Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How do you know when SVPreprocess has successfully finshed?
I apologize in advance if this is a stupid question.
I'm coming from the world of gotcloud where when a step in the pipeline finishes a file called
all.done gets created for that step. So in the event a pipeline crashe, I can re-execute the program and it will pickup where it left off.
I've been running SVPreprocess for over a week now. It's crashed a few times, usually due to memory limits but I've overcome those. At no point did I clear out the
tmp folders or files.
I can't tell if it ever finished completely and I can move on with the next step in the CNV pipeline or if I'm starting from scratch each time.
Is there a file or a specific message I should look for?