PCA with shellfish

1. Assuming  shellfish and all other related software have been installed correctly.
2. Assuming shellfish.py exists
3. then prepare a pbs script, here I called it Shellfish.pbs and I have plink files calledABC.bim ABC.bed ABC.fam
4. cat Shellfish.pbs

5. #!/bin/bash
   
    #PBS -N shellfish
   
    #PBS -S /bin/bash
   
    #PBS -j oe
   
    #PBS -l walltime=24:00:00
   
    #PBS -l ncpus=20
   
    #PBS -l mem=100G
   
   hostname
    cd $PBS_O_WORKDIR
    echo "shellfish.py  --pca --numpcs 10 --ignore-sge --maxprocs  20 --file ${bim_file} --out ${bim_file}_pca"
    shellfish.py  --pca --numpcs 10 --ignore-sge --maxprocs  20 --file ${bim_file} --out ${bim_file}_pca

to submit this job, type

qsub -v bim_file=ABC Shellfish.pbs

 

This script will produce 10 PCA components with 20 CPUs