Hi everyone,

So I'm trying to generate some axtFiles from a whole-genome alignment - using this walkthrough http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto ... however at the stage where I am trying to convert net files to axt files I get the following error

Duplicate chain 1 ending line 476476 of all.pre.chain

Does anyone know where this error is coming from? And where to begin fixing it - I honestly don't know where to start.

Many thanks in advance