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SystemsGenetics / GEMmaker

A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
https://gemmaker.readthedocs.io/en/latest/
MIT License
33 stars 16 forks source link

Running on Back queue #233

Closed JohnHadish closed 2 years ago

JohnHadish commented 3 years ago

If users are running on a back queue on a University Cluster, they may encounter being preempted by another user:

SLurm Example:

slurmstepd: error: *** JOB 32391783 ON cn119 CANCELLED AT 2021-06-18T13:05:36 DUE TO PREEMPTION ***

This will cause their run to end. To avoid this, the user can modify the nextflow.config parameter maxRetries:

maxRetries = 3

Which will attempt to re-run jobs which failed, including those which have been preempted.

This information can be added to the Troubleshooting Section

spficklin commented 3 years ago

I think this is something we can add to the docs to help user's out.

spficklin commented 2 years ago

Fixed by recent PR.