10x Genomics
Spatial Gene Expression
Space Ranger, printed on 12/22/2024
System Requirements
Table of Contents
Hardware
Space Ranger pipelines run on Linux systems that meet these minimum requirements:
- 8-core Intel or AMD processor (32 cores recommended)
- 64GB RAM (128GB recommended)
- 1TB free disk space
- 64-bit CentOS/RedHat 7.0 or Ubuntu 14.04; See the 10x Genomics OS Support page for details.
Note: Space Ranger v1.3 was the last version that supported CentOS/RedHat 6 or Ubuntu 12.04.
The pipeline can also run on clusters that meet these additional minimum requirements:
- Shared filesystem (e.g. NFS)
- SGE or LSF batch scheduling system
Software dependencies
In order to run spaceranger mkfastq, the following software needs to be installed:
- Illumina® bcl2fastq: bcl2fastq must be version 2.20 or higher.
Resource limits
- Space Ranger runs with
--jobmode=localby default, using 90% of available memory and all available cores. To restrict resource usage, please see the--localcoresand--localmemflags for spaceranger count. - Many Linux systems have default user limits (ulimits) for maximum open files and maximum user processes as low as 1024 or 4096. Because Space Ranger spawns multiple processes per core, jobs that use a large number of cores can exceed these limits. 10x Genomics recommends higher limits.
| Limit | Recommendation |
|---|---|
| user open files | 16k |
| system max files | 10k per GB RAM available to Space Ranger |
| user processes | 64 per core available to Space Ranger |
How CPU and memory affects runtime
| The following plots are based on time trials using Amazon EC2 m5 instances, version 1.0 of Space Ranger, and a dataset with 574 million reads. These plots will be updated for subsequent releases of Space Ranger if pipeline performance changes significantly. |
Shown below is spaceranger 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. If your system has ≫128GB of memory, you may want to run with --localmem=128 since there is notable diminishing return beyond 128GB.
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Here is spaceranger 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.
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