Space Ranger, printed on 04/01/2023
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=localby default, using 90% of available memory and all available cores. To restrict resource usage, please see the
--localmemflags for spaceranger count.
|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.
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.