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 four 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 cannot fix the error.