10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger3.0, printed on 11/05/2024

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 5.5 or Ubuntu 10.04

Note: Cell Ranger 2.1 is expected to be the last version of Cell Ranger to support CentOS/RedHat 5 and Ubuntu 10. Future versions of Cell Ranger will require CentOS/RedHat 6 or Ubuntu 12 or later. See the 10x OS Support page for further information.

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, please 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: