Space Ranger, printed on 11/21/2024
Space Ranger pipelines run on Linux systems that meet these minimum requirements:
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:
In order to run spaceranger mkfastq, the following software needs to be installed:
--jobmode=local by default, using 90% of available memory and all available cores. To restrict resource usage, please see the --localcores and --localmem flags for spaceranger count.| 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 |
| 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.
.png)
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.
.png)