There are a number of issues here:

• "i'm a beginner so happy to give me more info." — OK, that's fair enough, there are missing pieces of information that would help us to help you. These include things like: example input, actual output, expected output and diagnostic messages. See "How do I post a question effectively?" and "SSCCE" for details.
• "$ cat annotation_files_path ...":
  • To be honest, I'm questioning whether "cat" was intended: two of the three arguments shown are directories.
  • If "cat" was intended, where's the output?
  • Please wrap commands and output in <code>...</code> tags: it's easier to read; output format is not lost; and, you don't need to do anything about special characters (e.g. there's no need to change '<' to '&lt;').
  • The two pathnames starting with "~/home/usr/" look wrong: "/home/usr/", "~usr/", or just "~/" would be more usual. If it's not wrong (e.g. perhaps it expands to "/home/your_uname/home/usr/") you should mention this because, as it stands, it's confusing.
• There are a number of issues with your code:
  • "i'm a beginner" — take a look at "perlintro - Perl introduction for beginners".
  • The shebang line (#!usr/bin/perl) looks wrong: there should probably be a slash before usr (i.e. #!/usr/bin/perl).
  • Always use the strict and warnings pragmata. If you followed the perlintro link (above), you'll know why.
  • @ARGV:
    • This is a special variable: see "perlvar - Perl predefined variables".
    • You've declared a lexical variable (my @ARGV) with the same name: this is rarely, if ever, a good idea.
    • It's an array variable but you've assigned a scalar value to it (@ARGV = []). While that works syntactically, it's unlikely to work as functionally intended. You possibly meant '()' instead of '[]'; however, that's redundant anyway.
    • Having populated that array, you don't subsequently use it!
    • My code below has examples of @ARGV usage and array declaration.

The following code (pm_1192233_multi_file_output.pl) may do roughly what you want. If not, there should be sufficient examples of techniques to get you on the right track.

#!/usr/bin/env perl

use strict;
use warnings;
use autodie;
use constant {
    GENE_FILE    => 'pm_1192233_genes.txt',
    MISSING_FILE => 'pm_1192233_missing.txt',
    OUT_PREFIX   => 'pm_1192233_out_',
};

my @ano_files = @ARGV;

my ($gene_list, $gene_re) = get_gene_data(GENE_FILE);

for my $ano_file (@ano_files) {
    open my $fh, '<', $ano_file;
    while (<$fh>) {
        print { get_out_fh($1) } $_ if /$gene_re/;
    }
}

gen_missing_report($gene_list);

{
    my %fh_for;

    sub get_out_fh {
        unless (exists $fh_for{$_[0]}) {
            open $fh_for{$_[0]}, '>', OUT_PREFIX . $_[0];
        }
        return $fh_for{$_[0]};
    }

    sub gen_missing_report {
        my ($genes) = @_;
        open my $fh, '>', MISSING_FILE;
        print $fh "--- START MISSING LIST ---\n";
        print $fh "$_\n" for grep { ! exists $fh_for{$_} } @$genes;
        print $fh "--- END MISSING LIST ---\n";
    } 
} 

sub get_gene_data {
    my ($file) = @_;
    my @list;
    open my $fh, '<', $file;
    push @list, $_ while <$fh>;
    chomp @list;
    @list = sort { length $b <=> length $a } @list;
    my $alt = join '|', @list;
    return (\@list, qr{($alt)});
}
[download]

I created some dummy input:

$ cat pm_1192233_genes.txt
ACMSD
CRYM
ARIB1B
GENE_NOT_ANOTATED
ALSO_ABSENT
$ cat pm_1192233_anot_1.txt
ACMSD 1
XXXX 1
CRYM 1
$ cat pm_1192233_anot_2.txt
ARIB1B 2
YYYY 2
ACMSD 2
$ cat pm_1192233_anot_3.txt
WWWW 3
CRYM 3
ARIB1B 3
ZZZZ 3
[download]

I ran the script like this:

$ pm_1192233_multi_file_output.pl pm_1192233_anot_*
$
[download]

These files were produced:

$ cat pm_1192233_out_ACMSD
ACMSD 1
ACMSD 2
$ cat pm_1192233_out_ARIB1B
ARIB1B 2
ARIB1B 3
$ cat pm_1192233_out_CRYM
CRYM 1
CRYM 3
$ cat pm_1192233_missing.txt
--- START MISSING LIST ---
GENE_NOT_ANOTATED
ALSO_ABSENT
--- END MISSING LIST ---
[download]

Feel free to post follow-up questions, but please adhere to the guidelines I linked to at the start. You might also consider registering so that we can tell you apart from others posting anonymously.

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