I am attempting to align 2 whole genomes of closely related fish species (zebrafish and another sucker species) using the LASTZ plugin in Geneious. The zebrafish genome was downloaded from UCSC and the other species' sequence was generated using Illumina. I have tried several different parameter changes in LASTZ and I continue to get the following error message: "Cannot import results file for job KN149692.1: There are no alignment results."
According to the NCBI, the zebrafish genome (GRCz10) contains some scaffolds that have been located on a chromosome and these are given a "CM" file name. The location of other scaffolds are not known and are therefore given a "KN" file name. LASTZ always gets through the CM files with no problem and fails once it reaches the KN files. Is there a way to prune or trim the zebrafish genome down to just the CM files? These files contain most of the information and will therefore allow me to map the majority of the genome to the closely related species that I'm interested in.
Any comments or suggestions would be very helpful. I'm using Red Hat Linux 6.7.