Open yzliu01 opened 3 months ago
It's unlikely that the reference proteins would be close enough for some members of the genus but not for others.
This looks like some technical issue, possibly with the assembly of that one genome. You can send me the assembly of one of the genomes where the algorithm works well, the assembly of the problematic one, and the protein database. I'll take a look (please share by email, bruna.tomas@gmail.com, if you don't want your data to appear here).
OK, it is a bit too big and I just sent the data to you by email. Please check it. Appreciated!
Hi @tomasbruna,
I ran Braker to predict gene structure and got the problem in the step running Genmark-EX as below. I used the reference genome and customized amino acid sequence database with the following command, which worked well with all species in the same genus except for the reference genome of one species. I am NOT use RNA-Seq data.
braker.pl --genome="$genome" --prot_seq="$Apodiea_gene_AA"
braker.log
output error file tail -30 gene_annotation_AndBic.40649391.e The number of mairs aligned (8804/8804 (100%) pairs aligned) is much smaller than other reference genomes (448747/448747 (100%) pairs aligned). It seems that this reference genome is very distant from the protein database. Can you give any hints to address this issue?