Error calculating consensus

Patusco
2010-05-27
2013-04-18
  • Patusco
    Patusco
    2010-05-27

    Hi,

    when I run gap4 with a set of 5000 sequences, with the option of Normal shotgun assembly, I get this error - Error calculating consensus, and the assembly stops, and it only assembled 358 sequences.
    Does anyone knows why it appears?
    I have the staden 1.7 for windows installed.

    thanks

     
  • James Bonfield
    James Bonfield
    2010-05-27

    This is probably hitting some arbitrary limits. Try going to the main Gap4 options menu and setting the maximum consensus length to something much higher (eg 10 million).  I ought to change the defaults to something far larger, given the typical size of a modern machine.