I had encountered an ERROR when I used MAKER to annotate my genome.
It is a large plant genome (more than 3Gb). I included a TE (gff) data, one Transcriptome data (fasta),
and three protein sequences (fasta) for the homology annotation. There are, in total, 29 scaffolds. Three scaffolds faced the “ERROR: Failed while processing all repeats,” while the other 26 finished successfully.
I have tried the following methods from the online forum. However, I still can’t fix the error.
Check the RepeatMasker configuration
Check the maker_exe.ctl, and set a updated BLAST (ncbi-blast-2.7.1)