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10x Genomics
Spatial Gene Expression

System Requirements


Space Ranger pipelines run on Linux systems that meet these minimum requirements:

Note: Version 1.3 is the last version that will support CentOS/RedHat 6 or Ubuntu 12.04. Future versions will require CentOS/RedHat 7 or newer, or Ubuntu 14.04 or newer.

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 spaceranger mkfastq, the following software needs to be installed:

Resource 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 Affect Runtime

Here 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's 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.