Cluster related questions

What is cold storage?

On most clusters, a difference is being made between repositories designed to IO-intensive computations (hot storage), and repositories designed to archive (cold storage). Locally, system administrators allow (or not) the users to compute on archive-designed repositories.

Yet, copying all your fastq files at once before starting to work is time consuming and requires two copies of all your fastq files at the beginning of your work. Let Snakemake handle both copy creation and removal. This will save you time!

Slurm : partition time limit error

This error is not related to the pipeline itself, but with your use of Snakemake. This issue is raised because too much time was required for the queue you specified.

Your command line looks like : –qsub –time={resources.time} –mem={resources.mem_mb}

The time provided by the pipeline through the argument –time is too high for the queue YOU specified. Your command line should look like: –qsub –time={resources.time} –mem={resources.mem_mb} -p mediumq

Or else, you could use a profile! Snakemake profile allows to choose automatically the best queue! If you are in Gustave Roussy Institute, then look at: slurm