add log file to gmap step

bin/gmapRescue.sh

@@ -48,10 +48,10 @@ do
 		targetindexdir=$gmapdbdir
 		targetgff=$rootdir'/gmap.wholeGenome.gff3'
 		gmapexe='gmapl'
-		eval $gmapexe --min-identity 0.90 --min-trimmed-coverage 0.80 --ordered -n 1 -d $targetindex -D $targetindexdir -f 2 $rootdir'/query.mrna.fasta' 1> $targetgff 
+		eval $gmapexe --min-identity 0.90 --min-trimmed-coverage 0.80 --ordered -n 1 -d $targetindex -D $targetindexdir -f 2 $rootdir'/query.mrna.fasta' 1> $targetgff 2> $rootdir'/gmap.wg.log'
 	else
 		echo "running gmap on target"
-		eval gmap --ordered -n 1 -g $rootdir'/target.fasta' -f 2 $rootdir'/query.mrna.fasta' 1> $targetgff
+		eval gmap --ordered -n 1 -g $rootdir'/target.fasta' -f 2 $rootdir'/query.mrna.fasta' 1> $targetgff 2> $rootdir'/gmap.target.log'
 	fi
 	eval gmap --ordered -n 1 -g $rootdir'/query.fasta' -f 2 $rootdir'/query.mrna.fasta' 1> $rootdir'/gmap.query.gff3'