Aligned sequential 01b to cluster

01b_MesobromionCluster.R

@@ -72,9 +72,9 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
   species <- read_delim(species.path, delim="\t") %>%
 		as.data.frame()
   traits <- read_delim(traits.path, delim="\t") %>%
-		as.data.frame() %>% 
+		as.data.frame()# %>% 
 ### TEMPORARY FOR TESTING!
-    dplyr::select(1:11)
+#    dplyr::select(1:11)
   
   
   traits <- traits %>% 

cli_01b.r

@@ -65,7 +65,7 @@ parser <- OptionParser(
        epilogue    = "use with caution, the awesomeness might slap you in the face!"
 )
 
-cli <- parse_args(parser, positional_arguments = 4)
+cli <- parse_args(parser, positional_arguments = 5)
 
 # ------------------------------------------------------------------------------
 # assign a few shortcuts

submit_01b.sh

@@ -9,12 +9,10 @@
 #$ -l h_rt=00:45:00:00
 #$ -l h_vmem=1G
 
-#$ -pe smp 1-1
+#$ -pe smp 24-32
 
 #$ -cwd
 
-#$ -t 24-32
-
 
 module load R
 
@@ -25,7 +23,7 @@ Rscript \
     --max.inter.t 20 \
     --chunk.i NA \
     --chunkn 32 \
-    --nperm 999 \
+    --nperm 99 \
     /data/splot/HIDDEN/species.out.10perc.txt \
     /data/splot/HIDDEN/traits.out.10perc.txt \
     "$output" \