update

Author: ShuXingYu94

multithreading.sh

@@ -220,7 +220,9 @@ cd ${stacks_dir}
 vcftools --vcf populations.snps.vcf --out mean_depth_stat --site-mean-depth
 awk '{$4="";print $0}' mean_depth_stat.ldepth.mean |  awk '$0=NR" "$0' > SNP_Mean_Depth.txt
 cd ${workdir}
-r -f r_plot.r
+cp ./stacks/SNP_Mean_Depth.txt tmp.txt
+R -f r_plot.r
+rm tmp.txt
 if test -f "Rectangular-Manhattan.MEAN_DEPTH_depth.jpg"; then
   mv Rectangular-Manhattan.MEAN_DEPTH_depth.jpg ./statistics/SNP_Depth_0.jpg
 else
@@ -232,9 +234,12 @@ cd ${stacks_dir}
 cat populations.snps.vcf | grep -E '#' > vcfform.txt
 sed -e '/#CHROM/r vcfform.txt' snps_depth_10.txt | sed '1d' > snps_depth_10.vcf
 rm vcfform.txt
-vcftools --vcf populations.snps.vcf --site-mean-depth | awk '{$4="";print $0}' mean_depth_stat.ldepth.mean |  awk '$0=NR" "$0' >> SNP_Mean_Depth.txt
+vcftools --vcf snps_depth_10.vcf --site-mean-depth --out mean_depth_stat_10
+awk '{$4="";print $0}' mean_depth_stat_10.ldepth.mean |  awk '$0=NR" "$0' > SNP_Mean_Depth_10.txt
 cd ${workdir}
-r -f r_plot.r
+cp ./stacks/SNP_Mean_Depth_10.txt tmp.txt
+R -f r_plot.r
+rm tmp.txt
 if test -f "Rectangular-Manhattan.MEAN_DEPTH_depth.jpg"; then
   mv Rectangular-Manhattan.MEAN_DEPTH_depth.jpg ./statistics/SNP_Depth_10.jpg
 else

r_plot.r

@@ -1,3 +1,3 @@
 library(CMplot);
 data<-read.table(file = "./tmp.txt",header = TRUE);
-CMplot(data,plot.type="m",cex=0.8, band=0.5,col=c("grey30","grey60"),threshold = 10,threshold.lty = 1,LOG10=FALSE,ylab = "Average Depth of SNP", file="jpg", memo="depth", dpi=300, file.output=TRUE, verbose=TRUE);
+CMplot(data,plot.type="m",cex=0.8, band=0.5,col=c("grey30","grey60"),threshold = 10,threshold.lty = 1,LOG10=TRUE,ylab = "Average Depth of SNP", file="jpg", memo="depth", dpi=300, file.output=TRUE, verbose=TRUE);