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
I am trying to use reference genome + transcriptome data of the same species for braker annotation. When I passed the job, within 5 days, I get an error.
Error display：
# WARNING: The number of threads was set to 88, which is greater than 48. GeneMark has in the past been reported to die if you set such a high number of threads. Please be aware that a very large number of threads also may not be used efficiently by optimize_augustus.pl during cross validation. braker.pl will automatically compute the number of threads that will effectively be used for optimizing AUGUSTUS parameter in such a way that each bucket will contain at least 200 training genes. We usually use 8 threads for 8-fold cross validation.
# Mon Sep 23 15:06:40 2024: Log information is stored in file /work/home/acn95ttd5d/gonglei/braker.log
ERROR in file /work/home/acn95ttd5d/mambaforge/envs/braker3/bin/braker.pl at line 8345
Failed to execute: /work/home/acn95ttd5d/software/braker3/TSEBRA-main/bin/tsebra.py --keep_gtf /work/home/acn95ttd5d/gonglei/augustus.hints.gtf,/work/home/acn95ttd5d/gonglei/GeneMark-ET/genemark.f.multi_anchored.gtf,/work/home/acn95ttd5d/gonglei/GeneMark-ET/genemark.f.single_anchored.gtf --cfg /work/home/acn95ttd5d/software/braker3/TSEBRA-main/bin/../config/braker3.cfg --out /work/home/acn95ttd5d/gonglei/braker.gtf -q 2>/work/home/acn95ttd5d/gonglei/errors/tsebra.stderr
/work/home/acn95ttd5d/gonglei/augustus.hints.gtf,/work/home/acn95ttd5d/gonglei/GeneMark-ET/genemark.f.multi_anchored.gtf,/work/home/acn95ttd5d/gonglei/GeneMark-ET/genemark.f.single_anchored.gtf
All three files are empty
braker.log file is :
mv /work/home/acn95ttd5d/gonglei/aug_hints_34733 /work/home/acn95ttd5d/gonglei/augustus_files_hints/aug_hints_34733
mv /work/home/acn95ttd5d/gonglei/aug_hints_34985 /work/home/acn95ttd5d/gonglei/augustus_files_hints/aug_hints_34985
mv /work/home/acn95ttd5d/gonglei/aug_hints_35900 /work/home/acn95ttd5d/gonglei/augustus_files_hints/aug_hints_35900
# Sat Sep 28 19:07:20 2024: Making a gtf file from /work/home/acn95ttd5d/gonglei/augustus.hints.gff
cat /work/home/acn95ttd5d/gonglei/augustus.hints.gff | /work/home/acn95ttd5d/mambaforge/envs/braker3/bin/perl -ne 'if(m/\tAUGUSTUS\t/) {print $_;}' | /work/home/acn95ttd5d/mambaforge/envs/braker3/bin/perl /work/home/acn95ttd5d/software/braker3/Augustus-3.4.0/scripts/gtf2gff.pl --printExon --out=/work/home/acn95ttd5d/gonglei/augustus.hints.tmp.gtf 2>/work/home/acn95ttd5d/gonglei/errors/gtf2gff.augustus.hints.gtf.stderr
# Sat Sep 28 19:07:20 2024: Making a fasta file with protein sequences of /work/home/acn95ttd5d/gonglei/augustus.hints.gtf
/work/home/acn95ttd5d/mambaforge/envs/braker3/bin/python3 /work/home/acn95ttd5d/software/braker3/Augustus-3.4.0/scripts/getAnnoFastaFromJoingenes.py -g /work/home/acn95ttd5d/gonglei/genome.fa -f /work/home/acn95ttd5d/gonglei/augustus.hints.gtf -o /work/home/acn95ttd5d/gonglei/augustus.hints 1> /work/home/acn95ttd5d/gonglei/getAnnoFastaFromJoingenes.augustus.hints_tmp.stdout 2>/work/home/acn95ttd5d/gonglei/errors/getAnnoFastaFromJoingenes.augustus.hints_tmp.stderr
# Sat Sep 28 19:12:51 2024: Making a fasta file with protein sequences of /work/home/acn95ttd5d/gonglei/augustus.hints.gtf
/work/home/acn95ttd5d/mambaforge/envs/braker3/bin/python3 /work/home/acn95ttd5d/software/braker3/Augustus-3.4.0/scripts/getAnnoFastaFromJoingenes.py -g /work/home/acn95ttd5d/gonglei/genome.fa -f /work/home/acn95ttd5d/gonglei/augustus.hints.gtf -o /work/home/acn95ttd5d/gonglei/augustus.hints 1> /work/home/acn95ttd5d/gonglei/getAnnoFastaFromJoingenes.augustus.hints_hints.stdout 2>/work/home/acn95ttd5d/gonglei/errors/getAnnoFastaFromJoingenes.augustus.hints_hints.stderr
# Sat Sep 28 19:17:33 2024: AUGUSTUS prediction complete
# Sat Sep 28 19:17:33 2024: Trying to create merged gene set from GeneMark-EX and AUGUSTUS predictions (braker.gtf/braker.utr.gtf)...
# Sat Sep 28 19:17:33 2024: Trying to create combined gene set with TSEBRA...
/work/home/acn95ttd5d/software/braker3/TSEBRA-main/bin/tsebra.py --keep_gtf /work/home/acn95ttd5d/gonglei/augustus.hints.gtf,/work/home/acn95ttd5d/gonglei/GeneMark-ET/genemark.f.multi_anchored.gtf,/work/home/acn95ttd5d/gonglei/GeneMark-ET/genemark.f.single_anchored.gtf --cfg /work/home/acn95ttd5d/software/braker3/TSEBRA-main/bin/../config/braker3.cfg --out /work/home/acn95ttd5d/gonglei/braker.gtf -q 2>/work/home/acn95ttd5d/gonglei/errors/tsebra.stderr
For the above question, could you provide some suggestions? Thank you for your valuable time and assistance. I sincerely look forward to your response！
Hi, KatharinaHoff,
I am trying to use reference genome + transcriptome data of the same species for braker annotation. When I passed the job, within 5 days, I get an error.
Error display：
/work/home/acn95ttd5d/gonglei/augustus.hints.gtf,/work/home/acn95ttd5d/gonglei/GeneMark-ET/genemark.f.multi_anchored.gtf,/work/home/acn95ttd5d/gonglei/GeneMark-ET/genemark.f.single_anchored.gtf
All three files are empty
braker.log file is :
For the above question, could you provide some suggestions? Thank you for your valuable time and assistance. I sincerely look forward to your response！