{"action":"created","issue":{"url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51","labels_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51/labels{/name}","comments_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51/comments","events_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51/events","html_url":"https://github.com/pcingola/BigDataScript/issues/51","id":52470703,"number":51,"title":"SGE: qsub: command required for a binary job","user":{"login":"floerhard","id":10242442,"avatar_url":"https://avatars.githubusercontent.com/u/10242442?v=3","gravatar_id":"","url":"https://api.github.com/users/floerhard","html_url":"https://github.com/floerhard","followers_url":"https://api.github.com/users/floerhard/followers","following_url":"https://api.github.com/users/floerhard/following{/other_user}","gists_url":"https://api.github.com/users/floerhard/gists{/gist_id}","starred_url":"https://api.github.com/users/floerhard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/floerhard/subscriptions","organizations_url":"https://api.github.com/users/floerhard/orgs","repos_url":"https://api.github.com/users/floerhard/repos","events_url":"https://api.github.com/users/floerhard/events{/privacy}","received_events_url":"https://api.github.com/users/floerhard/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/pcingola/BigDataScript/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":44,"created_at":"2014-12-19T10:54:43Z","updated_at":"2015-01-24T21:52:05Z","closed_at":null,"body":"Dear Pablo,\r\n\r\nfirst of all, nice work, bds looks like a really nice platform to build pipelines on!\r\n\r\nI wanted to try a minimal example (Hello World with 'task') on our SGE cluster using BigDataScript 0.99c (build 2014-12-15)\r\n\r\n```\r\n#!/usr/bin/env bds\r\ntask echo Hello world\r\n```\r\n\r\n```\r\nbds -system sge -debug -l -v hello_world.bds\r\n```\r\n\r\nThe output is\r\n```\r\n00:00:00.214\tExecutioner: ExecutionerClusterSge, task hello_world.bds.20141219_114332_240/task.line_3.id_1\r\n00:00:00.214\tRunning command: echo \"bds exec 86400 '/home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout' '/home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr' '/home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.exitCode' '/home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.sh' \" | qsub -pe serial 1 -o /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout.cluster -e /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr.cluster \r\n00:00:00.215\tCommand (CmdCluster): CmdCluster: qsub -pe serial 1 -o /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout.cluster -e /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr.cluster \r\n00:00:00.216\tCmdCluster 'hello_world.bds.20141219_114332_240/task.line_3.id_1': Start\r\n00:00:00.216\tExecutionerClusterSge 'ClusterSge[11]': Queue: No task to run.\r\n00:00:00.216\tCmdLocal: Executing  qsub -pe serial 1 -o /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout.cluster -e /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr.cluster\r\nWARNING: Process closed stdout prematurely. Could not read PID\r\nCmdCluster: qsub -pe serial 1 -o /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stdout.cluster -e /home/users/erhard/test/bds/hello_world.bds.20141219_114332_240/task.line_3.id_1.stderr.cluster \r\nqsub: command required for a binary job\r\n```\r\n\r\nIs the shell script is missing from the qsub call?\r\n\r\nBest,\r\nFlorian"},"comment":{"url":"https://api.github.com/repos/pcingola/BigDataScript/issues/comments/71339243","html_url":"https://github.com/pcingola/BigDataScript/issues/51#issuecomment-71339243","issue_url":"https://api.github.com/repos/pcingola/BigDataScript/issues/51","id":71339243,"user":{"login":"pcingola","id":1334427,"avatar_url":"https://avatars.githubusercontent.com/u/1334427?v=3","gravatar_id":"","url":"https://api.github.com/users/pcingola","html_url":"https://github.com/pcingola","followers_url":"https://api.github.com/users/pcingola/followers","following_url":"https://api.github.com/users/pcingola/following{/other_user}","gists_url":"https://api.github.com/users/pcingola/gists{/gist_id}","starred_url":"https://api.github.com/users/pcingola/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pcingola/subscriptions","organizations_url":"https://api.github.com/users/pcingola/orgs","repos_url":"https://api.github.com/users/pcingola/repos","events_url":"https://api.github.com/users/pcingola/events{/privacy}","received_events_url":"https://api.github.com/users/pcingola/received_events","type":"User","site_admin":false},"created_at":"2015-01-24T21:52:05Z","updated_at":"2015-01-24T21:52:05Z","body":"\r\nIf you can, please send me a sample of your qstat output (as a TXT file) and I'll debug it.\r\nBy default the procedure is:\r\n   i-) Use first column (separated by \"\\\\s+\")\r\n   ii-) Parse first column using pidRegex (form config file)\r\n   iii-) Split first column by \"\\\\.\" (dot) and use the first part\r\n\r\nIf none of these rules matches your qstat's output, I can try to add new rules or separate regex (in cds.config file) for parsing the jobIds.\r\n"}}