{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/57","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/57/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/57/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/57/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/57","id":71727780,"number":57,"title":"unable to run fc_run.py on SGE","user":{"login":"mahulchak","id":7537640,"avatar_url":"https://avatars.githubusercontent.com/u/7537640?v=3","gravatar_id":"","url":"https://api.github.com/users/mahulchak","html_url":"https://github.com/mahulchak","followers_url":"https://api.github.com/users/mahulchak/followers","following_url":"https://api.github.com/users/mahulchak/following{/other_user}","gists_url":"https://api.github.com/users/mahulchak/gists{/gist_id}","starred_url":"https://api.github.com/users/mahulchak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mahulchak/subscriptions","organizations_url":"https://api.github.com/users/mahulchak/orgs","repos_url":"https://api.github.com/users/mahulchak/repos","events_url":"https://api.github.com/users/mahulchak/events{/privacy}","received_events_url":"https://api.github.com/users/mahulchak/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-04-28T22:48:31Z","updated_at":"2015-04-30T19:53:44Z","closed_at":null,"body":"Hi,\r\nI am trying to run Falcon on SGE. I have a cfg file that is similar to the generic cfg file you have provided. However, I can't find the information on how to provide the job_type, sge_option for the pipeline. I tried entering them in the cfg file but the script prepare_db.sh that the first command generates in the 0-rawreads folder is not submitted to the grid by the pipeline. Am I missing something? I am appending first part of my cfg file for your convenience :\r\n\r\n[General]\r\njob_type = SGE\r\njob_name = tes\r\nsge_option = -q bio -ckpt blcr -l kernel=blcr \r\n# list of files of the initial subread fasta files\r\ninput_fofn = input.fofn\r\n#input_fofn = preads.fofn\r\n\r\ninput_type = raw\r\n#input_type = preads\r\n\r\n# The length cutoff used for seed reads used for initial mapping\r\nlength_cutoff = 12000\r\n\r\n# The length cutoff used for seed reads usef for pre-assembly\r\nlength_cutoff_pr = 12000\r\n\r\nThanks.\r\nMahul"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/97948355","html_url":"https://github.com/PacificBiosciences/FALCON/issues/57#issuecomment-97948355","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/57","id":97948355,"user":{"login":"mahulchak","id":7537640,"avatar_url":"https://avatars.githubusercontent.com/u/7537640?v=3","gravatar_id":"","url":"https://api.github.com/users/mahulchak","html_url":"https://github.com/mahulchak","followers_url":"https://api.github.com/users/mahulchak/followers","following_url":"https://api.github.com/users/mahulchak/following{/other_user}","gists_url":"https://api.github.com/users/mahulchak/gists{/gist_id}","starred_url":"https://api.github.com/users/mahulchak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mahulchak/subscriptions","organizations_url":"https://api.github.com/users/mahulchak/orgs","repos_url":"https://api.github.com/users/mahulchak/repos","events_url":"https://api.github.com/users/mahulchak/events{/privacy}","received_events_url":"https://api.github.com/users/mahulchak/received_events","type":"User","site_admin":false},"created_at":"2015-04-30T19:53:44Z","updated_at":"2015-04-30T19:53:44Z","body":"Thanks for the quick response. I spoke with the sys admins and they asked me if python virtual env is absolutely necessary for the pipeline to work. We are trying to figure out why automated job submission by the pipeline is not working. The admins want me to try the pipeline without the virtual env so the information about whether python virtual env is necessary or not will be helpful. "}}