diff --git a/scripts/mask_low_complexity.sh b/scripts/mask_low_complexity.sh
index e35151c..b631cb3 100755
--- a/scripts/mask_low_complexity.sh
+++ b/scripts/mask_low_complexity.sh
@@ -23,17 +23,26 @@ if ! which $MASKER > /dev/null; then
   exit 1
 fi
 
+function mask_data_chunk () {
+  # Removes empty records and performs masking, all in pipes
+  MASKER=$1
+  awk -v RS=">" -v FS="\n" -v ORS="" ' { if ($2) print ">"$0 } ' |\
+  $MASKER -in - -outfmt fasta |\
+  sed -e '/^>/!s/[a-z]/x/g'
+}
+export -f mask_data_chunk
+
 if [ -d $target ]; then
   for file in $(find $target '(' -name '*.fna' -o -name '*.faa' ')'); do
     if [ ! -e "$file.masked" ]; then
-      $MASKER -in $file -outfmt fasta | sed -e '/^>/!s/[a-z]/x/g' > "$file.tmp"
+      cat $file | parallel --pipe --recstart '>' --blocksize 100M mask_data_chunk $MASKER > "$file.tmp"
       mv "$file.tmp" $file
       touch "$file.masked"
     fi
   done
 elif [ -f $target ]; then
   if [ ! -e "$target.masked" ]; then
-    $MASKER -in $target -outfmt fasta | sed -e '/^>/!s/[a-z]/x/g' > "$target.tmp"
+    cat $target | parallel --pipe --recstart '>' --blocksize 100M mask_data_chunk $MASKER > "$target.tmp"
     mv "$target.tmp" $target
     touch "$target.masked"
   fi