{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/18","labels_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/18/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/18/comments","events_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/18/events","html_url":"https://github.com/PacificBiosciences/cDNA_primer/issues/18","id":118964636,"number":18,"title":"P_IsoSeqCluster/cluster OSError: [Errno 2] No such file or directory: '..data/clusterOutDir/scripts/gcon_test_dir/g_consensus.fa'","user":{"login":"52teth","id":14286330,"avatar_url":"https://avatars.githubusercontent.com/u/14286330?v=3","gravatar_id":"","url":"https://api.github.com/users/52teth","html_url":"https://github.com/52teth","followers_url":"https://api.github.com/users/52teth/followers","following_url":"https://api.github.com/users/52teth/following{/other_user}","gists_url":"https://api.github.com/users/52teth/gists{/gist_id}","starred_url":"https://api.github.com/users/52teth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/52teth/subscriptions","organizations_url":"https://api.github.com/users/52teth/orgs","repos_url":"https://api.github.com/users/52teth/repos","events_url":"https://api.github.com/users/52teth/events{/privacy}","received_events_url":"https://api.github.com/users/52teth/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":17,"created_at":"2015-11-26T03:27:09Z","updated_at":"2015-12-14T18:09:38Z","closed_at":null,"body":"when I use the follwing cmd to do my Isoseq work with SGE:\r\n         smrtpipe.py --params=settings.xml xml:cfg/input.xml \r\nthe following error occurs:\r\n\r\n[ERROR] 2015-11-26 01:14:47,115 [smrtpipe.status refreshTargets 413] *** Failed task task://Anonymous/P_IsoSeqC\r\nluster/cluster\r\n[INFO] 2015-11-26 01:14:47,116 [smrtpipe.status execute 627] Found 1 failed tasks.\r\n[INFO] 2015-11-26 01:14:47,116 [smrtpipe.status execute 629] task cluster FAILED\r\n[ERROR] 2015-11-26 01:14:47,582 [SMRTpipe.SmrtPipeMain run 608] SmrtExit task://Anonymous/P_IsoSeqCluster/cluster Failed\r\nTraceback (most recent call last):\r\n  File \"/share/nas2/genome/biosoft/smrtanalysis/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py\", line 571, in run\r\n    self._runTasks(pModules)\r\n  File \"/share/nas2/genome/biosoft/smrtanalysis/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/SmrtPipeMain.py\", line 300, in _runTasks\r\n    workflow.execute()\r\n  File \"/share/nas2/genome/biosoft/smrtanalysis/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/SMRTpipe/engine/SmrtPipeWorkflow.py\", line 640, in execute\r\n    raise SmrtExit(str(e))\r\nSmrtExit: SmrtExit task://Anonymous/P_IsoSeqCluster/cluster Failed\r\n[ERROR] 2015-11-26 01:14:47,583 [SMRTpipe.SmrtPipeMain exit 690] SmrtExit task://Anonymous/P_IsoSeqCluster/cluster Failed\r\n[INFO] 2015-11-26 01:14:47,584 [SMRTpipe.SmrtPipeMain exit 692] Beginning exit process\r\n\r\nThen i checked the P_IsoSeqCluster/cluster.log, then the following error information is given:\r\nTraceback (most recent call last):\r\n  File \"/share/nas2/genome/biosoft/smrtanalysis/smrtanalysis/current/analysis/bin/pbtranscript.py\", line 146, in run\r\n    obj.run()\r\n  File \"/share/nas2/genome/biosoft/smrtanalysis/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/pbtools/pbtranscript/Cluster.py\", line 245, in run\r\n    fastq_filename=first_split_fq)\r\n  File \"/share/nas2/genome/biosoft/smrtanalysis/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/pbtools/pbtranscript/ice/IceIterative.py\", line 95, in __init__\r\n    sanity_check_sge(self.script_dir)\r\n  File \"/share/nas2/genome/biosoft/smrtanalysis/smrtanalysis/current/redist/python2.7/lib/python2.7/site-packages/pbtools/pbtranscript/ice/IceUtils.py\", line 81, in sanity_check_sge\r\n    if not filecmp.cmp(consensusFa, GCON_OUT_FA):\r\n  File \"/share/nas2/genome/biosoft/smrtanalysis/smrtanalysis/current/redist/python2.7/lib/python2.7/filecmp.py\", line 42, in cmp\r\n    s1 = _sig(os.stat(f1))\r\nOSError: [Errno 2] No such file or directory: '/lustre/tengh/SMRT/test_TOFU_v2/result/BasicAnalysis/MCF1/data/clusterOutDir/scripts/gcon_test_dir/g_consensus.fa'\r\n\r\nI have checked the dir '/lustre/tengh/SMRT/test_TOFU_v2/result/BasicAnalysis/MCF1/data/clusterOutDir/scripts/gcon_test_dir/', only gcon_in.fa can be found. So what's the matter with my job submit? What can I do with this problem?\r\n\r\nBy the way, I have tested a job without the use of SGE, and it has completed successfull. So I can make sure that there's somthing with my SGE. So what can I with it?\r\n\r\nThanks a lot for any adviceO(∩_∩)O"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/comments/164513599","html_url":"https://github.com/PacificBiosciences/cDNA_primer/issues/18#issuecomment-164513599","issue_url":"https://api.github.com/repos/PacificBiosciences/cDNA_primer/issues/18","id":164513599,"user":{"login":"bowhan","id":1703619,"avatar_url":"https://avatars.githubusercontent.com/u/1703619?v=3","gravatar_id":"","url":"https://api.github.com/users/bowhan","html_url":"https://github.com/bowhan","followers_url":"https://api.github.com/users/bowhan/followers","following_url":"https://api.github.com/users/bowhan/following{/other_user}","gists_url":"https://api.github.com/users/bowhan/gists{/gist_id}","starred_url":"https://api.github.com/users/bowhan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bowhan/subscriptions","organizations_url":"https://api.github.com/users/bowhan/orgs","repos_url":"https://api.github.com/users/bowhan/repos","events_url":"https://api.github.com/users/bowhan/events{/privacy}","received_events_url":"https://api.github.com/users/bowhan/received_events","type":"User","site_admin":false},"created_at":"2015-12-14T18:09:38Z","updated_at":"2015-12-14T18:09:38Z","body":"Yes, please edit both `start.tmpl ` and `interactive.tmpl` files to reflect the queue to use in smrtanalysis. \r\nIf you run `pbtranscript.py` or `tofu` directly on the command line, please do the switch using option `--sge_queue`."}}