Your code can be simplified to: 

my %file_hash;
open my $fh, '<', $fasta_file or die "Cannot open '$fasta_file' $!";
while ( <$fh> ) {
    my ( $name ) = m!/([^/]+)$!;
    $name =~ m!((?<=^.{3})\d{4}|(?<=^.{2})\d{8})([FPR])$! or do {
        print "$name is crap\n";
        next;
        };
    $file_hash{ "$1.\L$2" } = $name;
    }
close $fh;

open my $qh, '<', $qual_file or die "Cannot open '$qual_file' $!";
while ( my $file = <$qh> ) {
    chomp $file;
    next unless $file =~ m!/((?:\d{4}|\d{8})\.[frp])!;
    if ( exists $file_hash{ $1 } ) {
        rename $file, "$dir/$file_hash{$1}" or die "Cannot rename '$fi
+le' $!";
        }
    else {
        print "no key $1\n";
        }
    }

[download]
Hopefully :) that may be faster, depending on the size of %file_hash of course.

In reply to Re: performance problems with renaming multiple files using another file name by jwkrahn
in thread performance problems with renaming multiple files using another file name by mav3067

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