Cell Ranger ATAC, printed on 08/04/2021
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:
| 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 |
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 |
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.
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.
