Only check existence of toassemble files if stage<=1.

run-trust4

@@ -183,7 +183,7 @@ if ( @bamFiles > 0 )
 		push @singleFiles, "${prefix}_toassemble.fq" ;
 		$mainArgs .= " -u ${prefix}_toassemble.fq" ;
 	}
-	else
+	elsif ( $stage <= 1 )
 	{
 		die "Could not find files like ${prefix}_toassemble*.fq\n" ;
 	}