgat/), version: 0.3.2 2020-09-20T12:57:10,865 Found link https://files.pythonhosted.org/packages/af/31/d29170e58d6fc06571753b9b54f6aad686a376d310e87b0810099e8bbbac/CGAT-0.3.3.tar.gz#sha256=f00686ab3bb22b2d69acd608cd9d4db7786b06988afcef55d499b064d1e855bd (from https://pypi.org/simple/cgat/), version: 0.3.3 2020-09-20T12:57:10,866 Found link https://files.pythonhosted.org/packages/46/9f/4131b77f952d136662feba4cdc9562115f3eddf2dddf6cbc2bb7c0f3299c/cgat-0.5.1.tar.gz#sha256=5254102752cab2c7ee4fc056eb5e2df288d813cd3ffd3dd9b759c22a9bf9d2c3 (from https://pypi.org/simple/cgat/), version: 0.5.1 2020-09-20T12:57:10,866 Found link https://files.pythonhosted.org/packages/9e/8e/83ff5d238ac6bc75be300a50bcfbb64ebe77d90b053ef094db1af962abda/cgat-0.5.2.tar.gz#sha256=0a2f1a1047aebdbb3c2240ebca85cf136b63baca99661353235cc95e3a45ac50 (from https://pypi.org/simple/cgat/), version: 0.5.2 2020-09-20T12:57:10,866 Found link https://files.pythonhosted.org/packages/d7/05/6518cd6bf64bc0d15f474ea707979b8a47d502b2ee7c043d3a5e33f602c9/cgat-0.5.3.tar.gz#sha256=2ea78bcee73c0aa2427466efe4dab3d6b035089bb42cc735480dafe5ceb2f191 (from https://pypi.org/simple/cgat/), version: 0.5.3 2020-09-20T12:57:10,867 Found link https://files.pythonhosted.org/packages/b6/58/4a88bde62300df47727a502c91b91a1e5d3399c4f72715c3a802bcd19faa/cgat-0.5.4.tar.gz#sha256=df54c25707ba87e42c853cd6e851ba672de1f1ffea6c122e1408229a53b007a8 (from https://pypi.org/simple/cgat/), version: 0.5.4 2020-09-20T12:57:10,867 Found link https://files.pythonhosted.org/packages/dc/54/bce4257afde6befa7728b1911c1b2499b8a6edbc51e5ab6bca7d7c5dd70a/cgat-0.5.5.tar.gz#sha256=e03ceddbd8b94be3cf92c720b42a0fc36f2b228b6cce88a097c26c646bef092c (from https://pypi.org/simple/cgat/), version: 0.5.5 2020-09-20T12:57:10,867 Found link https://files.pythonhosted.org/packages/c6/30/6c6b3d2820998a407c14b540e0b656de4177d36cb427ffe1ac8bb90c2e82/cgat-0.5.6.tar.gz#sha256=e728f51696f9d23bea1553b3f11474b024e13902bf6ecd13a14481966b166ae1 (from https://pypi.org/simple/cgat/), version: 0.5.6 2020-09-20T12:57:10,868 Found link https://files.pythonhosted.org/packages/0e/10/ebbb6959f3d636e59a3572e3f864dacf9f89246406bf962baf17e041da8b/cgat-0.6.0.tar.gz#sha256=d851076158ac9244bb71b36bf8637cddbcf92c681af89bb0a379963bd32e2e64 (from https://pypi.org/simple/cgat/), version: 0.6.0 2020-09-20T12:57:10,876 Given no hashes to check 1 links for project 'cgat': discarding no candidates 2020-09-20T12:57:10,877 Using version 0.2.6 (newest of versions: 0.2.6) 2020-09-20T12:57:10,881 Collecting cgat==0.2.6 2020-09-20T12:57:10,882 Created temporary directory: /tmp/pip-unpack-uthslkkq 2020-09-20T12:57:10,930 Downloading CGAT-0.2.6.tar.gz (615 kB) 2020-09-20T12:57:11,559 Added cgat==0.2.6 from https://files.pythonhosted.org/packages/fe/86/be2a14843dc272abe33dd0de754e8ba142fc07c3cfe11410be7230d27078/CGAT-0.2.6.tar.gz#sha256=a7f1ffe13981fe95ecface2ae86c80a48914799713e674512b6355be8c7f8b0b to build tracker '/tmp/pip-req-tracker-gnby2sky' 2020-09-20T12:57:11,560 Running setup.py (path:/tmp/pip-wheel-2tq3a4ej/cgat/setup.py) egg_info for package cgat 2020-09-20T12:57:11,561 Created temporary directory: /tmp/pip-pip-egg-info-tg_vfs93 2020-09-20T12:57:11,562 Running command python setup.py egg_info 2020-09-20T12:57:12,613 Traceback (most recent call last): 2020-09-20T12:57:12,614 File "/tmp/pip-wheel-2tq3a4ej/cgat/setup.py", line 29, in 2020-09-20T12:57:12,614 import pysam 2020-09-20T12:57:12,615 ModuleNotFoundError: No module named 'pysam' 2020-09-20T12:57:12,616 During handling of the above exception, another exception occurred: 2020-09-20T12:57:12,617 Traceback (most recent call last): 2020-09-20T12:57:12,617 File "", line 1, in 2020-09-20T12:57:12,618 File "/tmp/pip-wheel-2tq3a4ej/cgat/setup.py", line 32, in 2020-09-20T12:57:12,618 "the CGAT code collection requires pysam to " 2020-09-20T12:57:12,619 ImportError: the CGAT code collection requires pysam to be installed before running setup.py (pip install pysam) 2020-09-20T12:57:12,690 ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. 2020-09-20T12:57:12,691 Exception information: 2020-09-20T12:57:12,691 Traceback (most recent call last): 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/base_command.py", line 228, in _main 2020-09-20T12:57:12,691 status = self.run(options, args) 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/cli/req_command.py", line 182, in wrapper 2020-09-20T12:57:12,691 return func(self, options, args) 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/commands/wheel.py", line 156, in run 2020-09-20T12:57:12,691 reqs, check_supported_wheels=True 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/legacy/resolver.py", line 183, in resolve 2020-09-20T12:57:12,691 discovered_reqs.extend(self._resolve_one(requirement_set, req)) 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/legacy/resolver.py", line 388, in _resolve_one 2020-09-20T12:57:12,691 abstract_dist = self._get_abstract_dist_for(req_to_install) 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/resolution/legacy/resolver.py", line 340, in _get_abstract_dist_for 2020-09-20T12:57:12,691 abstract_dist = self.preparer.prepare_linked_requirement(req) 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 483, in prepare_linked_requirement 2020-09-20T12:57:12,691 req, self.req_tracker, self.finder, self.build_isolation, 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/prepare.py", line 91, in _get_prepared_distribution 2020-09-20T12:57:12,691 abstract_dist.prepare_distribution_metadata(finder, build_isolation) 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/distributions/sdist.py", line 40, in prepare_distribution_metadata 2020-09-20T12:57:12,691 self.req.prepare_metadata() 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 555, in prepare_metadata 2020-09-20T12:57:12,691 self.metadata_directory = self._generate_metadata() 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/req/req_install.py", line 535, in _generate_metadata 2020-09-20T12:57:12,691 details=self.name or "from {}".format(self.link) 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 73, in generate_metadata 2020-09-20T12:57:12,691 command_desc='python setup.py egg_info', 2020-09-20T12:57:12,691 File "/usr/local/lib/python3.7/dist-packages/pip/_internal/utils/subprocess.py", line 242, in call_subprocess 2020-09-20T12:57:12,691 raise InstallationError(exc_msg) 2020-09-20T12:57:12,691 pip._internal.exceptions.InstallationError: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. 2020-09-20T12:57:12,698 Removed cgat==0.2.6 from https://files.pythonhosted.org/packages/fe/86/be2a14843dc272abe33dd0de754e8ba142fc07c3cfe11410be7230d27078/CGAT-0.2.6.tar.gz#sha256=a7f1ffe13981fe95ecface2ae86c80a48914799713e674512b6355be8c7f8b0b from build tracker '/tmp/pip-req-tracker-gnby2sky' 2020-09-20T12:57:12,699 Removed build tracker: '/tmp/pip-req-tracker-gnby2sky'