{"action":"created","issue":{"url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/52","labels_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/52/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/52/comments","events_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/52/events","html_url":"https://github.com/PacificBiosciences/pbsmrtpipe/issues/52","id":105717857,"number":52,"title":"TaskChunkingError: Starting to chunk task-id ...","user":{"login":"pb-cdunn","id":12086299,"avatar_url":"https://avatars.githubusercontent.com/u/12086299?v=3","gravatar_id":"","url":"https://api.github.com/users/pb-cdunn","html_url":"https://github.com/pb-cdunn","followers_url":"https://api.github.com/users/pb-cdunn/followers","following_url":"https://api.github.com/users/pb-cdunn/following{/other_user}","gists_url":"https://api.github.com/users/pb-cdunn/gists{/gist_id}","starred_url":"https://api.github.com/users/pb-cdunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pb-cdunn/subscriptions","organizations_url":"https://api.github.com/users/pb-cdunn/orgs","repos_url":"https://api.github.com/users/pb-cdunn/repos","events_url":"https://api.github.com/users/pb-cdunn/events{/privacy}","received_events_url":"https://api.github.com/users/pb-cdunn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-09-10T02:00:34Z","updated_at":"2015-09-10T02:06:56Z","closed_at":null,"body":"The scatter task succeeds. Then, the chunked task does not even have its directory created. There is no command-line for it either. All I get is this error message:\r\n```python\r\nTaskChunkingError: Starting to chunk task-id falcon_ns.tasks.task_falcon1_run_daligner_jobs with chunk-group 9647db9e-beb0-4de2-8c94-45917b17dbf1\r\n[ERROR] 2015-09-10 01:54:31,442Z Traceback (most recent call last):\r\n  File \"/lustre/hpcprod/cdunn/repo/gh/FALCON-integrate/pbsmrtpipe/pbsmrtpipe/driver.py\", line 875, in _wrapper\r\n    state = func(*args, **kwargs)\r\n  File \"/lustre/hpcprod/cdunn/repo/gh/FALCON-integrate/pbsmrtpipe/pbsmrtpipe/driver.py\", line 970, in run_pipeline\r\n    workflow_level_opts, output_dir, service_uri)\r\n  File \"/lustre/hpcprod/cdunn/repo/gh/FALCON-integrate/pbsmrtpipe/pbsmrtpipe/driver.py\", line 842, in exe_workflow\r\n    workers, shutdown_event, service_uri)\r\n  File \"/lustre/hpcprod/cdunn/repo/gh/FALCON-integrate/pbsmrtpipe/pbsmrtpipe/driver.py\", line 389, in __exe_workflow\r\n    B.apply_chunk_operator(bg, global_registry.chunk_operators, global_registry.tasks, max_nchunks)\r\n  File \"/lustre/hpcprod/cdunn/repo/gh/FALCON-integrate/pbsmrtpipe/pbsmrtpipe/graph/bgraph.py\", line 1228, in apply_chunk_operator\r\n    chunked_nodes = add_chunkable_task_nodes_to_bgraph(bg, tnode_, pipeline_chunks, chunk_operators, registered_tasks_d)\r\n  File \"/lustre/hpcprod/cdunn/repo/gh/FALCON-integrate/pbsmrtpipe/pbsmrtpipe/graph/bgraph.py\", line 1127, in add_chunkable_task_nodes_to_bgraph\r\n    raise TaskChunkingError(\"Starting to chunk task-id {i} with chunk-group {g}\".format(i=task_type_to_scatter.task_id, g=chunk_group_id))\r\nTaskChunkingError: Starting to chunk task-id falcon_ns.tasks.task_falcon1_run_daligner_jobs with chunk-group 9647db9e-beb0-4de2-8c94-45917b17dbf1\r\n\r\nShutting down.\r\n[INFO] 2015-09-10 01:54:31,446Z Completed execution pbsmrtpipe v0.30.7. Workflow Failed in 47.22 sec (0.79 min)\r\nCompleted execution pbsmrtpipe v0.30.7. Workflow Failed in 47.22 sec (0.79 min)\r\n```"},"comment":{"url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/comments/139095179","html_url":"https://github.com/PacificBiosciences/pbsmrtpipe/issues/52#issuecomment-139095179","issue_url":"https://api.github.com/repos/PacificBiosciences/pbsmrtpipe/issues/52","id":139095179,"user":{"login":"mpkocher","id":868552,"avatar_url":"https://avatars.githubusercontent.com/u/868552?v=3","gravatar_id":"","url":"https://api.github.com/users/mpkocher","html_url":"https://github.com/mpkocher","followers_url":"https://api.github.com/users/mpkocher/followers","following_url":"https://api.github.com/users/mpkocher/following{/other_user}","gists_url":"https://api.github.com/users/mpkocher/gists{/gist_id}","starred_url":"https://api.github.com/users/mpkocher/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mpkocher/subscriptions","organizations_url":"https://api.github.com/users/mpkocher/orgs","repos_url":"https://api.github.com/users/mpkocher/repos","events_url":"https://api.github.com/users/mpkocher/events{/privacy}","received_events_url":"https://api.github.com/users/mpkocher/received_events","type":"User","site_admin":false},"created_at":"2015-09-10T02:06:56Z","updated_at":"2015-09-10T02:06:56Z","body":"It's reading in your pipeline chunks. If those are not well formed. This might be the source of your error. \r\n\r\nCan you post the output of scatter tasks (i.e., scatter.chunk.json)."}}