Running a program via CGI is very different from running a program from command line, and also has much more security issues.

summary:

#!/usr/bin/perl -wT
use CGI;
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Update:

After reading your post again, it seems your problem is indeed related to permissions. Make shure the files are writeable for the user the webserver is running as.

Try checking the results of your system call like this:

system("command ...") == 0 or die "System error: $?";
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You could also take a look at the error logs and see the error code your script outputs.

-- 
Joost       downtime n. The period during which a system
            is error-free and immune from user input.
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The OP is using the single-argument form, with part of that argument taken directly from the form input. Bad Idea. Use the multiple-argument form of system after validating the form input, that each variable contains only data that's expected:

system ("/var/www/perl/cgi_classification.pl", $outfile, $input_sequen
+ce, $name);
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This line looks hairy, as well:

open OUTFILE, ">/var/www/data/$ARGV[0]" or die "cannot....";
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my $filename = $ARGV[0];
# Use whatever regex suits your needs. this is just an example.
if ($filename =~ /^([\w]+\.[\w]+)$/) { 
  $filename = $1;
  } else {
  # handle the error here
}
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HTH

--

There are 10 kinds of people -- those that understand binary, and those that don't.