Bgc 2016
Introduction
bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. Models are available for linked loci, genotype uncertainty and sequence errors. Models for genotype uncertainty and sequence error can be used to estimate genomic cline parameters from next-generation sequence data.
Installed versions
On environment hpc-env/6.4:
bgc/1.03-intel-2018a
Using bgc on the HPC cluster
You need to switch to the new environment hpc-env/6.4 before loading the bgc module:
module load hpc-env/6.4 module load bgc
Example job scripts
If you want to use bgc, it can be of use to create a job script. For example, it could look like this:
~ #!/bin/bash #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --mem=24G #SBATCH --time=0-18:00:00 #SBATCH --output=slurm.%j.out #SBATCH --error=slurm.%j.err #SBATCH --mail-type=END,FAIL #SBATCH --mail-user=fynn.schwietzer1@uol.de ml hpc-env/6.4 ml bgc/1.03-intel-2018a mkdir ~/bgc_test cp -r $EBROOTBGC/example/* ~/bgc_test cd ~/bgc_test bgc -a p0in.txt -b p1in.txt -h admixedin.txt -M map.txt -O 0 -x 50000 -n 25000 -p 1 -q 1 -N 1 -m 1 -D 0.5 -t 5 -E 0.0001 -d 1 -s 1 -I 0 -u 0.04 done ~
In this example, the corresponding modules being loaded, a test folder is getting created at your home directory (~/), and some test files get copied in it.
At the end, the script starts to analyze the given data set.
This could take up to 18 hours, so this should just be seen as an example of a fitting job script.
Documentation
If you want a short introduction to the available commands, you can use the help function after loading the module. Just type in:
bgc --help
The full documentation of AUGUSTUS can be found here. For further information you can find the manual here