Some bug fixes in SLURM and with CPU

CPU/juicer.sh

@@ -320,10 +320,10 @@ fi
 
 # Get version numbers of all software
 echo -ne "Juicer version $juicer_version;" >> $headfile
-bwa 2>&1 | awk '\$1=="Version:"{printf(" BWA %s; ", \$2)}' >> $headfile 
+bwa 2>&1 | awk '$1=="Version:"{printf(" BWA %s; ", $2)}' >> $headfile 
 echo -ne "$threads threads; " >> $headfile
-java -version 2>&1 | awk 'NR==1{printf("%s; ", \$0);}' >> $headfile 
-${juiceDir}/scripts/juicer_tools -V 2>&1 | awk '\$1=="Juicer" && \$2=="Tools"{printf("%s; ", \$0);}' >> $headfile
+java -version 2>&1 | awk 'NR==1{printf("%s; ", $0);}' >> $headfile 
+${juiceDir}/scripts/juicer_tools -V 2>&1 | awk '$1=="Juicer" && $2=="Tools"{printf("%s; ", $0);}' >> $headfile
 echo "$0 $@" >> $headfile
 
 ## ALIGN FASTQ AS SINGLE END, SORT BY READNAME, HANDLE CHIMERIC READS

SLURM/scripts/juicer.sh

@@ -100,9 +100,9 @@ then
     long_queue_time="3600"
 else
     isVoltron=1
-
     export PATH=/gpfs0/biobuild/biobuilds-2016.11/bin:$PATH 
-    unset MALLOC_ARENA_MAX 
+    unset MALLOC_ARENA_MAX
+    load_gpu="CUDA_VISIBLE_DEVICES=0,1,2,3" 
     # Juicer directory, contains scripts/, references/, and restriction_sites/
     # can also be set in options via -D
     juiceDir="/gpfs0/juicer/"
@@ -1023,6 +1023,7 @@ DUPCHECK`
 			echo "***! Found errorfile. Exiting." 
 			exit 1 
 		fi 
+		${load_java}
 		export IBM_JAVA_OPTIONS="-Xmx16384m -Xgcthreads1"
 		tail -n1 $headfile | awk '{printf"%-1000s\n", \\\$0}' > $outputdir/inter.txt