STQ icon indicating copy to clipboard operation
STQ copied to clipboard

where to specify amount of memory?

Open WagnerPatrickResearch opened this issue 1 year ago • 4 comments

Hey STQ Team! First of all, thank you for this great Package! If I can get it to work this will greatly help my work. I recently ran my first PDX Visium Experiment and was trying to run your Nextflow pipeline on a HPC (slurm submission). I adapted the node specification in the submit.sb script and the nextflow.config files. Unfortunately I ran into some more issues when trying to run the Demo. This is the execution error that I got. The memory specification is specified in the submit.sb

Error executing process > 'TWO:SEQ:LOAD_SAMPLE_INFO (Demo_S1)'

Caused by: Failed to submit process to grid scheduler for execution

Command executed:

sbatch .command.run

Command exit status: 1

Command output: sbatch: error: Mem flag not set for partial node allocation. sbatch: error: Please specify the amount of memory for the job with: "--mem xxG". sbatch: error: Batch job submission failed: Job size specification needs to be provided

Any Help will be greatly appreciated! Thank you! All the best, Patrick

WagnerPatrickResearch avatar May 16 '24 09:05 WagnerPatrickResearch