{"action":"created","issue":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/205","repository_url":"https://api.github.com/repos/compomics/peptide-shaker","labels_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/205/labels{/name}","comments_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/205/comments","events_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/205/events","html_url":"https://github.com/compomics/peptide-shaker/issues/205","id":178954268,"number":205,"title":"-log option not processed?","user":{"login":"paulstodghill","id":18268434,"avatar_url":"https://avatars.githubusercontent.com/u/18268434?v=3","gravatar_id":"","url":"https://api.github.com/users/paulstodghill","html_url":"https://github.com/paulstodghill","followers_url":"https://api.github.com/users/paulstodghill/followers","following_url":"https://api.github.com/users/paulstodghill/following{/other_user}","gists_url":"https://api.github.com/users/paulstodghill/gists{/gist_id}","starred_url":"https://api.github.com/users/paulstodghill/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/paulstodghill/subscriptions","organizations_url":"https://api.github.com/users/paulstodghill/orgs","repos_url":"https://api.github.com/users/paulstodghill/repos","events_url":"https://api.github.com/users/paulstodghill/events{/privacy}","received_events_url":"https://api.github.com/users/paulstodghill/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/compomics/peptide-shaker/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":{"login":"hbarsnes","id":13151214,"avatar_url":"https://avatars.githubusercontent.com/u/13151214?v=3","gravatar_id":"","url":"https://api.github.com/users/hbarsnes","html_url":"https://github.com/hbarsnes","followers_url":"https://api.github.com/users/hbarsnes/followers","following_url":"https://api.github.com/users/hbarsnes/following{/other_user}","gists_url":"https://api.github.com/users/hbarsnes/gists{/gist_id}","starred_url":"https://api.github.com/users/hbarsnes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hbarsnes/subscriptions","organizations_url":"https://api.github.com/users/hbarsnes/orgs","repos_url":"https://api.github.com/users/hbarsnes/repos","events_url":"https://api.github.com/users/hbarsnes/events{/privacy}","received_events_url":"https://api.github.com/users/hbarsnes/received_events","type":"User","site_admin":false},"assignees":[{"login":"hbarsnes","id":13151214,"avatar_url":"https://avatars.githubusercontent.com/u/13151214?v=3","gravatar_id":"","url":"https://api.github.com/users/hbarsnes","html_url":"https://github.com/hbarsnes","followers_url":"https://api.github.com/users/hbarsnes/followers","following_url":"https://api.github.com/users/hbarsnes/following{/other_user}","gists_url":"https://api.github.com/users/hbarsnes/gists{/gist_id}","starred_url":"https://api.github.com/users/hbarsnes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hbarsnes/subscriptions","organizations_url":"https://api.github.com/users/hbarsnes/orgs","repos_url":"https://api.github.com/users/hbarsnes/repos","events_url":"https://api.github.com/users/hbarsnes/events{/privacy}","received_events_url":"https://api.github.com/users/hbarsnes/received_events","type":"User","site_admin":false}],"milestone":null,"comments":3,"created_at":"2016-09-23T19:20:51Z","updated_at":"2016-09-27T14:41:19Z","closed_at":"2016-09-27T14:41:19Z","body":"I tried to change the directory into which logs are written using the \"-log\" option. This results in a error message that -log option isn't recognized.\r\n\r\nHere's what the -help message says,\r\n\r\n```\r\nOptional Log Folder:\r\n\r\n-log                                 Folder where to write logs.\r\n\r\n```\r\nHere's what happens,\r\n\r\n```\r\ndaffy$ java -Djava.awt.headless=true -Xmx4g -cp /storage/ps27/work/projects/proteomic-pipeline/bin/../lib/PeptideShaker/PeptideShaker-1.13.3.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -log .\r\n<CompomicsError>PeptideShaker processing failed. See the PeptideShaker log for details.</CompomicsError>\r\norg.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -log\r\n        at org.apache.commons.cli.Parser.processOption(Parser.java:363)\r\n        at org.apache.commons.cli.Parser.parse(Parser.java:199)\r\n        at org.apache.commons.cli.Parser.parse(Parser.java:85)\r\n        at eu.isas.peptideshaker.cmd.PeptideShakerCLI.main(PeptideShakerCLI.java:928)\r\ndaffy$ \r\n```\r\n\r\nThanks!"},"comment":{"url":"https://api.github.com/repos/compomics/peptide-shaker/issues/comments/249885386","html_url":"https://github.com/compomics/peptide-shaker/issues/205#issuecomment-249885386","issue_url":"https://api.github.com/repos/compomics/peptide-shaker/issues/205","id":249885386,"user":{"login":"hbarsnes","id":13151214,"avatar_url":"https://avatars.githubusercontent.com/u/13151214?v=3","gravatar_id":"","url":"https://api.github.com/users/hbarsnes","html_url":"https://github.com/hbarsnes","followers_url":"https://api.github.com/users/hbarsnes/followers","following_url":"https://api.github.com/users/hbarsnes/following{/other_user}","gists_url":"https://api.github.com/users/hbarsnes/gists{/gist_id}","starred_url":"https://api.github.com/users/hbarsnes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hbarsnes/subscriptions","organizations_url":"https://api.github.com/users/hbarsnes/orgs","repos_url":"https://api.github.com/users/hbarsnes/repos","events_url":"https://api.github.com/users/hbarsnes/events{/privacy}","received_events_url":"https://api.github.com/users/hbarsnes/received_events","type":"User","site_admin":false},"created_at":"2016-09-27T14:41:18Z","updated_at":"2016-09-27T14:41:18Z","body":"Hi Paul,\r\n\r\nWe've just released PeptideShaker v1.13.4 which should fix this issue. If this is not the case please let us know and we'll reopen the issue.\r\n\r\nBest regards,\r\nHarald"}}
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