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Bug report - find internal joins

John Nash
  • John Nash

    John Nash - 2011-07-13

    Good afternoon,

    I was just using gap5 to clean up some sequence after a Newbler assembly.  I converted the 454Contigs.ace to a gap5 database, opened gap5 and immediately did a "find internal joins".  It crashed and here is the last part of the crash report:

    Level 1: FIJ_OK_Pressed .fij io=0x101188be0 .fij.infile .fij.sel_task .fij.match.blocks .fij.match.min_overlap .fij.match.word_length .fij.match.f.min_match .fij.match.f.use_band .fij.match.s.max_diag .fij.match.s.band_size .fij.match.max_mis .fij.hidden.yn .fij.sel_mode.rl .fij.ops .fij.align_length .fij.match.f.use_filter .fij.match.f.filter_cutoff
    Wed 13 Jul 15:51:02 2011 signal_handler: Program terminated unexpectedly with signal 11.
    Wed 13 Jul 15:51:02 2011 signal_handler: This is probably a bug.
    Wed 13 Jul 15:51:02 2011 signal_handler: Please report all bug reports at
    Abort trap

    I'm using the Staden package which was downloaded from svn and compiled on May 3rd, 2011.  I'm running it on a MacBook Air with 4 GB RAM.

    The genome is a 5 megabase Salmonella genome, with reads representing 14-fold coverage, and there are about 171K reads and 206 contigs.

    If you need any more info, I'll happily oblige.


  • James Bonfield

    James Bonfield - 2011-07-14

    It's probably worth trying the latest SVN release. I've been spending a lot of time checking for and fixing bugs, although some have lead to inconsistencies in the database itself so they show up elsewhere too. That's one reason I haven't done a new release for a while - I want to try and consolidate what I have and make it less buggy first.


  • John Nash

    John Nash - 2011-07-21

    Just to draw a line under this… the 21 July 2011 version in SVN fixes this.

    Thanks James.


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