Post date: Feb 07, 2015 7:38:33 PM
I am running entropy on the Ithomia hybrid zone data. I already have results from structure as a comparison. The Ithomia data set includes 112 individuals and 43,344 SNPs, and the Oleria data set includes 149 individuals and 55,365 SNPs. I am analyzing each hybrid zone with the Q-matrix and admixture proportion models. I am running three chains for each one, using the SNP count format data with locus-specific error rates, running 15,000 iteration chains with 5000 iteration burnin and and thinning interval of 5. I am not using LDA for starting values (but I might need to try this if the initial results don't look good). Here are the example commands (infiles and outfiles will be in /labs/evolution/projects/ithom_hybrid_zones/entropy/):
cd /local/scratch/
sleep 10
~/bin/entropy -i /labs/evolution/projects/ithom_hybrid_zones/entropy/snps_oleria.txt -l 15000 -b 5000 -t 5 -k 2 -e 9 -Q 0 -o entout_oleriaChain2.hdf5 -m 0 -w 0
scp entout_oleriaChain2.hdf5 /labs/evolution/projects/ithom_hybrid_zones/entropy/
rm entout_oleriaChain2.hdf5
cd /local/scratch/
sleep 10
~/bin/entropy -i /labs/evolution/projects/ithom_hybrid_zones/entropy/snps_oleria.txt -l 15000 -b 5000 -t 5 -k 2 -e 9 -Q 1 -o entoutQ_oleriaChain2.hdf5 -m 0 -w 0
scp entoutQ_oleriaChain2.hdf5 /labs/evolution/projects/ithom_hybrid_zones/entropy/
rm entoutQ_oleriaChain2.hdf5