Hiii.....I'm ruuning maker annotation pipeline for the first time. It is given that in the maker tutorial the output folder contains number of files and a directory.
ie, contig-dpp-500-500.gff contig-dpp-500-500.maker.proteins.fasta contig-dpp-500-500.maker.transcripts.fasta run.log theVoid.contig-dpp-500-500
But my output folder contains only the following files. why didn't generate the protein and transcript sequence files?
contig-dpp-500-500.gff run.log theVoid.contig-dpp-500-500
For us, it was possible to run MAKER only after reffering this link written by darencard.
He has explained each step in very nice manner. I think it will be useful to you too.