{"action":"created","issue":{"url":"https://api.github.com/repos/pcingola/BigDataScript/issues/114","labels_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/114/labels{/name}","comments_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/114/comments","events_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/114/events","html_url":"https://github.com/pcingola/BigDataScript/issues/114","id":109662946,"number":114,"title":"qstat not found in starcluster created cluster, but qstat is in path.","user":{"login":"golharam","id":671079,"avatar_url":"https://avatars.githubusercontent.com/u/671079?v=3","gravatar_id":"","url":"https://api.github.com/users/golharam","html_url":"https://github.com/golharam","followers_url":"https://api.github.com/users/golharam/followers","following_url":"https://api.github.com/users/golharam/following{/other_user}","gists_url":"https://api.github.com/users/golharam/gists{/gist_id}","starred_url":"https://api.github.com/users/golharam/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/golharam/subscriptions","organizations_url":"https://api.github.com/users/golharam/orgs","repos_url":"https://api.github.com/users/golharam/repos","events_url":"https://api.github.com/users/golharam/events{/privacy}","received_events_url":"https://api.github.com/users/golharam/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":25,"created_at":"2015-10-04T04:47:02Z","updated_at":"2015-10-16T17:18:56Z","closed_at":null,"body":"java.lang.RuntimeException: Cannot execute commnads: 'qstat -f -j 969'\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.osCmd.Exec.run(Exec.java:80)\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.osCmd.Exec.exec(Exec.java:37)\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.executioner.ExecutionerCluster.postMortemInfo(ExecutionerCluster.java:343)\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.executioner.Executioner.taskUpdateFinished(Executioner.java:717)\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.executioner.Executioner.taskUpdateStates(Executioner.java:778)\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.executioner.Executioner.reportsChecksUpdates(Executioner.java:304)\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.executioner.Executioner.runExecutionerLoop(Executioner.java:426)\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.executioner.Executioner.runExecutioner(Executioner.java:383)\r\n        at ca.mcgill.mcb.pcingola.bigDataScript.executioner.Executioner.run(Executioner.java:367)\r\n"},"comment":{"url":"https://api.github.com/repos/pcingola/BigDataScript/issues/comments/148776759","html_url":"https://github.com/pcingola/BigDataScript/issues/114#issuecomment-148776759","issue_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/114","id":148776759,"user":{"login":"pcingola","id":1334427,"avatar_url":"https://avatars.githubusercontent.com/u/1334427?v=3","gravatar_id":"","url":"https://api.github.com/users/pcingola","html_url":"https://github.com/pcingola","followers_url":"https://api.github.com/users/pcingola/followers","following_url":"https://api.github.com/users/pcingola/following{/other_user}","gists_url":"https://api.github.com/users/pcingola/gists{/gist_id}","starred_url":"https://api.github.com/users/pcingola/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pcingola/subscriptions","organizations_url":"https://api.github.com/users/pcingola/orgs","repos_url":"https://api.github.com/users/pcingola/repos","events_url":"https://api.github.com/users/pcingola/events{/privacy}","received_events_url":"https://api.github.com/users/pcingola/received_events","type":"User","site_admin":false},"created_at":"2015-10-16T17:18:56Z","updated_at":"2015-10-16T17:18:56Z","body":"\r\nRyan,\r\n   Let me repeat once more. What I need is: i) a minimal script that I can run in a similar setting and can reproduce the error condition; ii) a log file from your run of that minimal script. If you scripts runs on SGE, then your command line should add the proper \"-s sge\" options (similarly, I don't expect your script to be named 'minimal_script.bds', it can certainly have another name). I'm giving general guidelines as opposed to specific commands for you to copy&paste because I assume you are knowledgable and intelligent enough to understand this.\r\n   The standard way to capture the STDOUT and STDERR when running a unix command is to use \"> log.txt 2>&1\". If you don't know how to do this, please get advise from someone who has minimal knowledge of unix command line. Again, the output file does not have to be called 'log.txt', you can use another name.\r\n   The way to create a minimal script is to remove all \"non-error causing code\" and replace 'task' by simple statements that still capture the error condition.\r\n   I'm not asking for all this just to make your life miserable, I'm doing it in order to be able to replicate the error condition and then debug the problem.\r\n   Yours\r\n\r\n     Pablo\r\n\r\n\r\n"}}