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10x Genomics
Single Cell ATAC

System Requirements

Hardware

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

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-atac 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 ATAC
user processes 64 per core available to Cell Ranger ATAC

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 ATAC. 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 ATAC, unless pipeline performance changes significantly.

Instance Threads Memory (GB) Core hours Wall time Storage HWM (GB)
r3.8xlarge (Ivy Bridge) 32 64 129 5h 14m 285
m5.24xlarge (Skylake) 96 384 92 1h 59m 233
r4.16xlarge (Broadwell) 64 488 111 2h 58m 233
r1.32xlarge (Haswell) 128 1952 137 2h 37m 233

How CPU and Memory Affect Runtime

Here is cellranger-atac count walltime as a function of available memory for a variety of CPU architectures. In general, you can improve performance by allocating more than the minimum 64GB of memory to the pipeline. There is notable diminishing return beyond 160GB.

Memory

Here's cellranger-atac count walltime as a function of threads. If your system has ≫48 logical cores, you may want to run with --localcores=48 since there is diminishing return beyond 48 threads.

Threads