The reason being that the original file is 8GB in size,

Which file is 8GB? You're processing 2 files. are they both 8GB?

Other important pieces of information:

  1. how many sequences are there in each of those files?

    A simple grep '>' file | wc -l will tell you.

  2. The same number in both?
  3. Do the sequences appear in the same order in both files?

With the right answers, your problem could be much simpler and quicker than your current approach. Even if the answers aren't so helpful, there is almost certainly a better approach than your current one, but you do need to provide the information,

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
"Too many [] have been sedated by an oppressive environment of political correctness and risk aversion."

In reply to Re: When the input file is huge !!! by BrowserUk
in thread When the input file is huge !!! by sugar

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.