<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello,<div><br></div><div>I does appear than my genome.ann file from maker2zff script has data in it. However, the SNAP steps after that have created empty files. The following are all empty:</div><div><br></div><div>alt.dna err.dna export.dna genome.dna olp.dna uni.dna wrn.dna</div><div><div>alt.ann err.ann export.ann genome.ann olp.ann uni.ann wrn.ann</div><div><br></div><div>When I tried to get gene stats or validate genome.ann, I get errors like this for all of them:</div><div><br></div><div>fathom genome.ann genome.dna -gene-stats |more</div><div><div>MODEL5547 1 1 6 + errors(6): exon-1:out_of_bounds exon-2:out_of_bounds exon-3:out_of_bounds exon-4:out_of_bounds exon-5:out_of_bounds exon-6:out_of_bounds</div><div>MODEL5568 1 1 6 - errors(6): exon-6:out_of_bounds exon-5:out_of_bounds exon-4:out_of_bounds exon-3:out_of_bounds exon-2:out_of_bounds exon-1:out_of_bounds</div><div>MODEL5589 1 1 5 + errors(5): exon-1:out_of_bounds exon-2:out_of_bounds exon-3:out_of_bounds exon-4:out_of_bounds exon-5:out_of_bounds</div><div>MODEL5195 1 1 21 + errors(21): exon-1:out_of_bounds exon-2:out_of_bounds exon-3:out_of_bounds exon-4:out_of_bounds exon-5:out_of_bounds exon-6:out_of_bounds exon-7:out_of_bounds exon-8:out_of_bounds exon-9:out_of_bounds exon-10:out_of_bounds exon-11:out_of_bounds exon-12:out_of_bounds exon-13:out_of_bounds exon-14:out_of_bounds exon-15:out_of_bounds exon-16:out_of_bounds exon-17:out_of_bounds exon-18:out_of_bounds exon-19:out_of_bounds exon-20:out_of_bounds exon-21:out_of_bounds</div></div><div><br></div><div>I'm not sure why the annotation I'm seeing in genome.ann are all showing up as errors. I realize this may be an issue with snap, but are you familiar with anything like this? Snippet of my genome.ann file is attached (since its too big for the list) for reference.</div><div><br></div><div>Thanks</div><div>Dhivya</div></div><div><br></div><div></div></body></html>