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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.
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.