Added additional arguments, clarified error msg

New arguments:
-The two arguments speciePos_genome and speciePos_proteomes gives the position of the species identifier in the proteomes and genomes files respectively.
-gapLength: Sequences starting with more than this number of gaps will be sent to findAltStart
-cores: The number of cores/threads to use.

Added and clarified error messages when ids are not found in hashes of annotation and genome files