If you had printed the system command that you were running you would have figured this out.

Update

Just to show what I meant consider what happens when your code is modified like so: 


my $command = qq("svr_submit_RAST_job --user "$username" --passwd "$Pa
+ssword" --fasta "$fasta" --domain "$domain" --genetic_code "$Genetic_
+code") ;

print "\n\n\nGoing to run the following through system:\n $command\n";

[download]
Output 
Enter the Rast Username
username
Enter the Rast Password
password
Enter the fasta file Name
filename
Enter the Domain Name
domainname
Enter Genetic_Code
geneticcode



Going to run the following through system:
 "svr_submit_RAST_job --user "username
" --passwd "password
" --fasta "filename
" --domain "domainname
" --genetic_code "geneticcode
"

[download]

And the newlines are there for you to see, as plain as daylight.

In reply to Re: Perl calling Linux commands by tmharish
in thread Perl calling Linux commands by MVRS

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.