Zombie runs, jobs has been killed in local but state is still running on Seqera

[Phi_Nguyen_Truong (Phi Nguyen)]

Hi, Seqera community.

When running a pipeline with CLI, runs are failed/canceled and I already checked the state with slurm. But the state is still running on Seqera. The success run’s state is success normally.

As I see, this phenomenon especially happens with this pipeline.
What are the possible causes in a pipeline that leads to the “zombie runs” problem in general? Also, how do I cancel a “zombie” job on Seqera?

Review developing history, I see:

• Zombie runs, redux: Jobs still shown as running · Issue #354 · seqeralabs/nf-tower · GitHub
• Zombie run · Issue #313 · seqeralabs/nf-tower · GitHub

They also met the same problem. It seems they solved this by providing workflow_id and the Tower administrator has canceled for them. Is this way possible now?

Thanks for the great platform.

[bpoli]

I always get these “zombie runs” when I kill a nextflow run that I have submitted to the cluster with slurm using “scancel”. The PID gets killed as expected and the run interrupts, but the pipeline is shown as running in seqera cloud forever.