{"action":"created","issue":{"url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/76","repository_url":"https://api.github.com/repos/cancerit/cgpBattenberg","labels_url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/76/labels{/name}","comments_url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/76/comments","events_url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/76/events","html_url":"https://github.com/cancerit/cgpBattenberg/issues/76","id":303530567,"number":76,"title":"Callsubclones error","user":{"login":"mjz1","id":19936589,"avatar_url":"https://avatars1.githubusercontent.com/u/19936589?v=4","gravatar_id":"","url":"https://api.github.com/users/mjz1","html_url":"https://github.com/mjz1","followers_url":"https://api.github.com/users/mjz1/followers","following_url":"https://api.github.com/users/mjz1/following{/other_user}","gists_url":"https://api.github.com/users/mjz1/gists{/gist_id}","starred_url":"https://api.github.com/users/mjz1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mjz1/subscriptions","organizations_url":"https://api.github.com/users/mjz1/orgs","repos_url":"https://api.github.com/users/mjz1/repos","events_url":"https://api.github.com/users/mjz1/events{/privacy}","received_events_url":"https://api.github.com/users/mjz1/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-03-08T15:54:47Z","updated_at":"2018-03-22T17:18:37Z","closed_at":"2018-03-22T17:18:20Z","author_association":"NONE","body":"Hi there,\r\n\r\nGetting an error in the callsubclones step:\r\nError in t.test.default(logR[logR$Chromosome == subclones$chr[i - 1] &  :\r\n  not enough 'x' observations\r\nCalls: callSubclones -> merge_segments -> t.test -> t.test.default\r\n\r\nNot sure if it is related, but the fitcn step mentions that 'reference segment did not provide a possible solution':\r\n[1] \"ploidy=1.78246500278682,rho=0.81,goodness=84.6365342478127,percentzero=0.292220227244316, perczerAbb=0.292220227244316\"\r\n[1] \"ploidy=3.51630145168029,rho=0.68,goodness=77.8766478542867,percentzero=0.289668502443199, perczerAbb=0.289668502443199\"\r\n[1] \"goodnessOfFit from grid=0.52666849231385\"\r\n[1] \"reference segment did not provide a possible solution\"\r\n\r\nI have this pipeline working for the majority of my samples, but would like to know if there is a way to resolve these sorts of issues. It results in the finalise step failing as it can't find the subclones.txt file. Are these samples for which there is simply no solution? \r\n\r\nAny help would be greatly appreciated! Thanks!"},"comment":{"url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/comments/375387528","html_url":"https://github.com/cancerit/cgpBattenberg/issues/76#issuecomment-375387528","issue_url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/76","id":375387528,"user":{"login":"mjz1","id":19936589,"avatar_url":"https://avatars1.githubusercontent.com/u/19936589?v=4","gravatar_id":"","url":"https://api.github.com/users/mjz1","html_url":"https://github.com/mjz1","followers_url":"https://api.github.com/users/mjz1/followers","following_url":"https://api.github.com/users/mjz1/following{/other_user}","gists_url":"https://api.github.com/users/mjz1/gists{/gist_id}","starred_url":"https://api.github.com/users/mjz1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mjz1/subscriptions","organizations_url":"https://api.github.com/users/mjz1/orgs","repos_url":"https://api.github.com/users/mjz1/repos","events_url":"https://api.github.com/users/mjz1/events{/privacy}","received_events_url":"https://api.github.com/users/mjz1/received_events","type":"User","site_admin":false},"created_at":"2018-03-22T17:18:37Z","updated_at":"2018-03-22T17:18:37Z","author_association":"NONE","body":"Issue is resolved in battenberg R 2.2.8 update."}}
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