{"action":"closed","issue":{"url":"https://api.github.com/repos/mothur/mothur/issues/139","labels_url":"https://api.github.com/repos/mothur/mothur/issues/139/labels{/name}","comments_url":"https://api.github.com/repos/mothur/mothur/issues/139/comments","events_url":"https://api.github.com/repos/mothur/mothur/issues/139/events","html_url":"https://github.com/mothur/mothur/issues/139","id":99756871,"number":139,"title":"set.dir not working correctly","user":{"login":"tracykteal","id":889238,"avatar_url":"https://avatars.githubusercontent.com/u/889238?v=3","gravatar_id":"","url":"https://api.github.com/users/tracykteal","html_url":"https://github.com/tracykteal","followers_url":"https://api.github.com/users/tracykteal/followers","following_url":"https://api.github.com/users/tracykteal/following{/other_user}","gists_url":"https://api.github.com/users/tracykteal/gists{/gist_id}","starred_url":"https://api.github.com/users/tracykteal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tracykteal/subscriptions","organizations_url":"https://api.github.com/users/tracykteal/orgs","repos_url":"https://api.github.com/users/tracykteal/repos","events_url":"https://api.github.com/users/tracykteal/events{/privacy}","received_events_url":"https://api.github.com/users/tracykteal/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-08-08T01:08:54Z","updated_at":"2015-08-11T17:46:22Z","closed_at":"2015-08-11T17:46:22Z","body":"There seems to be something with set.dir where if you run it more than once, then it won't set the directories the second time you run it. It will output that you did it, but if you look at get.current() you can see that it's not set. \r\n\r\nDetails below. \r\n\r\ne.g. \r\n\r\nmothur > set.dir(input=../data/MiSeq_SOP)\r\nMothur's directories:\r\ninputDir=/Users/tracyt/Desktop/mothur-project/data/MiSeq_SOP/\r\n\r\nmothur > set.dir(output=../analyses/)\r\nMothur's directories:\r\noutputDir=/Users/tracyt/Desktop/mothur-project/analyses/\r\n\r\nmothur > get.current()\r\n\r\nCurrent files saved by mothur:\r\n\r\nCurrent output directory saved by mothur: /Users/tracyt/Desktop/mothur-project/analyses/\r\n\r\nCurrent default directory saved by mothur: ./\r\n\r\nCurrent working directory: /Users/tracyt/Desktop/mothur-project/mothur/\r\n\r\nThen gives:\r\n\r\nmothur > make.contigs(file=stability.files, processors=8)\r\nUnable to open stability.files. Trying default ./stability.files\r\nUnable to open ./stability.files. Trying output directory /Users/tracyt/Desktop/mothur-project/analyses/stability.files\r\nUnable to open /Users/tracyt/Desktop/mothur-project/analyses/stability.files\r\n\r\nBut if I set the output dir and then the input dir, then I get \r\n\r\nget.current()\r\n\r\nmothur > get.current()\r\n\r\nCurrent input directory saved by mothur: /Users/tracyt/Desktop/mothur-project/data/MiSeq_SOP/\r\n\r\nCurrent default directory saved by mothur: ./\r\n\r\nCurrent working directory: /Users/tracyt/Desktop/mothur-project/mothur/\r\n\r\nThen, make.contigs(file=stability.files, processors=8) works, but it writes the files out to the input directory.\r\n"}}