At a first glance, it seems you need a pair of braces around the print statement. And the file handle in the print statement.

while ($line=<in>) { 
        if($line=~/>/) { 
                @vettore=split(/\s+/, $line); 
                open my $fh, ">>seq_id.txt" or die "Cannot open output
+.txt: $!"; 
                foreach (@vettore) { # { was missing here, removed ;
                        print $fh $_ . "\n"; # file handle was missing
                } # } was missing here
                close $fh; # removed my 
        } 
}
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UPDATE: The regex for > at the beginning of line is /^>/. The name of the file you are trying to open for writing is inconsistent with the error message.