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print "@ids\n";
print "@files\n";

foreach my $id (@ids) {
    foreach my $fasta (@files) {
        open my $fh, '<', $fasta or die "can not open file $fasta: $!"
+;
...
        close $fh;
    }
}

my $pattern = join '|', @ids;
print grep {/$pattern/} <>;