In addition to what others have said, these two lines look like a problem: 
my $newRefFile = "$pathName\newRefFile.txt";
my $newBlastFile = "$pathName\newBlastFile.txt";

[download]
Those backslashes won't show up the way you expect unless you double them -- all they're doing here is inserting a newline in the strings. If $pathName is being defined the same way, the problem is compounded. I'm doubtful that this code works from the command line.

You might as well just use a plain old forward slash for separating directory names, because perl will know what you mean by that and do the Right Thing. (Or you could use the appropriate File:: module(s) to construct path names in an OS-neutral manner.)

In reply to Re: Cannot open files using CGI by graff
in thread Cannot open files using CGI by MonkPaul

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.