{"action":"opened","issue":{"url":"https://api.github.com/repos/moonso/genmod/issues/58","repository_url":"https://api.github.com/repos/moonso/genmod","labels_url":"https://api.github.com/repos/moonso/genmod/issues/58/labels{/name}","comments_url":"https://api.github.com/repos/moonso/genmod/issues/58/comments","events_url":"https://api.github.com/repos/moonso/genmod/issues/58/events","html_url":"https://github.com/moonso/genmod/issues/58","id":150444966,"number":58,"title":"GENMOD on bigger VCF file - IO Error","user":{"login":"tinuthomas","id":3639243,"avatar_url":"https://avatars.githubusercontent.com/u/3639243?v=3","gravatar_id":"","url":"https://api.github.com/users/tinuthomas","html_url":"https://github.com/tinuthomas","followers_url":"https://api.github.com/users/tinuthomas/followers","following_url":"https://api.github.com/users/tinuthomas/following{/other_user}","gists_url":"https://api.github.com/users/tinuthomas/gists{/gist_id}","starred_url":"https://api.github.com/users/tinuthomas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tinuthomas/subscriptions","organizations_url":"https://api.github.com/users/tinuthomas/orgs","repos_url":"https://api.github.com/users/tinuthomas/repos","events_url":"https://api.github.com/users/tinuthomas/events{/privacy}","received_events_url":"https://api.github.com/users/tinuthomas/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2016-04-22T18:49:20Z","updated_at":"2016-04-22T18:49:20Z","closed_at":null,"body":"Hi, \r\n\r\nWhen we tried to run GENMOD on a VCF with ~400 members in ~140 families, the code broke with this error. Why does this happen ?\r\n```\r\nProcess VariantPrinter-6:\r\nTraceback (most recent call last):\r\n  File \"/usr/lib64/python2.7/multiprocessing/process.py\", line 258, in _bootstrap\r\nProcess VariantAnnotator-2:\r\nProcess VariantAnnotator-5:\r\nTraceback (most recent call last):\r\nTraceback (most recent call last):\r\nTraceback (most recent call last):\r\n  File \"/usr/lib64/python2.7/multiprocessing/process.py\", line 258, in _bootstrap\r\n  File \"/usr/lib64/python2.7/multiprocessing/process.py\", line 258, in _bootstrap\r\n  File \"/usr/lib64/python2.7/multiprocessing/process.py\", line 258, in _bootstrap\r\n    self.run()\r\n  File \"build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py\", line 160, in run\r\n    self.run()\r\n  File \"build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py\", line 160, in run\r\n  File \"build/bdist.linux-x86_64/egg/genmod/utils/variant_printer.py\", line 70, in run\r\n    self.run()\r\n  File \"build/bdist.linux-x86_64/egg/genmod/annotate_models/variant_annotator.py\", line 160, in run\r\n    variant = self.task_queue.get()\r\n  File \"<string>\", line 2, in get\r\n    self.results_queue.put(variant)\r\n    self.results_queue.put(variant)\r\n  File \"<string>\", line 2, in put\r\n  File \"<string>\", line 2, in put\r\n    self.results_queue.put(variant)\r\n  File \"<string>\", line 2, in put\r\n  File \"/usr/lib64/python2.7/multiprocessing/managers.py\", line 759, in _callmethod\r\n    kind, result = conn.recv()\r\n    kind, result = conn.recv()\r\n    kind, result = conn.recv()\r\nEOFError\r\n    kind, result = conn.recv()\r\nIOError: [Errno 104] Connection reset by peer\r\nIOError: [Errno 104] Connection reset by peer\r\nIOError: [Errno 104] Connection reset by peer\r\n    self.results_queue.put(variant)\r\n  File \"<string>\", line 2, in put\r\n  File \"/usr/lib64/python2.7/multiprocessing/managers.py\", line 759, in _callmethod\r\n    kind, result = conn.recv()\r\nIOError: [Errno 104] Connection reset by peer\r\n```\r\n\r\n\r\nAlso in another machine, got the error that 'no space left on the device'\r\n\r\nBoth are Linux machines. Is GENMOD creating any .tmp files/folder, if so is there a way to specify where the tmp file/folder should be generated ?\r\n"}}