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Structure

Structure is a software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.

It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

License

  • Structure is free to use and open source, but no license is specified.
  • StrAuto is free to use and open source, but no license is specified.
  • strasuto-puhti is free to use and open source, but no license is specified.
  • structureHarvester is free to use and open source under its own License
  • CLUMPP is free to use, but no license is specified.

Available

  • Puhti: 2.3.4

Usage

To use Structure in Puhti, run first the following setup commands:

module load biokit
module load structure

In addition to the structure command, the Structure module makes available programs CLUMPP and structureHarvester that can be used for post-processing Structure results.

On Puhti, we recommend that you submit your Structure jobs using a help tool called strauto-puhti. This tool is a modified version of StrAuto Structure job submission tool. Note that many details in the StrAuto manual do not apply to strauto-puhti.

Next, move to the scratch directory of your project. Any subdirectory inside your scratch area will do. For example:

cd /scratch/project_xxxxxx/$USER

Create a new empty directory:

mkdir structure_job1

Next, you need to copy or create to this directory the two input files used by strauto-puhti program. The parameter file must always be named as input.py. The name of the actual data file is defined in input.py. The data file name should end with .str or .ustr.

A sample file provided by StrAuto can be copied to your current directory with the commands:

cd structure_job1
cp /appl/soft/bio/structure/strauto/input.py ./  
cp /appl/soft/bio/structure/strauto/sim.str ./

When the input file has been prepared, the Structure job can be launched with the command:

strauto-puhti

StrAuto first asks you to check and accept Structure parameters and after that submits the Structure job to the batch job system of Puhti. After that it starts monitoring the progress of your job.

You can leave the monitor process running, but if you want to stop it, press Ctrl-c.

The structure jobs will still continue their execution in the batch job system of Puhti. If you run the command:

strauto-puhti

in the same directory again it will check the status of structure jobs and do the post-processing of the results if all the Structure-related tasks have finished.

Note that strauto-puhti does not use the internal, GNU-parallel based, parallelization. Instead, parallelization is based on array jobs. Because of this, you should not change the parallel parameter value to True in the structure input file.

More information