{"action":"closed","issue":{"url":"https://api.github.com/repos/opencb/hpg-bigdata/issues/20","labels_url":"https://api.github.com/repos/opencb/hpg-bigdata/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/opencb/hpg-bigdata/issues/20/comments","events_url":"https://api.github.com/repos/opencb/hpg-bigdata/issues/20/events","html_url":"https://github.com/opencb/hpg-bigdata/issues/20","id":92481981,"number":20,"title":"Vcf2AvroMR job fails before map-reduce stage","user":{"login":"mh11","id":946740,"avatar_url":"https://avatars.githubusercontent.com/u/946740?v=3","gravatar_id":"","url":"https://api.github.com/users/mh11","html_url":"https://github.com/mh11","followers_url":"https://api.github.com/users/mh11/followers","following_url":"https://api.github.com/users/mh11/following{/other_user}","gists_url":"https://api.github.com/users/mh11/gists{/gist_id}","starred_url":"https://api.github.com/users/mh11/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mh11/subscriptions","organizations_url":"https://api.github.com/users/mh11/orgs","repos_url":"https://api.github.com/users/mh11/repos","events_url":"https://api.github.com/users/mh11/events{/privacy}","received_events_url":"https://api.github.com/users/mh11/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/opencb/hpg-bigdata/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":{"login":"mh11","id":946740,"avatar_url":"https://avatars.githubusercontent.com/u/946740?v=3","gravatar_id":"","url":"https://api.github.com/users/mh11","html_url":"https://github.com/mh11","followers_url":"https://api.github.com/users/mh11/followers","following_url":"https://api.github.com/users/mh11/following{/other_user}","gists_url":"https://api.github.com/users/mh11/gists{/gist_id}","starred_url":"https://api.github.com/users/mh11/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mh11/subscriptions","organizations_url":"https://api.github.com/users/mh11/orgs","repos_url":"https://api.github.com/users/mh11/repos","events_url":"https://api.github.com/users/mh11/events{/privacy}","received_events_url":"https://api.github.com/users/mh11/received_events","type":"User","site_admin":false},"milestone":null,"comments":2,"created_at":"2015-07-01T20:49:46Z","updated_at":"2015-07-01T21:09:02Z","closed_at":"2015-07-01T21:09:02Z","body":"Running the command with an vcf text file (uncompressed) \r\n<code>\r\n./build/bin/hpg-bigdata.sh variant convert -i hdfs:///my/genome.vcf -o /my/genome.avro.snappy -x deflate --to-avro\r\n</code>\r\nfails with \r\n<code>\r\nContainer id: container_1433243773280_0038_02_000001\r\nExit code: 1\r\nStack trace: ExitCodeException exitCode=1: \r\n        at org.apache.hadoop.util.Shell.runCommand(Shell.java:538)\r\n        at org.apache.hadoop.util.Shell.run(Shell.java:455)\r\n        at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:715)\r\n        at org.apache.hadoop.yarn.server.nodemanager.DefaultContainerExecutor.launchContainer(DefaultContainerExecutor.java:211)\r\n        at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:302)\r\n        at org.apache.hadoop.yarn.server.nodemanager.containermanager.launcher.ContainerLaunch.call(ContainerLaunch.java:82)\r\n        at java.util.concurrent.FutureTask.run(FutureTask.java:266)\r\n        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\r\n        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\r\n        at java.lang.Thread.run(Thread.java:745)\r\n</code>\r\n"}}