Any ideas?

Yes. You are naming both files the same, so the second overwrites the first. 

   my $out = Bio::SeqIO->new(
                    -file    => ">$file"."_fasta",
                    -format    => 'Fasta');

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In reply to Re: splitting fasta file into individual fasta files by BrowserUk
in thread splitting fasta file into individual fasta files by lomSpace

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