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10x Genomics
Single Cell ATAC

System Requirements


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:


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

How CPU and Memory Affect Runtime

Here is cellranger-atac count walltime as a function of available memory. In general, you can improve performance by allocating more than the minimum 64GB of memory to the pipeline. There is notable diminishing return beyond 128GB.


Here's cellranger-atac count walltime as a function of threads. If your system has ≫32 logical cores, you may want to run with --localcores=32 since there is diminishing return beyond 32 threads.