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Scatter/gather tasks cannot depend upon each other #300

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nh13 opened this issue Jun 15, 2017 · 0 comments
Open

Scatter/gather tasks cannot depend upon each other #300

nh13 opened this issue Jun 15, 2017 · 0 comments

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@nh13
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nh13 commented Jun 15, 2017

For example, see this pipeline: https://github.com/fulcrumgenomics/dagr/blob/master/pipelines/src/main/scala/dagr/pipelines/ParallelHaplotypeCaller.scala

If I change this:

root ==> scatter
 gather ==> new DeleteFiles(dir)

to this:

root ==> scatter ==> gather ==> new DeleteFiles(dir)

I get an exception:

ArrayBuffer(WrappedArray(Failed getTasks for [SingleGather]: ), dagr.core.execsystem.TaskException: java.lang.IllegalStateException: Gather.getTasks called before sources populated.
	at dagr.core.execsystem.TaskManager.invokeGetTasks(TaskManager.scala:382)
	at dagr.core.execsystem.TaskManager.$anonfun$invokeCallbacksAndGetTasks$2(TaskManager.scala:451)
	at dagr.core.execsystem.TaskManager.$anonfun$invokeCallbacksAndGetTasks$2$adapted(TaskManager.scala:447)
	at scala.collection.immutable.Set$Set2.foreach(Set.scala:130)
	at dagr.core.execsystem.TaskManager.invokeCallbacksAndGetTasks(TaskManager.scala:447)
	at dagr.core.execsystem.TaskManager.stepExecution(TaskManager.scala:511)
	at dagr.core.execsystem.TaskManager.runToCompletion(TaskManager.scala:548)
	at dagr.core.cmdline.DagrCoreArgs.execute(DagrCoreMain.scala:190)
	at dagr.core.cmdline.DagrCoreMain.makeItSo(DagrCoreMain.scala:237)
	at dagr.core.cmdline.DagrCoreMain.makeItSoAndExit(DagrCoreMain.scala:213)
	at dagr.core.cmdline.DagrCoreMain$.main(DagrCoreMain.scala:55)
	at dagr.core.cmdline.DagrCoreMain.main(DagrCoreMain.scala)
Caused by: java.lang.IllegalStateException: Gather.getTasks called before sources populated.
	at dagr.tasks.ScatterGather$SingleGather.getTasks(ScatterGather.scala:83)
	... 12 more
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