Hardware
Cell Ranger pipelines run on Linux systems that meet these minimum requirements:
- 8-core Intel or AMD processor (16 cores recommended)
- 64GB RAM (128GB recommended)
- 1TB free disk space
- 64-bit CentOS/RedHat 6.0 or Ubuntu 12.04
| | The minimum requirement of 64GB RAM will allow <samp style="box-sizing: border-box; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 13px; color: rgb(51, 51, 51); background: none; border-radius: 3px; padding: 0px; white-space: nowrap;">cellranger aggr</samp> to aggregate up to 250k cells, more memory will be required beyond that. |
See the 10x Genomics OS Support page for further information.
In order to run in cluster mode, the cluster needs to meet these additional minimum requirements:
- 8-core Intel or AMD processor per node
- 6GB RAM per core
- Shared filesystem (e.g. NFS)
- SGE or LSF batch scheduling system
Software
In order to run <samp style="box-sizing: border-box; font-family: Menlo, Monaco, Consolas, "Courier New", monospace; font-size: 13px; color: rgb(51, 51, 51); background: rgb(229, 229, 229); border-radius: 3px; padding: 2px 5px; white-space: nowrap;">cellranger mkfastq</samp>, the following software needs to be installed:
- Illumina® bcl2fastq: bcl2fastq must be version 2.20 or higher.
Resource Limits
| Limit | Recommendation |
|---|---|
| user open files | 16k |
| system max files | 10k per GB RAM available to Cell Ranger |
| user processes | 64 per core available to Cell Ranger |
How CPU and Memory Affect Runtime
| | The following plots are based on time trials using Amazon EC2 instances, one of our public datasets, and version 4.0 of Cell Ranger. These plots will not be updated with every subsequent release of Cell Ranger, unless pipeline performance changes significantly. |
