I have recently used MAKER2 for genome annotation. The run appears to have been successful, but when I came to use
fasta_merge -d there was no output!
gff3_merge -d worked fine, producing a new file AGND01.1.all.gff. I decided to check if any FASTAs had been generated using
find . -type f -name "*.fa" in the AGND01.1_datastore directory generated by MAKER, but there were no results. Does this mean that MAKER did not produce and FASTAs for the contigs it annotated? If so, how do I fix this? Is there an option I must choose in the .ctl files?