Post date: Jul 01, 2015 8:55:13 PM
I found a bug in the popanc source code. Ancestry was not consistently polarized (i.e. whether population 0 or 1 ancestry was being 'counted'). I have fixed this and a quick initial test suggests that it will (not surprisingly) improve the analysis quite a bit. So, I am re-running everything. Here are the commands for the simulated data.
# DEMOGRAPHY, 4, 10, or 20 SNPs
cd /local/scratch/
sleep 5
popanc -o estpanc_n4demogGens50Rep9Chain1.hdf5 -m 30000 -b 10000 -t 5 -n 4 -d 20 -s 1 -u 10 -l 0.1 -a 0.1 -z 1 /labs/evolution/projects/popanc_sims/sims/demog/genoP0F_r9gen_demog_gens50.txt /labs/evolution/projects/popanc_sims/sims/demog/genoP1F_r9gen_demog_gens50.txt /labs/evolution/projects/popanc_sims/sims/demog/genoAdmxF_r9gen_demog_gens50.txt
scp estpanc_n4demogGens50Rep9Chain1.hdf5 /labs/evolution/projects/popanc_sims/mcmc/
cd /local/scratch/
sleep 5
popanc -o estpanc_n10demogGens50Rep9Chain1.hdf5 -m 30000 -b 10000 -t 5 -n 10 -d 20 -s 1 -u 10 -l 0.1 -a 0.1 -z 1 /labs/evolution/projects/popanc_sims/sims/demog/genoP0F_r9gen_demog_gens50.txt /labs/evolution/projects/popanc_sims/sims/demog/genoP1F_r9gen_demog_gens50.txt /labs/evolution/projects/popanc_sims/sims/demog/genoAdmxF_r9gen_demog_gens50.txt
scp estpanc_n10demogGens50Rep9Chain1.hdf5 /labs/evolution/projects/popanc_sims/mcmc/
cd /local/scratch/
sleep 5
popanc -o estpanc_n20demogGens50Rep9Chain1.hdf5 -m 30000 -b 10000 -t 5 -n 20 -d 20 -s 1 -u 10 -l 0.1 -a 0.1 -z 1 /labs/evolution/projects/popanc_sims/sims/demog/genoP0F_r9gen_demog_gens50.txt /labs/evolution/projects/popanc_sims/sims/demog/genoP1F_r9gen_demog_gens50.txt /labs/evolution/projects/popanc_sims/sims/demog/genoAdmxF_r9gen_demog_gens50.txt
scp estpanc_n20demogGens50Rep9Chain1.hdf5 /labs/evolution/projects/popanc_sims/mcmc/
## SELECTION, 4, 10, or 20 SNPs
cd /local/scratch/
sleep 5
popanc -o estpanc_n4weakselGens50Rep9Chain1.hdf5 -m 30000 -b 10000 -t 5 -n 4 -d 20 -s 1 -u 10 -l 0.1 -a 0.1 -z 1 /labs/evolution/projects/popanc_sims/sims/selection/genoP0F_r9gen_weaksel_gens50.txt /labs/evolution/projects/popanc_sims/sims/selection/genoP1F_r9gen_weaksel_gens50.txt /labs/evolution/projects/popanc_sims/sims/selection/genoAdmixF_r9gen_weaksel_gens50.txt
scp estpanc_n4weakselGens50Rep9Chain1.hdf5 /labs/evolution/projects/popanc_sims/mcmc/
cd /local/scratch/
sleep 5
popanc -o estpanc_n10weakselGens50Rep9Chain1.hdf5 -m 30000 -b 10000 -t 5 -n 10 -d 20 -s 1 -u 10 -l 0.1 -a 0.1 -z 1 /labs/evolution/projects/popanc_sims/sims/selection/genoP0F_r9gen_weaksel_gens50.txt /labs/evolution/projects/popanc_sims/sims/selection/genoP1F_r9gen_weaksel_gens50.txt /labs/evolution/projects/popanc_sims/sims/selection/genoAdmixF_r9gen_weaksel_gens50.txt
scp estpanc_n10weakselGens50Rep9Chain1.hdf5 /labs/evolution/projects/popanc_sims/mcmc/
cd /local/scratch/
sleep 5
popanc -o estpanc_n20weakselGens50Rep9Chain1.hdf5 -m 30000 -b 10000 -t 5 -n 20 -d 20 -s 1 -u 10 -l 0.1 -a 0.1 -z 1 /labs/evolution/projects/popanc_sims/sims/selection/genoP0F_r9gen_weaksel_gens50.txt /labs/evolution/projects/popanc_sims/sims/selection/genoP1F_r9gen_weaksel_gens50.txt /labs/evolution/projects/popanc_sims/sims/selection/genoAdmixF_r9gen_weaksel_gens50.txt
scp estpanc_n20weakselGens50Rep9Chain1.hdf5 /labs/evolution/projects/popanc_sims/mcmc/