sbatch error - Requested time limit is invalid

[alisonrocco]

Hi,

I am getting an error while trying to run this software on a SLURM engine (configured using Singularity):

Error executing process > 'Trimming (sample1)'
Caused by:
Failed to submit process to grid scheduler for execution
Command executed:
sbatch .command.run
Command exit status:
1
Command output:
sbatch: error: Batch job submission failed: Requested time limit is invalid (missing or exceeds some limit)

Any advice or suggestions for troubleshooting this would be greatly appreciated.

Sincerely,
Alison

[Nick-Eagles]

Hello,

First, I'm assuming you installed SPEAQeasy (perhaps with bash install_software.sh "singularity"-- I wasn't sure if you meant Singularity was being used with SPEAQeasy or with SLURM), and secondly that you're submitting some variation of run_pipeline_slurm.sh with sbatch to run SPEAQeasy. Let me know if I've misunderstood. Have you configured SLURM yourself on some machine, or is it part of a computing cluster you have access to? If the former, I'd check what time constraints exist for jobs. Trimming specifically should request 4 hours, but can be manually adjusted if needed. If Trimming was about to start, then PreprocessInputs must have already run, which requests 30 minutes. It's possible a very low limit (e.g. 2 hours) was accidentally set by SLURM.

Best,
-Nick