Stacks

Description

From the Stacks home page: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography

Version

  • 2.3e

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Stacks requires the following module file to run:

  • apps/stacks/2.3e

Running Stacks on CIRCE/SC

The Stacks user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting a Job

Use a submit script like the following to run Stacks:

#!/bin/bash
#
#SBATCH --job-name=stacks-test
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --mem-per-cpu=1024
#SBATCH --output=output.%j.stacks-test
#SBATCH --time=01:00:00

#### SLURM single node Stacks test 
#### to run for 1 hour 
#### using 4 processor cores and 4 GB of memory

module purge
module add apps/stacks/2.3e

denovo_map.pl -T 4 -m 3 -M 4 -n 4 -o ./stacks/ --samples ./samples --popmap ./popmaps/popmap

 

Next, be sure that you are in your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./stacks-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources


More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Stacks to the IT Help Desk: rc-help@usf.edu