10x Genomics
Single Cell ATAC

Cell Ranger ATAC , printed on 01/20/2019

System Requirements

Cell Ranger ATAC

Cell Ranger ATAC 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 the 10x Genomics 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 file system (e.g. NFS)
• SGE or LSF batch scheduling system

Software Dependencies

Most software dependencies come bundled in the Cell Ranger ATAC package, but certain pipeline pieces may require other software. cellranger-atac mkfastq also requires Illumina® bcl2fastq. bcl2fastq must be version 2.17 or higher. It supports most sequencers running RTA version 1.18.54 or higher. If you are using NovaSeq™, the pipelines require version 2.20 or higher. If your sequencer is running an older version of RTA, then the pipelines require bcl2fastq 1.8.4.

Resource Limits

• Cell Ranger ATAC 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 see the --localmem and --localcores flags for cellranger-atac count at the link here for more information.
• 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 ATAC spawns multiple processes per core, jobs that use a large number of cores can exceed these limits. 10x Genomics recommends higher limits.