aug_ab_initio error!

[sunnycqcn]

Hello Developer, When I run my command, I met an aug_ab_initio error. I still can get the results. my command as following: braker.pl --genome=./${line}.mask.fa --prot_seq=Eukaryota.fa --softmasking \ --threads=80 --species=striga --crf --useexisting --AUGUSTUS_ab_initio --gff3 --overwrite --nocleanup --eval_pseudo=pseudo.gff3 \ --bam=./ST.bam --addUTR=on && touch ${line}.braker.addUTR.successfully

Failed to execute: /isilon/projects/J-002571_clubroot_src_chen/fuf/StGenome/genome/annotation/braker/aug_ab_initio_417! ERROR in file /isilon/projects/J-002571_clubroot_src_chen/fuf/miniconda/envs/braker3/bin/braker.pl at line 7686 Thanks, Fuyou

[jwli-code]

Hi, I was wondering - does the eval parameter refer to adding a gff file of a related reference species for homology annotation? And what does the --eval_pseudo parameter refer to and what does it do, the help documentation is not clear, thank you

[sunnycqcn]

Hello, Thanks for your reply. You mean I need to refer a related reference species for using --AUGUSTUS_ab_initio. If I did not refer one, I do not need to use it. Fuyou

Hi, I was wondering - does the eval parameter refer to adding a gff file of a related reference species for homology annotation? And what does the --eval_pseudo parameter refer to and what does it do, the help documentation is not clear, thank you

[KatharinaHoff]

The --eval and --eval_pseudo commands are developer options that we use to benchmark braker gene sets. However that's a fragile implementation, and I am not even using it anymore, myself. I evaluate accuracy after the braker run as completed. The options do not influence annotation.

Just don't use these options.

If you want to reproduce our accuracy results from publications, use the evaluation scripts by Alex that sit in the BRAKER scripts folder.

Why do you run AUGUSTUS in ab inito mode? This is usually only interesting for development purposes. For genome annotation in practice, this burns runtime.

[sunnycqcn]

Thanks, I will try more.