diff --git a/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm b/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm
index e86ed38b41127cbfe3b4dd0f0342eb94f28fe6aa..d8b6aaf432440859006b2157529fd9a2f291db0c 100644
--- a/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/FASTA/DumpFile.pm
@@ -505,7 +505,7 @@ sub _generate_file_name {
 
   my $file_name = join( '.', @name_bits );
 
-  $data_type =~ s/_rm$//;    # remove repeatmask designation from path component
+  $data_type =~ s/_[rs]m$//;    # remove repeatmask or softmask designation from path component
   my $data_type_dir = $self->fasta_path($data_type);
   $self->_remove_files_from_dir($data_type_dir);
   return File::Spec->catfile( $data_type_dir, $file_name );