10x Genomics
Chromium Single Cell Immune Profiling
Cell Ranger7.1 (latest), printed on 11/14/2024
System Requirements
Table of Contents
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 7.0 or Ubuntu 14.04; See the 10x Genomics OS Support page for details.
Note: Cell Ranger v6.1 was the last version that supported CentOS/RedHat 6 or Ubuntu 12.04.
The pipelines also run on clusters that meet these additional minimum requirements:
- Shared filesystem (e.g. NFS).
- SGE or LSF batch scheduling system.
Software dependencies
Most software dependencies come bundled in the Cell Ranger package. However, cellranger mkfastq also requires:
- Illumina bcl2fastq. Version 2.20 or higher is required.
Resource limits
- Cell Ranger runs locally by default (or when specified as --jobmode=local), using 90% of available memory and all of the available cores. To restrict resource usage, please use the --localmem and --localcores options (see cellranger vdj --help).
- Many Linux systems have default user limits (ulimits) for maximum open files and maximum user processes as low as 1024 or 4096. Because Cell Ranger spawns multiple processes per core, jobs that use a large number of cores can exceed these limits. We recommend higher 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 memory affects runtime for the cellranger vdj pipeline
This graph is based on time trials using Amazon EC2 instances. Observed performance will be impacted by other factors besides memory, including read depth, number of cells, number of cores/threads, and I/O. The graph is meant to convey how increasing memory beyond the minimum and recommended levels may impact runtime for large datasets run with cellranger vdj. Similar graphs for cellranger multi, cellranger count, and cellranger aggr are provided on the 3' Single Cell Gene Expression's System Requirements page, but may not be representative of your dataset.
Walltime as a function of memory for a 10k PBMC V(D)J T cell dataset, read depth ~6,500 reads/cell, run with Cell Ranger v6.1.2:
Walltime as a function of memory for a 10k PBMC BCR Antigen Capture dataset run with Cell Ranger v7.1.0:
For similar inputs, walltime as a function of memory is similar for TCR and BCR Antigen Capture datasets.