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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

Structure Harvester

Structure Harvester parses the output of Pritchard's Structure program, applies the Evanno ΔK method to help detect the number of clusters, and can optionally emit CLUMPP-compatible indfiles and popfiles.

License

Free to use and open source under the MIT License.

Available

  • Roihu: 0.7, via the bio-apps module.

Usage

Structure Harvester is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the module:

module load bio-apps/v202603
module load structureharvester/0.7

Run structureHarvester.py on a directory of Structure result files:

structureHarvester.py --dir=structure_results --out=harvester_out --evanno --clumpp

Structure Harvester is often used as part of an automated Structure workflow — see StrAuto, which runs it as part of its post-processing.

Example batch script

#!/bin/bash
#SBATCH --job-name=structureharvester
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G

module load bio-apps/v202603
module load structureharvester/0.7

structureHarvester.py --dir=structure_results --out=harvester_out --evanno --clumpp

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information