Why the busco scores for the annotated example arabidopsis thaliana genome proteins are very low ?

[bioinformaticspcj]

Dear the authors,

Thanks a lot for your valuable and user-friendly software. I have tried the finder programe to annotate the example arabidopsis thaliana genome, but found the proteins extrated from FINDER_BRAKER_PROT.gtf file only achieved 54% BUSCO scores of embryophyta_odb10. It is very low compared with the genome itself BUSCO scores 99.3% with the same database and means near half of coding genes were not annotated. I do not know why. The command I used to run finder is as fellows: finder -no_cleanup -mf Arabidopsis_thaliana_metadata.csv -n 30 -gdir_star $PWD/star_index_without_transcriptome -out_dir $PWD/FINDER_test_ARATH -g $PWD/Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa -p $PWD/uniprot_ARATH.fasta -gdir_olego olego_index -preserve 1> $PWD/FINDER_test_ARATH.output 2> $PWD/FINDER_test_ARATH.error

Could you give me some advice to improve the performence of the annotation?

Thanks again for your reading. Looking forward to your timely respons. Best, Bob