Space Ranger pipelines run on Linux systems that meet these minimum requirements:
- 8-core Intel or AMD processor (32 cores recommended), with support for instruction sets including at least SSE4.2. This includes Intel CPUs released since 2008 (Core i5/i7 or newer) and any AMD CPU since 2011. Future versions of Cell Ranger will require CPUs supporting AVX instructions; Intel and AMD CPUs have supported these since 2011 (Intel Xeon E3/E5 or newer).
- 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.
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)
- Slurm batch scheduling system
In order to run
spaceranger mkfastq, the following software needs to be installed:
- Illumina® bcl2fastq: bcl2fastq must be version 2.20 or higher.
- Space Ranger runs with
--jobmode=localby default, using 90% of available memory and all available cores. To restrict resource usage, please see the
- 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.
|user open files||16k|
|system max files||10k per GB RAM available to Space Ranger|
|user processes||64 per core available to Space Ranger|
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.
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.