correct genome sequence number in the TEanno.sum file #73

oushujun · Apr 3, 2020 · 5b9b9fe · 5b9b9fe
1 parent 7cf1214
commit 5b9b9fe
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/EDTA.pl b/EDTA.pl
@@ -607,7 +607,7 @@
 	`perl $make_masked -genome $genome -rmout $genome.out -maxdiv 30 -minscore 1000 -minlen 1000 -hardmask 1 -misschar N -threads $threads -exclude $exclude`;
 	`mv $genome.new.masked $genome.MAKER.masked`;
 	my $maker_TE = `perl $count_base $genome.MAKER.masked`;
-	$maker_TE = (split /\s+/, $maker_TE)[-1];
+	$maker_TE = (split /\s+/, $maker_TE)[3];
 	$maker_TE = sprintf("%.2f%%", $maker_TE*100);
 
 	# check results and report status

diff --git a/util/buildSummary.pl b/util/buildSummary.pl
@@ -691,7 +691,7 @@ sub usage {
 ##
 print "Repeat Stats\n";
 print "============\n";
-print "Total Sequences: " . scalar( keys( %seqs ) ) . "\n";
+print "Total Sequences: " . $totalSeqNum . "\n";
 print "Total Length: $totalSeqLen bp\n";
 if ( $taxDB ) {
   print "Ancestral Repeats: $ancestralCount ( $ancestralBPMasked bp )\n";