{"action":"opened","issue":{"url":"https://api.github.com/repos/etal/cnvkit/issues/167","repository_url":"https://api.github.com/repos/etal/cnvkit","labels_url":"https://api.github.com/repos/etal/cnvkit/issues/167/labels{/name}","comments_url":"https://api.github.com/repos/etal/cnvkit/issues/167/comments","events_url":"https://api.github.com/repos/etal/cnvkit/issues/167/events","html_url":"https://github.com/etal/cnvkit/issues/167","id":195073831,"number":167,"title":"Correcting for density bias...true_divide","user":{"login":"ramaniak","id":6088710,"avatar_url":"https://avatars.githubusercontent.com/u/6088710?v=3","gravatar_id":"","url":"https://api.github.com/users/ramaniak","html_url":"https://github.com/ramaniak","followers_url":"https://api.github.com/users/ramaniak/followers","following_url":"https://api.github.com/users/ramaniak/following{/other_user}","gists_url":"https://api.github.com/users/ramaniak/gists{/gist_id}","starred_url":"https://api.github.com/users/ramaniak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ramaniak/subscriptions","organizations_url":"https://api.github.com/users/ramaniak/orgs","repos_url":"https://api.github.com/users/ramaniak/repos","events_url":"https://api.github.com/users/ramaniak/events{/privacy}","received_events_url":"https://api.github.com/users/ramaniak/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-12T20:13:54Z","updated_at":"2016-12-12T20:13:54Z","closed_at":null,"body":"Hello Eric,\r\n\r\nI am running cnvkit fix step as follows:\r\n\r\n```\r\ncnvkit.py fix A2.targetcoverage.cnn A2.antitargetcoverage.cnn Reference.cnn -o A2.cnr\r\n\r\n```\r\nand am seeing the following log which I am not sure how to interpret/fix.\r\n\r\n```\r\nProcessing target: A2\r\nKeeping 254401 of 256375 bins\r\nCorrecting for GC bias...\r\nCorrecting for density bias...\r\n/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/CNVkit-0.8.1-py2.7.egg/cnvlib/fix.py:170: : divide by zero encountered in true_divide\r\n/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/CNVkit-0.8.1-py2.7.egg/cnvlib/fix.py:175: RuntimeWarning: divide by zero encountered in true_divide\r\n/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/CNVkit-0.8.1-py2.7.egg/cnvlib/fix.py:175: RuntimeWarning: invalid value encountered in subtract\r\n/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/CNVkit-0.8.1-py2.7.egg/cnvlib/fix.py:198: RuntimeWarning: divide by zero encountered in true_divide\r\n/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/CNVkit-0.8.1-py2.7.egg/cnvlib/fix.py:204: RuntimeWarning: divide by zero encountered in true_divide\r\n/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/CNVkit-0.8.1-py2.7.egg/cnvlib/fix.py:204: RuntimeWarning: invalid value encountered in subtract\r\nProcessing antitarget: A2\r\nTraceback (most recent call last):\r\n  File \"/hpf/tools/centos6/python/2.7.12/bin/cnvkit.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('CNVkit==0.8.1', 'cnvkit.py')\r\n  File \"/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/pkg_resources/__init__.py\", line 742, in run_script\r\n    self.require(requires)[0].run_script(script_name, ns)\r\n  File \"/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/pkg_resources/__init__.py\", line 1504, in run_script\r\n    exec(script_code, namespace, namespace)\r\n  File \"/hpf/tools/centos6/python/2.7.12/lib/python2.7/site-packages/CNVkit-0.8.1-py2.7.egg/EGG-INFO/scripts/cnvkit.py\", line 13, in <module>\r\n    \r\n  File \"build/bdist.linux-x86_64/egg/cnvlib/commands.py\", line 677, in _cmd_fix\r\n    \r\n  File \"build/bdist.linux-x86_64/egg/cnvlib/commands.py\", line 691, in do_fix\r\n    \r\n  File \"build/bdist.linux-x86_64/egg/cnvlib/fix.py\", line 24, in load_adjust_coverages\r\n  File \"build/bdist.linux-x86_64/egg/cnvlib/fix.py\", line 94, in match_ref_to_sample\r\nValueError: Reference is missing 7309 bins found in A2\r\n```\r\n\r\nThanks\r\nArun"}}
{"actor":{"display_login":"ramaniak"}}