Hi, I’m having an issue with the latest version of the nf-core RNA-seq pipeline (version 3.17 on github.com/nf-core/rnaseq). While the pipeline completes all individual tasks successfully, it remains in the “Running” status and doesn’t transition to “Succeeded,” requiring me to manually cancel the run to terminate the associated EC2 instance. I didn’t encounter this issue with the same pipeline and dataset using version 3.9. Any suggestions on how to resolve this?
execution_report_2024-11-08_05-21-25.html (3.1 MB)
Thanks, Mahmoud
EDIT:
nf-5EIABhRgGgX1tp.log (277.8 KB)
Hi Mahmoud,
Welcome to the community forum. This sounds a lot like a recent identified bug and we’re currently investigating what may be leading to this. I will get back to you as soon as possible with more info.
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Dear @Mahmoud_Ghandi,
We identified the issue but we don’t have a solution yet. In the meantime, a workaround seems to be commenting/removing the email sending within the onComplete handler.
Could you please comment lines 122-140 (check here) and share if it is not getting stuck at running anymore?
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Hi Marcel,
Yes I tested that and it fixed the problem. Thank you so much!
Best,
Mahmoud
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