I have been able to use exonerate to map a large set of transctiptome-derived cDNA sequences (~10,000) to an assembled genome (~300 Mb). But I am only able to use the default parameters for exonerate. For instance, if I were to specity anything using parameters --bestn and --percent, I do not get any output, and the program seems to be stuck in its paths. If I include --showquerygff or --showtargetgff, the program runs with no problem.
I am using the exonerate version 2.2.0-x86_64 on a linux cluster, after securing a node with 16 processors.
Any help is appreciated.
(My first post to BioStars)