diff --git a/scripts/confirm_genes.pl b/scripts/confirm_genes.pl
index db2560a76..9d87bc330 100755
--- a/scripts/confirm_genes.pl
+++ b/scripts/confirm_genes.pl
@@ -623,14 +623,16 @@ sub create_transcript_file {
 	}else {
 		$prefix = $wormbase->chromosome_prefix."${chrom}_";
 	}
-        my $trinity = -e "${gffdir}/${prefix}BLAT_Trinity_BEST.gff" ? "${prefix}BLAT_Trinity_BEST.gff" : '';
-	my $isoseq  = -e "${gffdir}/${prefix}BLAT_IsoSeq_BEST.gff"  ? "${prefix}BLAT_IsoSeq_BEST.gff"  : '';
 
-	$wormbase->run_command("cd $gffdir; cat ${prefix}BLAT_EST_BEST.gff ${prefix}BLAT_mRNA_BEST.gff $trinity $isoseq > ${prefix}BLAT_TRANSCRIPT_BEST.gff", $log);
+	my $file = "${prefix}BLAT_TRANSCRIPT_BEST.gff";
+
+	return if $file; # don't rebuild the file every single time
 
-	# only elegans has OSTs and RSTs
-	$wormbase->run_command("cd $gffdir; cat ${prefix}BLAT_OST_BEST.gff ${prefix}BLAT_RST_BEST.gff >>  ${prefix}BLAT_TRANSCRIPT_BEST.gff", $log) if ($wormbase->species eq 'elegans');
+        my $trinity = -e "${gffdir}/${prefix}BLAT_Trinity_BEST.gff" ? "${prefix}BLAT_Trinity_BEST.gff" : '';
+	my $isoseq  = -e "${gffdir}/${prefix}BLAT_IsoSeq_BEST.gff"  ? "${prefix}BLAT_IsoSeq_BEST.gff"  : '';
+	my $more = ($wormbase->species eq 'elegans') ? "${prefix}BLAT_OST_BEST.gff ${prefix}BLAT_RST_BEST.gff" : ''; # only elegans has OSTs and RSTs
 
+	$wormbase->run_command("cd $gffdir; cat ${prefix}BLAT_EST_BEST.gff ${prefix}BLAT_mRNA_BEST.gff $trinity $isoseq $more > $file", $log);
 }
 ################