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10x Genomics
Single Cell Multiome ATAC + Gene Exp.

System Requirements

Table of Contents

Hardware

Cell Ranger ARC pipelines run on Linux systems that meet these minimum requirements:

Note: Version 2.0 is the last version that will support CentOS/RedHat 6 or Ubuntu 12.04. Future versions will require CentOS/RedHat 7 or newer, or Ubuntu 14.04 or newer.

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:

Software

In order to run cellranger-arc mkfastq, the following software needs to be installed:

Resource limits

Limit Recommendation
user open files 16k
system max files 10k per GB RAM available to Cell Ranger ARC
user processes 64 per core available to Cell Ranger ARC

Computational performance

The following data is based on time trials using Amazon EC2 instances, our PBMC 10k dataset, and version 2.0 of Cell Ranger ARC. Performance is dependent on both the number of cells and the number of reads per cell. These plots will not be updated with every subsequent release of Cell Ranger ARC, unless pipeline performance changes significantly.

Instance Threads Memory (GB) Core hours Wall time Storage HWM (GB)
r3.8xlarge (Ivy Bridge) 32 64 220 8h 22m 428
m5.24xlarge (Skylake) 96 384 198 3h 15m 356
r4.16xlarge (Broadwell) 64 488 196 4h 26m 484

How CPU and memory affect runtime

Here is cellranger-arc count walltime as a function of available memory based on the r3.8xlarge Ivy Bridge architecture. In general, you can improve performance by allocating more than the minimum 64GB of memory to the pipeline. There is notable diminishing return beyond 320GB.

Memory

Here's cellranger-arc count walltime as a function of threads. If your system has ≫96 logical cores, you may want to run with --localcores=96 since there is diminishing return beyond 96 threads.

Threads