{"action":"created","issue":{"url":"https://api.github.com/repos/rajanil/msCentipede/issues/8","labels_url":"https://api.github.com/repos/rajanil/msCentipede/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/rajanil/msCentipede/issues/8/comments","events_url":"https://api.github.com/repos/rajanil/msCentipede/issues/8/events","html_url":"https://github.com/rajanil/msCentipede/issues/8","id":116465471,"number":8,"title":"error: cvxopt and mscentipede.pyx","user":{"login":"gsteinhardt","id":15808320,"avatar_url":"https://avatars.githubusercontent.com/u/15808320?v=3","gravatar_id":"","url":"https://api.github.com/users/gsteinhardt","html_url":"https://github.com/gsteinhardt","followers_url":"https://api.github.com/users/gsteinhardt/followers","following_url":"https://api.github.com/users/gsteinhardt/following{/other_user}","gists_url":"https://api.github.com/users/gsteinhardt/gists{/gist_id}","starred_url":"https://api.github.com/users/gsteinhardt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gsteinhardt/subscriptions","organizations_url":"https://api.github.com/users/gsteinhardt/orgs","repos_url":"https://api.github.com/users/gsteinhardt/repos","events_url":"https://api.github.com/users/gsteinhardt/events{/privacy}","received_events_url":"https://api.github.com/users/gsteinhardt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-11-12T02:20:44Z","updated_at":"2015-12-02T00:28:54Z","closed_at":null,"body":"hello,\r\nWhen running the default model and the model using purified genomic dna (default and --model msCentipede_flexbg) the tool throws 2 different errors during the learning phase of the footprint calling:\r\n\r\nFLEXBG MODEL: \r\n...\r\nlearning a flexible background model ...\r\nNan in Tau\r\nError:\r\nFile \"mscentipede.pyx\", line 410, in mscentipede.Tau.update (mscentipede.c:12756)\r\n    raise ValueError\r\nValueError\r\n\r\nDEFAULT MODEL:\r\n...\r\nstarting model estimation (restart 1)\r\ninitial log likelihood = -6.32e+01\r\nError:\r\nFile \"dir/.conda/envs/msCentipede/lib/python2.7/site-packages/cvxopt/cvxprog.py\", line 788, in cpl\r\n    raise ValueError(\"Rank(A) < p or \"\\\r\nValueError: Rank(A) < p or Rank([H(x); A; Df(x); G]) < n\r\n\r\nI tried this with 2 different read sets.\r\nPlease let me know if more info is needed\r\nthanks\r\ngeorge"},"comment":{"url":"https://api.github.com/repos/rajanil/msCentipede/issues/comments/161140733","html_url":"https://github.com/rajanil/msCentipede/issues/8#issuecomment-161140733","issue_url":"https://api.github.com/repos/rajanil/msCentipede/issues/8","id":161140733,"user":{"login":"rajanil","id":320245,"avatar_url":"https://avatars.githubusercontent.com/u/320245?v=3","gravatar_id":"","url":"https://api.github.com/users/rajanil","html_url":"https://github.com/rajanil","followers_url":"https://api.github.com/users/rajanil/followers","following_url":"https://api.github.com/users/rajanil/following{/other_user}","gists_url":"https://api.github.com/users/rajanil/gists{/gist_id}","starred_url":"https://api.github.com/users/rajanil/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rajanil/subscriptions","organizations_url":"https://api.github.com/users/rajanil/orgs","repos_url":"https://api.github.com/users/rajanil/repos","events_url":"https://api.github.com/users/rajanil/events{/privacy}","received_events_url":"https://api.github.com/users/rajanil/received_events","type":"User","site_admin":false},"created_at":"2015-12-02T00:28:54Z","updated_at":"2015-12-02T00:28:54Z","body":"Hi @mlendale @yuifu @gsteinhardt \r\n I'm working on this issue currently, sorry for the delayed response. It seems to happen for some motif sets, but I'm not sure why yet. I will keep you posted.\r\nthanks!\r\n-anil"}}