I have a problem about gene annotation with software exonerate.
I have a scaffold-level genome sequence (fasta, about 800Mb) of target species and protein sequences (fasta, about 1Mb) of closely related species.
When I executed
exonerate \ --model protein2genome \ -q protein.fasta \ -t genome.fa \ -B yes \ -M 30000 \ --showvulgar no \ --showalignment no \ --showcigar yes \ --showtargetgff yes \ -V 1 > exonerate_output.gff
the output file (exonerate_output.gff) contains
Command line: [/home../exonerate --model protein2genome -q protein.fasta -t genome.fa -B yes -M 30000 --showvulgar no --showalignment no --showcigar yes --showtargetgff yes -V 1] \ Hostname: [---]\ Message: Processing [......]\ Message: Processing [......]\ Message: Processing [......]\ Message: Processing [......]\ Message: Processing [......]\ Message: Processing [......]\ Message: Processing [......]\ .\ .\ .\ -- completed exonerate analysis
and no information about the result of annotation.
What should I do for getting annotation result output?
