{"action":"created","issue":{"url":"https://api.github.com/repos/PeeperLab/CopywriteR/issues/5","labels_url":"https://api.github.com/repos/PeeperLab/CopywriteR/issues/5/labels{/name}","comments_url":"https://api.github.com/repos/PeeperLab/CopywriteR/issues/5/comments","events_url":"https://api.github.com/repos/PeeperLab/CopywriteR/issues/5/events","html_url":"https://github.com/PeeperLab/CopywriteR/issues/5","id":91818090,"number":5,"title":"SSH error upon run ","user":{"login":"jdeligt","id":5850879,"avatar_url":"https://avatars.githubusercontent.com/u/5850879?v=3","gravatar_id":"","url":"https://api.github.com/users/jdeligt","html_url":"https://github.com/jdeligt","followers_url":"https://api.github.com/users/jdeligt/followers","following_url":"https://api.github.com/users/jdeligt/following{/other_user}","gists_url":"https://api.github.com/users/jdeligt/gists{/gist_id}","starred_url":"https://api.github.com/users/jdeligt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jdeligt/subscriptions","organizations_url":"https://api.github.com/users/jdeligt/orgs","repos_url":"https://api.github.com/users/jdeligt/repos","events_url":"https://api.github.com/users/jdeligt/events{/privacy}","received_events_url":"https://api.github.com/users/jdeligt/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-06-29T14:20:26Z","updated_at":"2015-06-30T11:19:41Z","closed_at":null,"body":"Script start normally;\r\n> The bin size for this analysis is 15000\r\n> The capture region file is not specified\r\n> This analysis will be run on 6 cpus\r\n\r\nBut then gives an ssh error:\r\n> ssh: connect to host 6 port 22: Invalid argument\r\n\r\nThe host that is reported is the same as the number of cpus specified.\r\ni.e if I run it with 12 CPUs it tries to connect to host 12\r\n\r\nI can't find any code relating to ssh in the CopywriteR package.\r\n\r\nI'm running under R 3.1.3 and followed your installation guide.\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/PeeperLab/CopywriteR/issues/comments/117128973","html_url":"https://github.com/PeeperLab/CopywriteR/issues/5#issuecomment-117128973","issue_url":"https://api.github.com/repos/PeeperLab/CopywriteR/issues/5","id":117128973,"user":{"login":"thomasKuilman","id":8489622,"avatar_url":"https://avatars.githubusercontent.com/u/8489622?v=3","gravatar_id":"","url":"https://api.github.com/users/thomasKuilman","html_url":"https://github.com/thomasKuilman","followers_url":"https://api.github.com/users/thomasKuilman/followers","following_url":"https://api.github.com/users/thomasKuilman/following{/other_user}","gists_url":"https://api.github.com/users/thomasKuilman/gists{/gist_id}","starred_url":"https://api.github.com/users/thomasKuilman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thomasKuilman/subscriptions","organizations_url":"https://api.github.com/users/thomasKuilman/orgs","repos_url":"https://api.github.com/users/thomasKuilman/repos","events_url":"https://api.github.com/users/thomasKuilman/events{/privacy}","received_events_url":"https://api.github.com/users/thomasKuilman/received_events","type":"User","site_admin":false},"created_at":"2015-06-30T11:19:41Z","updated_at":"2015-06-30T11:19:41Z","body":"Hi Joep,\r\n\r\nNope, still not. Maybe it is better to send it to my work mail: t.kuilman@nki.nl<mailto:t.kuilman@nki.nl>.\r\n\r\nBest,\r\n\r\nThomas\r\n\r\n\r\n--------------------------------------------------\r\nThomas Kuilman, PhD\r\nDepartment of Molecular Oncology\r\nNetherlands Cancer Institute\r\n1066 CX Amsterdam\r\nThe Netherlands\r\n\r\nPhone: +31-20-5121841\r\n\r\nOn 30 Jun 2015, at 12:34, Joep de Ligt <notifications@github.com<mailto:notifications@github.com>> wrote:\r\n\r\nhow about now?\r\nJoep\r\n\r\n\r\nOn 30 Jun 2015, at 11:13, thomasKuilman <notifications@github.com<mailto:notifications@github.com>> wrote:\r\n\r\n> Hi Joep,\r\n>\r\n> You did not add any attachment…\r\n>\r\n> Thomas\r\n>\r\n>\r\n> --------------------------------------------------\r\n> Thomas Kuilman, PhD\r\n> Department of Molecular Oncology\r\n> Netherlands Cancer Institute\r\n> 1066 CX Amsterdam\r\n> The Netherlands\r\n>\r\n> Phone: +31-20-5121841\r\n>\r\n> On 30 Jun 2015, at 10:10, Joep de Ligt <notifications@github.com<mailto:notifications@github.com><mailto:notifications@github.com>> wrote:\r\n>\r\n> Hi Thomas,\r\n>\r\n> Thanks for the quick reply.\r\n> I am not trying to paralyse over ssh, I' only using that to log on to the server.\r\n> The server does not have separate compute nodes or any other exotic configurations.\r\n> The script I use to run CopywriteR is attached.\r\n>\r\n> Cheers,\r\n>\r\n> Joep\r\n>\r\n>\r\n>\r\n>\r\n>\r\n> On 29 Jun 2015, at 22:38, thomasKuilman <notifications@github.com<mailto:notifications@github.com><mailto:notifications@github.com>> wrote:\r\n>\r\n> > Hi Joep,\r\n> >\r\n> > Thanks for your interest in copywriter. I have never seen your error before, but I guess it has something to do with the way in which CopywriteR is trying to perform parallel computing. Is it true that you are trying to parallelise via ssh? You might want to try another mode of parallel computing. Otherwise, I am not entirely sure how to fix this, but if you send me how you run CopywriteR in detail and the CopywriteR.log file I will have a look at them to see if there�s any clue there. In any case, if you solve the problem could you please let me know for other users?\r\n> >\r\n> > Best,\r\n> >\r\n> > Thomas\r\n> >\r\n> >\r\n> > --------------------------------------------------\r\n> > Thomas Kuilman, PhD\r\n> > Department of Molecular Oncology\r\n> > Netherlands Cancer Institute\r\n> > 1066 CX Amsterdam\r\n> > The Netherlands\r\n> >\r\n> > Phone: +31-20-5121841\r\n> >\r\n> > On 29 Jun 2015, at 16:20, Joep de Ligt <notifications@github.com<mailto:notifications@github.com><mailto:notifications@github.com><mailto:notifications@github.com>> wrote:\r\n> >\r\n> >\r\n> > Script start normally;\r\n> >\r\n> > The bin size for this analysis is 15000\r\n> > The capture region file is not specified\r\n> > This analysis will be run on 6 cpus\r\n> >\r\n> > But then gives an ssh error:\r\n> >\r\n> > ssh: connect to host 6 port 22: Invalid argument\r\n> >\r\n> > The host that is reported is the same as the number of cpus specified.\r\n> > i.e if I run it with 12 CPUs it tries to connect to host 12\r\n> >\r\n> > I can't find any code relating to ssh in the CopywriteR package.\r\n> >\r\n> > �\r\n> > Reply to this email directly or view it on GitHub<https://github.com/PeeperLab/CopywriteR/issues/5>.\r\n> >\r\n> > —\r\n> > Reply to this email directly or view it on GitHub.\r\n> >\r\n>\r\n>\r\n> —\r\n> Reply to this email directly or view it on GitHub<https://github.com/PeeperLab/CopywriteR/issues/5#issuecomment-117050589>.\r\n>\r\n> —\r\n> Reply to this email directly or view it on GitHub.\r\n>\r\n\r\n\r\n—\r\nReply to this email directly or view it on GitHub<https://github.com/PeeperLab/CopywriteR/issues/5#issuecomment-117118201>.\r\n\r\n"}}