performance problems with renaming multiple files using another file name

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#! /usr/bin/perl -w

...
  chomp($file);
  &rename($file, \%tmp_hash, $directory)
}

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./FASTA/LO-leaves_drought/LO45829460F
./FASTA/LO-leaves_drought/LO45815650F
...
./FASTA/LO-leaves_drought/LO45978413F
./FASTA/LO-leaves_drought/LO45866607F
./FASTA/LO-leaves_drought/LO46017397F

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./QUAL/48743192.f_a09_1.fasta.qual
./QUAL/51455741.f_b20_1.fasta.qual
...
./QUAL/48690145.f_l05_2.fasta.qual
./QUAL/46242796.f_g23_1.fasta.qual

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