{"action":"created","issue":{"url":"https://api.github.com/repos/cBio/cbio-cluster/issues/259","labels_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/259/labels{/name}","comments_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/259/comments","events_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/259/events","html_url":"https://github.com/cBio/cbio-cluster/issues/259","id":78582017,"number":259,"title":"problem with qsub","user":{"login":"qwangmsk","id":11812514,"avatar_url":"https://avatars.githubusercontent.com/u/11812514?v=3","gravatar_id":"","url":"https://api.github.com/users/qwangmsk","html_url":"https://github.com/qwangmsk","followers_url":"https://api.github.com/users/qwangmsk/followers","following_url":"https://api.github.com/users/qwangmsk/following{/other_user}","gists_url":"https://api.github.com/users/qwangmsk/gists{/gist_id}","starred_url":"https://api.github.com/users/qwangmsk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/qwangmsk/subscriptions","organizations_url":"https://api.github.com/users/qwangmsk/orgs","repos_url":"https://api.github.com/users/qwangmsk/repos","events_url":"https://api.github.com/users/qwangmsk/events{/privacy}","received_events_url":"https://api.github.com/users/qwangmsk/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":6,"created_at":"2015-05-20T15:58:29Z","updated_at":"2015-05-20T17:48:56Z","closed_at":null,"body":"Hi, I ran the following command trying to submit a job to hal. I received this error after keying in the command: \"[index issues]\". I wonder what does it mean and how to fix it.\r\n \r\nqsub -q batch -l walltime=24:00:00 -l nodes=1:ppn=8 -l mem=20G -d ~/studies/tcga/BLCA/0 -o job0.output.txt ~/scripts/calc-expression.pl 1.fastq.gz 2.fastq.gz\r\n\r\nMany thanks\r\nQingguo"},"comment":{"url":"https://api.github.com/repos/cBio/cbio-cluster/issues/comments/103972672","html_url":"https://github.com/cBio/cbio-cluster/issues/259#issuecomment-103972672","issue_url":"https://api.github.com/repos/cBio/cbio-cluster/issues/259","id":103972672,"user":{"login":"tatarsky","id":6439722,"avatar_url":"https://avatars.githubusercontent.com/u/6439722?v=3","gravatar_id":"","url":"https://api.github.com/users/tatarsky","html_url":"https://github.com/tatarsky","followers_url":"https://api.github.com/users/tatarsky/followers","following_url":"https://api.github.com/users/tatarsky/following{/other_user}","gists_url":"https://api.github.com/users/tatarsky/gists{/gist_id}","starred_url":"https://api.github.com/users/tatarsky/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tatarsky/subscriptions","organizations_url":"https://api.github.com/users/tatarsky/orgs","repos_url":"https://api.github.com/users/tatarsky/repos","events_url":"https://api.github.com/users/tatarsky/events{/privacy}","received_events_url":"https://api.github.com/users/tatarsky/received_events","type":"User","site_admin":false},"created_at":"2015-05-20T17:48:56Z","updated_at":"2015-05-20T17:48:56Z","body":"I would simply place: \r\n```\r\n~/scripts/calc-expression.pl 1.fastq.gz 2.fastq.gz\r\n```\r\n\r\nInto a submit script. \r\n\r\nI don't believe qsub takes its script arguments that way but I could be wrong. \r\n"}}