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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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No protein fasta generated #542

Closed AkshitaJain2709 closed 9 months ago

AkshitaJain2709 commented 1 year ago

Hi, I am running BRAKER2 on a fragmented assembly, and it doesn't produce any protein fasta file as an output. Also, is there a way to include accession numbers in the gff file while running BRAKER.

Script: module load Boost/1.76.0-GCC-10.3.0 source activate braker /group/pathogens/plant_pathology/personal/Akshita/programs/braker2/BRAKER-2.1.6/scripts/braker.pl --gff3 --cores 16 --AUGUSTUS_CONFIG_PATH=/group/pathogens/plant_pathology/personal/Akshita/programs/braker2/Augustus-3.5.0/config/ --AUGUSTUS_BIN_PATH=/group/pathogens/plant_pathology/personal/Akshita/programs/braker2/Augustus-3.5.0/bin/ --AUGUSTUS_SCRIPTS_PATH=/group/pathogens/plant_pathology/personal/Akshita/programs/braker2/Augustus-3.5.0/scripts/ --BAMTOOLS_PATH=/group/pathogens/plant_pathology/personal/Akshita/programs/braker2/bamtools-2.5.2/final/bin/ --GENEMARK_PATH=/group/pathogens/plant_pathology/personal/Akshita/programs/braker2/GeneMark-EX/ --PROTHINT_PATH=/group/pathogens/plant_pathology/personal/Akshita/programs/braker2/ProtHint-2.6.0/bin/ --DIAMOND_PATH=/group/pathogens/plant_pathology/personal/Akshita/programs/braker2/ProtHint-2.6.0/dependencies/ --genome=/group/pathogens/plant_pathology/personal/Akshita/Sequencing_Run3/Redundans_PE/REDUNDANS_PE_OUT/scaffolds.reduced.fa --species=c_elegans_trsk --useexisting --esmode --min_contig 500 --workingdir=/group/pathogens/plant_pathology/personal/Akshita/Test_Workflow/BRAKER/braker_Haustralis/

KatharinaHoff commented 9 months ago

There's not enough information to solve this problem. It was possibly resolved by various software updates. I will close, here.