Post date: Aug 12, 2015 9:10:3 PM
We have been having trouble with bayenv2 not finishing, so I am trying a run with all 25 populations with a revised perl script. I am running two chains total. All of my files are in /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/. My infiles out1_snps.txt and out2_snps.txt are identical to each other (184287 SNPs) and to Sam's bayen_snpsfile.txt (I just re-named this when I copied it). My new perl script for submitting these jobs is /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/wrap_qsub_rc.pl. It does a better job of keeping the directories clean. I have it set to use stndenvironfile.txt and onematrix.txt as infiles and to run 200,000 MCMC steps. It runs 500 SNPs per node. It is executed as follows (for chain 2, this can be changed by editing the script and giving a different directory):
perl wrap_qsub_rc_bayen.pl /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/out2/ /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/out2_snps.txt
Here is an example:
~/bin/bayenv2 -i snp2_497.txt -e /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/stndenvironfile.txt -m /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/onematrix.txt -k 200000 -t -r 779 -o out2_1 -n 1 -p 25
rm snp2_497.txt
rm snp2_497.txt.freqs
echo "0 7 0 0 0 2 0 0 0 0 0 0 0 00 0 0 0 0 0 0 0 0 0 0
38 33 40 46 20 38 40 40 36 48 40 40 38 38 40 32 36 40 40 26 40 40 40 40 34" > snp2_498.txt
~/bin/bayenv2 -i snp2_498.txt -e /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/stndenvironfile.txt -m /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/onematrix.txt -k 200000 -t -r 940 -o out2_1 -n 1 -p 25
rm snp2_498.txt
rm snp2_498.txt.freqs
echo "1 0 0 0 0 0 4 3 0 0 2 0 2 00 3 0 1 2 0 2 0 0 0 0
37 40 40 46 20 40 36 37 36 48 38 40 36 38 40 29 36 39 38 26 38 40 40 40 34" > snp2_499.txt
~/bin/bayenv2 -i snp2_499.txt -e /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/stndenvironfile.txt -m /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/onematrix.txt -k 200000 -t -r 537 -o out2_1 -n 1 -p 25
rm snp2_499.txt
rm snp2_499.txt.freqs
echo "0 0 0 0 0 0 0 0 0 3 0 0 0 00 0 0 0 0 0 0 0 0 0 0
38 40 40 46 20 40 40 40 36 45 40 40 38 38 40 32 36 40 40 26 40 40 40 40 34" > snp2_500.txt
~/bin/bayenv2 -i snp2_500.txt -e /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/stndenvironfile.txt -m /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/onematrix.txt -k 200000 -t -r 271 -o out2_1 -n 1 -p 25
rm snp2_500.txt
rm snp2_500.txt.freqs
rsync -avz out2_1.bf /labs/evolution/projects/Lmelissa_host_adaptation/zBayen2/out2/
rm out2_1.bf