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The job was aborted from outside Cromwell: How to get around this error?
DivyKangeyan
Member, Broadie ✭
I am processing a few very large TCGA samples and I am getting the following error The job was aborted from outside Cromwell. My workflows are in aryee-merkin/TCGA_WGBS_hg19 and submission id is 966b6728-387b-4415-a488-58db29e3a55e. There is some discussion on what this error means but it is not clear to me how to get around this error. Should I increase the memory or disk size or something else?
Best Answers
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Tiffany_at_Broad Cambridge, MA admin
Hi @DivyKangeyan the error is because your workflow took longer than 6 days to run. I will report back with advice on how to proceed.
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Hi @DivyKangeyan , essentially you want this method to run faster, so you will have to determine how to do that best based on what your method is doing. If it’s possible to split this into smaller intervals, that would be worth trying. Does this help?
Answers
Thanks for the workspace and submisison ID information @DivyKangeyan. Could you also go into that workspace and click the "Share" button to share it with
[email protected]?@KateN I just shared the workspace with you.
Hi @DivyKangeyan the error is because your workflow took longer than 6 days to run. I will report back with advice on how to proceed.
Hi @DivyKangeyan , essentially you want this method to run faster, so you will have to determine how to do that best based on what your method is doing. If it’s possible to split this into smaller intervals, that would be worth trying. Does this help?
Hi @Tiffany_at_Broad Thank you so much for getting back to me. It make sense now, I will try to see how I can speed up the analysis.