Post date: Nov 25, 2014 4:54:6 PM
I am setting up another batch of piMASS runs, but only including loci with MAF >= 5%. I had to create new geno* files for this, maf0.05geno_timemaA.txt (3,965,420 SNPs) and maf0.05geno_timemaC.txt (3,962,710 SNPs). I am running 100 chains for the mean genotypes (these were better than modal), with a 5 million iteration burnin, 10 million steps, and a thinning interval of 5000. Here is an example command (writing locally!):
cd /local/scratch/
mkdir maf05timemaC99
cd maf05timemaC99
sleep 495
pimass-lin -g /home/A01963476/projects/timema_wgexperiment/gemma/maf0.05geno_timemaC.txt -p /home/A01963476/projects/timema_wgexperiment/gemma/pheno_samplesC.txt -w 5000000 -s 10000000 -num 5000 -o pimass_timemaCrep99 -cc
cd ..
rsync -avz maf05timemaC99 /home/A01963476/projects/timema_wgexperiment/gemma/output_pimassMaf5/