10x Genomics
Chromium Single Cell Immune Profiling
Cell Ranger3.1, printed on 04/26/2024
System Requirements
Cell Ranger
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 (See also 10x OS Support).
The pipelines also run on clusters that 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 Dependencies
Most software dependencies come bundled in the Cell Ranger package. However, cellranger mkfastq also requires:
- Illumina bcl2fastq. Version 2.17 or higher is preferred and supports most sequencers running RTA version 1.18.54 or higher. If you are using a NovaSeq, use version 2.20 or higher. If your sequencer is running an older version of RTA, then bcl2fastq 1.8.4 is required by Illumina.
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
|
