{"action":"closed","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/805","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/805/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/805/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/805/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/805","id":64982838,"number":805,"title":"sge queue adds .q suffix which isn't recognized","user":{"login":"dwaggott","id":3149944,"avatar_url":"https://avatars.githubusercontent.com/u/3149944?v=3","gravatar_id":"","url":"https://api.github.com/users/dwaggott","html_url":"https://github.com/dwaggott","followers_url":"https://api.github.com/users/dwaggott/followers","following_url":"https://api.github.com/users/dwaggott/following{/other_user}","gists_url":"https://api.github.com/users/dwaggott/gists{/gist_id}","starred_url":"https://api.github.com/users/dwaggott/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dwaggott/subscriptions","organizations_url":"https://api.github.com/users/dwaggott/orgs","repos_url":"https://api.github.com/users/dwaggott/repos","events_url":"https://api.github.com/users/dwaggott/events{/privacy}","received_events_url":"https://api.github.com/users/dwaggott/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-03-28T20:15:51Z","updated_at":"2015-03-30T09:13:53Z","closed_at":"2015-03-30T09:13:53Z","body":"\r\nI'm working on getting bcbio running on a second sge cluster. The first pipeline is gatk joint calling on 4 whole genomes.\r\n\r\nIt seems to be getting stuck on my queue specification i.e. `-q extended`. From the logs it might be due to the addition of the q suffix `extended.q` which doesn't exist.\r\n\r\n```\r\n# sge submission\r\nqsub -q extended -cwd -w e -V -N tk_call_variants_gatk_joint \\\r\n   -l h_vmem=20G -l h_rt=168:00:00 -l s_rt=168:00:00 -pe shm 2 \\\r\n   -o /home/dwaggott/ashley1/tk/results/bcbio/tk_gatk_joint/ -e /home/dwaggott/ashley1/tk/results/bcbio/tk_gatk_joint/ \\\r\n   -b Y 'module load python/2.7 r/3.1.1 perl-scg/1.0;cd ../results/bcbio/tk_gatk_joint/work/;bcbio_nextgen.py --timeout 10000 --retries 2 ../config/tk_gatk_joint.yaml  -t ipython -n 160 -q extended -s sge -r \"timelimit=2-00:00:00\" -r \"conmem=6\"'\r\n\r\n```\r\n\r\n```\r\n# log\r\n[2015-03-28T20:00Z] scg3-1-3.local: Resource requests: bwa, sambamba, samtools; memory: 2.00; cores: 16, 1, 16\r\n[2015-03-28T20:00Z] scg3-1-3.local: Configuring 4 jobs to run, using 12 cores each with 24.1g of memory reserved for each job\r\nNo cluster queue or queue instance matches the phrase \"extended.q\"\r\n2015-03-28 13:00:04.048 [IPClusterStart] Config changed:\r\n2015-03-28 13:00:04.048 [IPClusterStart] {'ProfileDir': {'location': u'/srv/gs1/projects/ashley/tk/results/bcbio/tk_gatk_joint/work/log/ipython'}, 'SGELauncher': {'queue': 'extended'}, 'BcbioSGEEngineSetL\r\n2015-03-28 13:00:04.055 [IPClusterStart] Using existing profile dir: u'/srv/gs1/projects/ashley/tk/results/bcbio/tk_gatk_joint/work/log/ipython'\r\n2015-03-28 13:00:04.055 [IPClusterStart] Searching path [u'/srv/gs1/projects/ashley/tk/results/bcbio/tk_gatk_joint/work', u'/srv/gs1/projects/ashley/tk/results/bcbio/tk_gatk_joint/work/log/ipython', '/usr\r\n2015-03-28 13:00:04.055 [IPClusterStart] Attempting to load config file: ipython_config.py\r\n2015-03-28 13:00:04.056 [IPClusterStart] Loaded config file: /srv/gs1/projects/ashley/tk/results/bcbio/tk_gatk_joint/work/log/ipython/ipython_config.py\r\n2015-03-28 13:00:04.056 [IPClusterStart] Attempting to load config file: ipcluster_9facd73b_758a_46bb_b95b_09354c7a010c_config.py\r\n2015-03-28 13:00:04.057 [IPClusterStart] Loaded config file: /srv/gs1/projects/ashley/tk/results/bcbio/tk_gatk_joint/work/log/ipython/ipcontroller_config.py\r\n2015-03-28 13:00:04.057 [IPClusterStart] Attempting to load config file: ipcluster_9facd73b_758a_46bb_b95b_09354c7a010c_config.py\r\n2015-03-28 13:00:04.058 [IPClusterStart] Loaded config file: /srv/gs1/projects/ashley/tk/results/bcbio/tk_gatk_joint/work/log/ipython/ipengine_config.py\r\n2015-03-28 13:00:04.058 [IPClusterStart] Attempting to load config file: ipcluster_9facd73b_758a_46bb_b95b_09354c7a010c_config.py\r\n2015-03-28 13:00:04.059 [IPClusterStart] Loaded config file: /srv/gs1/projects/ashley/tk/results/bcbio/tk_gatk_joint/work/log/ipython/ipcluster_config.py\r\n```"}}