open (FILE, $ReferenceFilePath) or die "Can't open file"; chomp (@REFFILELIST = ()); open OUTFILE, ">$OUTPUTFILE" or die $!; foreach my $line (@REFFILELIST) { open (LARGEFILE, $LARGESIZEDFILE) or die "Can't open File"; while () { my $Result = index($_, $line); if ($Result > 0) { open(my $FDH, ">>$OUTPUTFILE"); print $FDH $_; } } close(LARGEFILE); } close(OUTFILE); close(FILE);