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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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Error:Not get the final gff3 file #770

Open Bank-tidy opened 4 months ago

Bank-tidy commented 4 months ago

Thanks to braker3, the team developed such an easy-to-use software, but I encountered some problems when using it. I used the latest version of Braker3’s singularity container，follows are my code: singularity exec -B $PWD:$PWD /public1/home/yinhang/software/apps/Braker3/braker3.sif braker.pl --genome=${DIR}/SH_TRF_TE_masked.fasta --prot_seq=${DIR}/combined_cds.fa –-bam=${DIR}/SH_trans_clean_sorted.bam --threads=30 --workingdir=${DIR} --species=tomato --gff3

But my result look loss some files image

files in error directory is empty: image diamond directory: image GeneMark-EP directory is empty:: GeneMark-ES directory: image spaln directory: image

this is my braker.log

image image image

Looking forward to your suggestions, thank you!

KatharinaHoff commented 4 months ago

Is it possible that your BRAKER run died during the ProtHint stage?

Bank-tidy commented 4 months ago

Is it possible that your BRAKER run died during the ProtHint stage?

Thank you for your reply！The problem has been solved. The Augustus directory was not specified when using the latestes singularity.