{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/55","labels_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/55/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/55/comments","events_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/55/events","html_url":"https://github.com/PacificBiosciences/FALCON/issues/55","id":70807237,"number":55,"title":"falcon crash","user":{"login":"dgordon562","id":11529099,"avatar_url":"https://avatars.githubusercontent.com/u/11529099?v=3","gravatar_id":"","url":"https://api.github.com/users/dgordon562","html_url":"https://github.com/dgordon562","followers_url":"https://api.github.com/users/dgordon562/followers","following_url":"https://api.github.com/users/dgordon562/following{/other_user}","gists_url":"https://api.github.com/users/dgordon562/gists{/gist_id}","starred_url":"https://api.github.com/users/dgordon562/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dgordon562/subscriptions","organizations_url":"https://api.github.com/users/dgordon562/orgs","repos_url":"https://api.github.com/users/dgordon562/repos","events_url":"https://api.github.com/users/dgordon562/events{/privacy}","received_events_url":"https://api.github.com/users/dgordon562/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-04-24T22:14:43Z","updated_at":"2015-04-24T23:02:16Z","closed_at":null,"body":"Hi, Jason,\r\n\r\nI've had fc_run.py crash on me a number of times with the python key error below.  It isn't a show-stopper because I just restart fc_run.py and it then completes successfully, but it is a minor problem because I might not notice it is dead for a few days.\r\n\r\nI believe the conditions under which it occurs are the following:  some jobs are running and they die (for one reason or another).  So I restart fc_run.py which restarts those jobs.  This time they complete.  fc_run.py sees their done files and then crashes with this key error.  \r\n\r\nI should mention that the crash doesn't always say:\r\n\r\n'task://localhost/build_p_rdb'\r\n\r\nSometimes it says:\r\n\r\n'task://localhost/m_00054_preads'\r\nor\r\n'task://localhost/ct_00102'\r\n\r\nIs there is a simple change I could make to controller.py so that it would handle this problem?\r\n\r\nThanks!\r\nDavid\r\n\r\n\r\n> fc_run.py fc_run_human.cfg\r\n No target specified, assuming \"assembly\" as target \r\nYour job 4419007 (\"ct_00353-06239db8\") has been submitted\r\nYour job 4419008 (\"ct_00050-083f149c\") has been submitted\r\nYour job 4419009 (\"ct_00333-0a7520bc\") has been submitted\r\nTraceback (most recent call last):\r\n  File \"/net/gs/vol1/home/dgordon/falcon3/FALCON-master/install/fc_env/bin/fc_run.py\", line 4, in <module>\r\n    __import__('pkg_resources').run_script('falcon-kit==0.2.1', 'fc_run.py')\r\n  File \"/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py\", line 505, in run_script\r\n    self.require(requires)[0].run_script(script_name, ns)\r\n  File \"/net/gs/vol3/software/modules-sw/python/2.7.3/Linux/RHEL6/x86_64/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/pkg_resources.py\", line 1245, in run_script\r\n    execfile(script_filename, namespace, namespace)\r\n  File \"/net/gs/vol1/home/dgordon/falcon3/FALCON-master/install/fc_env/lib/python2.7/site-packages/falcon_kit-0.2.1-py2.7-linux-x86_64.egg/EGG-INFO/scripts/fc_run.py\", line 801, in <module>\r\n    wf.refreshTargets(updateFreq = wait_time) #all            \r\n  File \"/net/gs/vol1/home/dgordon/falcon3/FALCON-master/install/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py\", line 519, in refreshTargets\r\n    self._refreshTargets(objs = objs, callback = callback, updateFreq = updateFreq, exitOnFailure = exitOnFailure)\r\n  File \"/net/gs/vol1/home/dgordon/falcon3/FALCON-master/install/fc_env/lib/python2.7/site-packages/pypeflow-0.1.1-py2.7.egg/pypeflow/controller.py\", line 649, in _refreshTargets\r\n    task2thread[URL].join()\r\nKeyError: 'task://localhost/build_p_rdb'\r\n(fc_env){dgordon}e183:/net/eichler/vol20/projects/pacbio/nobackups/users/dgordon/falcon_chm13\r\n"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/comments/96090960","html_url":"https://github.com/PacificBiosciences/FALCON/issues/55#issuecomment-96090960","issue_url":"https://api.github.com/repos/PacificBiosciences/FALCON/issues/55","id":96090960,"user":{"login":"pb-jchin","id":1071734,"avatar_url":"https://avatars.githubusercontent.com/u/1071734?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-jchin","html_url":"https://github.com/pb-jchin","followers_url":"https://api.github.com/users/pb-jchin/followers","following_url":"https://api.github.com/users/pb-jchin/following{/other_user}","gists_url":"https://api.github.com/users/pb-jchin/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-jchin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-jchin/subscriptions","organizations_url":"https://api.github.com/users/pb-jchin/orgs","repos_url":"https://api.github.com/users/pb-jchin/repos","events_url":"https://api.github.com/users/pb-jchin/events{/privacy}","received_events_url":"https://api.github.com/users/pb-jchin/received_events","type":"User","site_admin":false},"created_at":"2015-04-24T23:02:16Z","updated_at":"2015-04-24T23:02:16Z","body":"@dgordon562  I think this is a duplicated of https://github.com/PacificBiosciences/FALCON/issues/12 \r\nI have fixed it in a recent commit for pypeFlow."}}