Single Cell CNV
Cell Ranger DNA, printed on 07/03/2022
Cell Ranger DNA
Cell Ranger DNA pipelines are distributed for and run on 64-bit Linux systems. The runtime and storage requirements of Cell Ranger DNA scale linearly with the number of reads to be processed. In the recommended experiment (1000 cells at 750,000 read-pairs per cell) there will be 750 million read-pairs and the minimum system requirements are:
- 16-core Intel or AMD processor
- 128GB of RAM
- 2TB of free disk space per 750 million read-pairs. Cell Ranger DNA is very sensitive to IO speed so we highly recommend solid-state disks or RAID arrays.
- 64-bit Centos/RedHat 6.0 or Ubuntu 12.04.
The pipelines also run on clusters that meet these additional minimum requirements:
- 8-core Intel or AMD processor per node
- 6GB RAM per core
- Shared filesystem (e.g. NFS)
- SGE or LSF batch scheduling system
Most software dependencies come bundled in the Cell Ranger DNA package. However,
cellranger-dna mkfastq also requires:
- Illumina bcl2fastq. Version 2.17 or higher is preferred and supports most sequencers running RTA version 1.18.54 or higher. If you are using a NovaSeq, please use version 2.20 or higher. If your sequencer is running an older version of RTA, then bcl2fastq 1.8.4 is required by Illumina.
- Cell Ranger DNA runs locally by default (or when specified as --jobmode=local), using 90% of available memory and all of the available cores. To restrict resource usage, please use the --localmem and --localcores options (see cellranger-dna cnv --help).
- Many Linux systems have default user limits (ulimits) for maximum open files and maximum user processes as low as 1024 or 4096. Because Cell Ranger DNA spawns multiple processes per core, jobs that use a large number of cores can exceed these limits. We recommend higher limits:
user open files
system max files
10k per GB RAM available to Cell Ranger DNA
64 per core available to Cell Ranger DNA
Empirical Performance results
The performance data below was produced by running Cell Ranger DNA on a range of datasets and computers. Cell Ranger DNA runtime is almost entirely determined by the number of reads and is insensitive to the number of cells. The table below was created on hardware available from Amazon cloud services.
| Number of read-pairs || Small system || Medium system || Large system |
| 375 million || 12h || 6h || 4h |
| 1.2 billion || 25h || 13h || 11h |
| 7 billion || Not recommended || Not recommended || 114h |
| || CPU cores || RAM (GB) || CPU Generation || Disk |
| Small system || 16 || 128 || Ivy Bridge || HDD |
| Medium system || 32 || 256 || Broadwell || HDD |
| Large system || 48 || 384 || Skylake || SDD |