{"action":"closed","issue":{"url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/37","labels_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/37/comments","events_url":"https://api.github.com/repos/Ecogenomics/CheckM/issues/37/events","html_url":"https://github.com/Ecogenomics/CheckM/issues/37","id":102465404,"number":37,"title":"Placing bins in reference genome tree problem","user":{"login":"ezaikova","id":13909709,"avatar_url":"https://avatars.githubusercontent.com/u/13909709?v=3","gravatar_id":"","url":"https://api.github.com/users/ezaikova","html_url":"https://github.com/ezaikova","followers_url":"https://api.github.com/users/ezaikova/followers","following_url":"https://api.github.com/users/ezaikova/following{/other_user}","gists_url":"https://api.github.com/users/ezaikova/gists{/gist_id}","starred_url":"https://api.github.com/users/ezaikova/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ezaikova/subscriptions","organizations_url":"https://api.github.com/users/ezaikova/orgs","repos_url":"https://api.github.com/users/ezaikova/repos","events_url":"https://api.github.com/users/ezaikova/events{/privacy}","received_events_url":"https://api.github.com/users/ezaikova/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":7,"created_at":"2015-08-21T21:28:54Z","updated_at":"2015-08-25T00:14:27Z","closed_at":"2015-08-25T00:14:27Z","body":"Hi, \r\n\r\nI am having issues with \"checkm tree\". I installed checkm earlier this week and the \"test\" ran just fine. However, when I tried to analyze my bins, I got the error below. I tried running the \"tree\" command on the test data (which worked for \"test\") and still got the same error.\r\n\r\n*******************************************************************************\r\n [CheckM - tree] Placing bins in reference genome tree.\r\n*******************************************************************************\r\n\r\n  Identifying marker genes in 1 bins with 4 threads:\r\n    Finished processing 1 of 1 (100.00%) bins.\r\n  Saving HMM info to file.\r\n\r\n  Calculating genome statistics for 1 bins with 4 threads:\r\n    Finished processing 1 of 1 (100.00%) bins.\r\n\r\n  Extracting marker genes to align.\r\n  Parsing HMM hits to marker genes:\r\n    Finished parsing hits for 1 of 1 (100.00%) bins.\r\n  Extracting 43 HMMs with 4 threads:\r\n    Finished extracting 43 of 43 (100.00%) HMMs.\r\n  Aligning 43 marker genes with 4 threads:\r\n    Finished aligning 43 of 43 (100.00%) marker genes.\r\n\r\n  Reading marker alignment files.\r\n  Concatenating alignments.\r\n  Placing 1 bins into the genome tree with pplacer (be patient).\r\nKilled\r\nUncaught exception: Sys_error(\"./testOUT/storage/tree/concatenated.pplacer.json: No such file or directory\")\r\nFatal error: exception Sys_error(\"./testOUT/storage/tree/concatenated.pplacer.json: No such file or directory\")\r\n\r\n  { Current stage: 0:21:44.524 || Total: 0:21:44.524 }\r\n\r\n\r\nI tried updating the CheckM dependency data with \"sudo checkm data update\", which didn't help, so then I downloaded the CheckM data (v1.0.3) and used \"sudo checkm data setRoot\" to point to the new directory. I still got the same error. \r\n\r\nI am not sure if the issue is in my installation or if something is missing.\r\n\r\nBest, \r\n\r\nElena"}}