{"action":"closed","issue":{"url":"https://api.github.com/repos/cdshaffer/starterator/issues/15","repository_url":"https://api.github.com/repos/cdshaffer/starterator","labels_url":"https://api.github.com/repos/cdshaffer/starterator/issues/15/labels{/name}","comments_url":"https://api.github.com/repos/cdshaffer/starterator/issues/15/comments","events_url":"https://api.github.com/repos/cdshaffer/starterator/issues/15/events","html_url":"https://github.com/cdshaffer/starterator/issues/15","id":93029686,"number":15,"title":"starterator crash with empty sequence","user":{"login":"cdshaffer","id":2753234,"avatar_url":"https://avatars.githubusercontent.com/u/2753234?v=3","gravatar_id":"","url":"https://api.github.com/users/cdshaffer","html_url":"https://github.com/cdshaffer","followers_url":"https://api.github.com/users/cdshaffer/followers","following_url":"https://api.github.com/users/cdshaffer/following{/other_user}","gists_url":"https://api.github.com/users/cdshaffer/gists{/gist_id}","starred_url":"https://api.github.com/users/cdshaffer/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cdshaffer/subscriptions","organizations_url":"https://api.github.com/users/cdshaffer/orgs","repos_url":"https://api.github.com/users/cdshaffer/repos","events_url":"https://api.github.com/users/cdshaffer/events{/privacy}","received_events_url":"https://api.github.com/users/cdshaffer/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2015-07-04T16:52:44Z","updated_at":"2016-07-19T03:40:37Z","closed_at":"2016-07-19T03:40:37Z","body":"When doing whole phage of *Redi*, starterator crashed. Was logging everything at the time.  Starterator was working on pham 3635 which was for redi_64 according to log\r\n\r\n```\r\nERROR: Empty sequences found: Redi_69\r\n\r\n CLUSTAL 2.1 Multiple Sequence Alignments\r\nException in thread Thread-6:\r\nTraceback (most recent call last):\r\n  File \"starterator/uiStarterate.py\", line 297, in run: self.starterate()\r\n  File \"/starterator/uiStarterate.py\", line 302, in starterate: gui=self, event=self.stop_thread)\r\n  File \"starterator/starterate.py\", line 112, in starterate: final_file, short_final = phage.final_report()\r\n  File \"starterator/report.py\", line 52, in final_report: self.make_reports()\r\n  File \"starterator/report.py\", line 77, in make_reports: pham = gene_report.make_report(whole=True)\r\n  File \"starterator/report.py\", line 267, in make_report:    self.pham.align()\r\n  File \"starterator/phams.py\", line 133, in align:    self.call_clustal(file_name+\".fasta\")\r\n  File \"starterator/phams.py\", line 107, in call_clustal:    '-quicktree'])\r\n  File \"/usr/lib/python2.7/subprocess.py\", line 511, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nCalledProcessError: Command '['clustalw', '-infile=/home/seastudent/.starterator/Intermediate Files/Pham3635.fasta', '-quicktree']' returned non-zero exit status 255\r\n```\r\n\r\nI checked phamerator database, the translation is there in the database. Curiously this is the very last gene in the phage."}}
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