{"action":"created","issue":{"url":"https://api.github.com/repos/veg/hyphy/issues/316","labels_url":"https://api.github.com/repos/veg/hyphy/issues/316/labels{/name}","comments_url":"https://api.github.com/repos/veg/hyphy/issues/316/comments","events_url":"https://api.github.com/repos/veg/hyphy/issues/316/events","html_url":"https://github.com/veg/hyphy/issues/316","id":97500225,"number":316,"title":"Running MEME on the sever","user":{"login":"TashyK","id":13521013,"avatar_url":"https://avatars.githubusercontent.com/u/13521013?v=3","gravatar_id":"","url":"https://api.github.com/users/TashyK","html_url":"https://github.com/TashyK","followers_url":"https://api.github.com/users/TashyK/followers","following_url":"https://api.github.com/users/TashyK/following{/other_user}","gists_url":"https://api.github.com/users/TashyK/gists{/gist_id}","starred_url":"https://api.github.com/users/TashyK/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TashyK/subscriptions","organizations_url":"https://api.github.com/users/TashyK/orgs","repos_url":"https://api.github.com/users/TashyK/repos","events_url":"https://api.github.com/users/TashyK/events{/privacy}","received_events_url":"https://api.github.com/users/TashyK/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/veg/hyphy/labels/Bug","name":"Bug","color":"e10c02"},{"url":"https://api.github.com/repos/veg/hyphy/labels/How-tos","name":"How-tos","color":"c7def8"}],"state":"open","locked":false,"assignee":{"login":"spond","id":1018513,"avatar_url":"https://avatars.githubusercontent.com/u/1018513?v=3","gravatar_id":"","url":"https://api.github.com/users/spond","html_url":"https://github.com/spond","followers_url":"https://api.github.com/users/spond/followers","following_url":"https://api.github.com/users/spond/following{/other_user}","gists_url":"https://api.github.com/users/spond/gists{/gist_id}","starred_url":"https://api.github.com/users/spond/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/spond/subscriptions","organizations_url":"https://api.github.com/users/spond/orgs","repos_url":"https://api.github.com/users/spond/repos","events_url":"https://api.github.com/users/spond/events{/privacy}","received_events_url":"https://api.github.com/users/spond/received_events","type":"User","site_admin":false},"milestone":null,"comments":15,"created_at":"2015-07-27T16:16:16Z","updated_at":"2015-08-12T09:33:43Z","closed_at":null,"body":"Hi \r\n\r\nI have another question. I am trying to run MEME on the university server (for which a FUBAR analysis worked). I have the following script to direct the software what to do:\r\n\r\ninputRedirect = {};\r\ninputRedirect[\"01\"]=\"/scratch/akoch/NEWDATA/ResequencingRun/MEME/test/input/E_FUBARComplementAlign_renameRC_final.fas\";\r\ninputRedirect[\"02\"]=\"010010\";\r\ninputRedirect[\"03\"]=\"General Discrete\";\r\ninputRedirect[\"04\"]=\"3\";\r\ninputRedirect[\"05\"]=\"/scratch/akoch/NEWDATA/ResequencingRun/MEME/test/output/E_FUBARComplementAlign_renameRC_final.fas_meme_out\";\r\nExecuteAFile(\"/scratch/akoch/NEWDATA/ResequencingRun/MEME/test/bfiles/MEME_mf.bf\",inputRedirect);\r\n\r\nI've also asked the server administrator to update hyphyMPI to the current version to see if that would help. But I have a feeling there may be a problem with some of my parameters - it was amended for me from a similar GARD script. \r\n\r\nI'm very new to this so any advice would be greatly appreciated. \r\n\r\nMany thanks\r\nTasha\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/veg/hyphy/issues/comments/130236449","html_url":"https://github.com/veg/hyphy/issues/316#issuecomment-130236449","issue_url":"https://api.github.com/repos/veg/hyphy/issues/316","id":130236449,"user":{"login":"TashyK","id":13521013,"avatar_url":"https://avatars.githubusercontent.com/u/13521013?v=3","gravatar_id":"","url":"https://api.github.com/users/TashyK","html_url":"https://github.com/TashyK","followers_url":"https://api.github.com/users/TashyK/followers","following_url":"https://api.github.com/users/TashyK/following{/other_user}","gists_url":"https://api.github.com/users/TashyK/gists{/gist_id}","starred_url":"https://api.github.com/users/TashyK/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TashyK/subscriptions","organizations_url":"https://api.github.com/users/TashyK/orgs","repos_url":"https://api.github.com/users/TashyK/repos","events_url":"https://api.github.com/users/TashyK/events{/privacy}","received_events_url":"https://api.github.com/users/TashyK/received_events","type":"User","site_admin":false},"created_at":"2015-08-12T09:33:43Z","updated_at":"2015-08-12T09:33:43Z","body":"Hi Sergei\n\nI would greatly appreciate that. Thank you so much.\n\nI just tried to send the files via attachment but they are too large.\n\nSee below for a dropbox link to the codon alignment in fasta format, and\nthe tree in newick format.\n\nhttps://www.dropbox.com/s/5amz3nq6bcilsek/E_FUBARComplementAlign_renameRC_final.fas?dl=0\nhttps://www.dropbox.com/s/tf4kmcp11b2iwnr/E_FUBARComplementAlign_renameRC_final.nwk?dl=0\n\nMany thanks\nTasha\n\n\n\nOn 11 August 2015 at 20:14, Sergei Pond <notifications@github.com> wrote:\n\n> Hi Tasha,\n>\n> Can you send me your alignment / trees? I'll try to debug on our local\n> cluster. Of course I will keep your data confidential and will delete them\n> when the problem has been resolved.\n>\n> Sergei\n>\n> —\n> Reply to this email directly or view it on GitHub\n> <https://github.com/veg/hyphy/issues/316#issuecomment-130000458>.\n>\n"}}