diff --git a/dDocent b/dDocent
index f76051f..ae02de7 100755
--- a/dDocent
+++ b/dDocent
@@ -3,7 +3,7 @@ export LC_ALL=en_US.UTF-8
 export SHELL=bash
 
 ##########dDocent##########
-VERSION='2.9.5'; export VERSION
+VERSION='2.9.6'; export VERSION
 #This script serves as an interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD (SE or PE), ezRAD (SE or PE) data, or SE RAD data.
 #It requires that your raw data are split up by tagged individual and follow the naming convention of:
 
@@ -152,7 +152,7 @@ if [ "$TEST" -gt 0 ]; then
 fi
 
 #Count number of individuals in current directory
-NumInd=$(ls *.F.fq.gz 2> /dev/null | wc -l)
+NumInd=$(find . -maxdepth 1 -type f -name "*.F.fq.gz" | wc -l)
 NumInd=$(($NumInd - 0))
 
 #Test for file limits for current user and reset if necessary
@@ -168,7 +168,7 @@ if [ "$Flimit" != "unlimited" ]; then
 fi
 
 #Create list of sample names
-ls *.F.fq.gz > namelist 2> /dev/null
+find . -maxdepth 1 -type f -name "*.F.fq.gz" -printf "%f\n" > namelist
 sed -i'' -e 's/.F.fq.gz//g' namelist
 #Create an array of sample names
 NUMNAMES=$(mawk '/_/' namelist | wc -l)
@@ -416,7 +416,7 @@ fi
 
 if [ "$MAP" != "no" ]; then
 	echo -e "\nCreating alignment intervals"
-	ls *-RG.bam >bamlist.list
+	find . -maxdepth 1 -type f -name "*-RG.bam" -printf "%f\n" > bamlist.list
 	CreateIntervals 
 fi
 
@@ -424,7 +424,7 @@ fi
 
 if [ "$SNP" != "no" ]; then
 	#Create list of BAM files
-	ls *-RG.bam >bamlist.list
+	find . -maxdepth 1 -type f -name "*-RG.bam" -printf "%f\n" > bamlist.list
 	#If mapping is not being performed, but intervals do not exist they are created
 	if [[ "$MAP" == "no" && ! -f "cat-RRG.bam" ]]; then
 		CreateIntervals 
@@ -435,12 +435,11 @@ if [ "$SNP" != "no" ]; then
 	fi
 	#Check to make sure interval files have been created
 	if [[ "$MAP" == "no" && ! -f "mapped.bed" ]]; then
-        	#bedtools bamtobed -i cat-RRG.bam > cat-RRG.bed
+        #bedtools bamtobed -i cat-RRG.bam > cat-RRG.bed
 		#bedops --merge cat-RRG.bed > mapped.bed
 		cat namelist | parallel -j $FB2 "bedtools bamtobed -i {}-RG.bam | sort-bed - | bedops --merge - > {}-RG.bed"
 		bedops --merge *-RG.bed | bedtools sort -i - -faidx reference.fasta.fai > mapped.bed
-		rm *-RG.bed
-		
+		find . -maxdepth 1 -type f -name "*-RG.bed" -delete
 	fi
 	#This code estimates the coverage of reference intervals and removes intervals in 0.01% of depth
 	#This allows genotyping to be more effecient and eliminates extreme copy number loci from the data
@@ -563,8 +562,9 @@ if [ "$SNP" != "no" ]; then
 					len=$3-$2;lc=len*$4;cov = cov + lc
 					if ( cov < cutoff) {x="mapped."i".bed";print $1"\t"$2"\t"$3 > x}
 					else {i=i+1; x="mapped."i".bed"; print $1"\t"$2"\t"$3 > x; cov=0}
-				}'                
-			ls mapped.*.bed | sed -e 's/mapped.//g' | sed -e 's/.bed//g' | shuf | parallel --bar --halt now,fail=1 --env call_genos2 -j 4 --no-notice "call_genos2 {} "
+				}'
+			         
+			find . -maxdepth 1 -type f -name "mapped.*.bed" -printf "%f\n" | sed -e 's/mapped.//g' | sed -e 's/.bed//g' | shuf | parallel --bar --halt now,fail=1 --env call_genos2 -j 4 --no-notice "call_genos2 {} "
 					
 			if [ -f "freebayes.error" ]; then
 				echo -e "\n\n\nFreeBayes has failed when trying to finish a previously failed instance.  Memory and processor settings need to be drastically reconfigured"
@@ -588,8 +588,7 @@ if [ "$SNP" != "no" ]; then
 	export -f finish_genos
 	
 	rm freebayes.error freebayes.log &> /dev/null
-	
-	ls mapped.*.bed | sed -e 's/mapped.//g' | sed -e 's/.bed//g' | shuf | parallel --bar --halt now,fail=10 --env call_genos -j $NUMProc --no-notice --joblog ./par.log "call_genos {} "
+	find . -maxdepth 1 -type f -name "mapped.*.bed" -printf "%f\n" | sed -e 's/mapped.//g' | sed -e 's/.bed//g' | shuf | parallel --bar --halt now,fail=10 --env call_genos -j $NUMProc --no-notice --joblog ./par.log "call_genos {} "
 
 	if [ -f "freebayes.error" ]; then
 		FAILS=$( cat freebayes.error | wc -l )
@@ -601,7 +600,7 @@ if [ "$SNP" != "no" ]; then
 			rm freebayes.redos
 		else	
 			echo -e "\nmultiple instances of freebayes failed.  dDocent will now recalibrate run parameters to use less memory.\n"
-			rm mapped.*.bed
+			find . -maxdepth 1 -type f -name "mapped.*.bed" -delete
 			rm freebayes.error
 			LIM=$(( $SNPNUMProc * 4 ))
         	if head -1 reference.fasta | grep -e 'dDocent' 1>/dev/null; then
@@ -628,7 +627,7 @@ if [ "$SNP" != "no" ]; then
 			echo "Using FreeBayes to call SNPs again"
 			NumP=$(( $NUMProc / 4 ))
 			NumP=$(( $NumP * 3 ))
-			ls mapped.*.bed | sed -e 's/mapped.//g' | sed -e 's/.bed//g' | shuf | parallel --bar --halt now,fail=10 --env call_genos -j $NumP --no-notice --joblog ./par2.log "call_genos {} " 
+			find . -maxdepth 1 -type f -name "mapped.*.bed" -printf "%f\n" | sed -e 's/mapped.//g' | sed -e 's/.bed//g' | shuf | parallel --bar --halt now,fail=10 --env call_genos -j $NumP --no-notice --joblog ./par2.log "call_genos {} " 
         fi
     fi
 
@@ -666,7 +665,7 @@ if [ "$SNP" != "no" ]; then
 			NumP=$(( $NumP / 4 ))
 			NumP=$(( $NumP * 3 ))
 			echo "Using FreeBayes to call SNPs again"
-			ls mapped.*.bed | sed -e 's/mapped.//g' | sed -e 's/.bed//g' | shuf | parallel --bar --halt now,fail=10 --env call_genos -j $NumP --joblog ./par3.log --no-notice "call_genos {}"
+			find . -maxdepth 1 -type f -name "mapped.*.bed" -printf "%f\n" | sed -e 's/mapped.//g' | sed -e 's/.bed//g' | shuf | parallel --bar --halt now,fail=10 --env call_genos -j $NumP --joblog ./par3.log --no-notice "call_genos {}"
         fi
 	fi
 
@@ -677,9 +676,8 @@ if [ "$SNP" != "no" ]; then
 	else
         ERROR3=0
 		export ERROR3
-        fi
-
-	rm mapped.*.bed  
+	fi
+	find . -maxdepth 1 -type f -name "mapped.*.bed" -delete  
 
 	mv raw.1.vcf raw.01.vcf 2>/dev/null
 	mv raw.2.vcf raw.02.vcf 2>/dev/null
@@ -768,7 +766,7 @@ TrimReads () {
 	if [ $STACKS -gt 0 ]; then
 		echo "Removing the _1 character and replacing with /1 in the name of every sequence"
 		cat namelist | parallel -j $FB1 --no-notice "gunzip -c {}.F.fq.gz | sed -e 's:_1$:/1:g' > {}.F.fq"
-		rm -f *.F.fq.gz
+		find . -maxdepth 1 -type f -name "*.F.fq.gz" -delete
 		cat namelist | parallel -j $FB1 --no-notice "gzip {}.F.fq"
 	fi
 
@@ -778,7 +776,7 @@ TrimReads () {
 		if [ $STACKS -gt 0 ]; then
 			echo "Removing the _2 character and replacing with /2 in the name of every sequence"
 			cat namelist | parallel -j $FB1 --no-notice "gunzip -c {}.R.fq.gz | sed -e 's:_2$:/2:g' > {}.R.fq"
-			rm -f *.R.fq.gz
+			find . -maxdepth 1 -type f -name "*.R.fq.gz" -delete
 			cat namelist | parallel -j $FB1 --no-notice "gzip {}.R.fq"
 		fi
 	fi
@@ -1205,7 +1203,7 @@ wait
     	#bedops --merge cat-RRG.bed > mapped.bed
     	cat namelist | parallel -j $FB2 "bedtools bamtobed -i {}-RG.bam | sort-bed - | bedops --merge - > {}-RG.bed"
 	bedops --merge *-RG.bed | bedtools sort -i - -faidx reference.fasta.fai > mapped.bed
-	rm *-RG.bed
+	find . -maxdepth 1 -type f -name "*-RG.bed" -delete
 }
 
 #This checks that dDocent has detected the proper number of individuals and exits if incorrect