Dear confreres, I wrote a perl script using different modules. use SWISS::Entry; use integer; use Bio::Structure::IO; use Bio::AlignIO; use XML::Writer; use String::Approx qw /aslice/; use Bio::Tools::Run::StandAloneBlast; The program takes a list of ids (14_000) and makes calculations for each id. e.g a blast search (Protein sequence comparison) and string comparisons etc. The problem is that the program runs awhile (e.g. for 100 ids) and generates the appropiate output (a xml result file). But suddenly I get a segfault. I think that the problem is the blast executable (written in C) which is called by a module from bioperl. But I am not sure! What can I do to debug?????? Thanks in advance! Murcia

update (broquaint): title change (was segfault)

In reply to How to debug a segfault? by Anonymous Monk

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.