Post date: Aug 22, 2014 3:39:0 PM
I am using gemma to fit a BSLMM to the binary survival data (modelled with normal errors) for the 491 Timema genomes. I am running separate analyses for individuals transplanted to Adenostoma vs. Ceanothus. The genotype and phenotype data are in /home/A01963476/projects/timema_wgexperiment/gemma, and the phenotype data were extracted from /home/A01963476/projects/timema_wgexperiment/gemma/auxfiles/survivor_match_key.txt which lists the ids for all of the surviving individuals. I am running five replicate chains for each data set with 5 million iterations, a 1 million iteration burnin and thinning interval of 40. Here is an example of the submission commands:
cd /home/A01963476/projects/timema_wgexperiment/gemma/
sleep 0
gemma -g geno_timemaC.txt -p pheno_samplesC.txt -a annotation.txt -bslmm 1 -n 1 -o gemout_timemaCrep0 -rpace 40 -w 1000000 -s 5000000