Plink

Description

From the Plink Home Page: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).

Version

  • 1.07

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

Plink requires the following module file to run:

  • apps/plink/1.07

Running Plink on CIRCE/SC

The Plink 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.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for Plink, and execute the Plink binary:

[user@itn0 ~]$ srun --time=48:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
[user@svc-3024-9-12 ~]$ module load apps/plink/1.07
[user@svc-3024-9-12 ~]$ plink --file mydata 

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

For example, to perform all plink analyses, set up a submit script as described below, where we expect two files: in this case, file1.ped and file2.map.

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

#### SLURM single node 4 cpu test to run for 1 hour.

# Load the plink module:
module load apps/plink/1.07

# Start plink
plink --noweb --ped file1.ped --map file2.map --maf 0.05 --assoc

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

[user@itn0 ~]$ cd my/jobdir
[user@itn0 jobdir]$ sbatch ./plink-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

  • Example files
    • /apps/plink/1.07/test

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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