create directory at the very beginning

moved the function to create directory at the very beginning.
This is only needed for the image to quit properly in Condor and not hang forever in the system.

GWASSER.R

@@ -113,6 +113,13 @@ processArgs <- function(){
   return(arguments)
 }
 
+if(!interactive()){
+    if(!dir.exists(args$outdir)){
+        message("Output directory is missing, creating directory...")
+        dir.create(args$outdir, recursive = TRUE)
+    }
+}
+
 if(!interactive()) {
   args <- processArgs()
   if (!args$noplots) {
@@ -298,11 +305,6 @@ if(!interactive()){
     message("------------------------")
     message("Start Analysis:\n")
 
-    if(!dir.exists(args$outdir)){
-        message("Output directory is missing, creating directory...")
-        dir.create(args$outdir, recursive = TRUE)
-    }
-
     message("Now reading genotype file...")
     genotypes <- parseGeno(args$gfile)