Gaius-Augustus BRAKER issues

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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Very satisfying annotations ... Except for one species

#842 vpymerel opened 1 day ago
0
Continue a failed run?

#841 Artifice120 opened 1 day ago
2
The environment variable AUGUSTUS_CONFIG_PATH

#840 Adolfocp94 opened 1 week ago
0
The most common problem is an expired or not present file ~/.gm_key!

#839 Arodiansyah21 opened 2 weeks ago
0
ERROR in file .conda/envs/braker3/bin/braker.pl at line 5333

#838 kinoppyi opened 2 weeks ago
1
BRAKER is running network outages in singularity, the work end is gone!

#837 452jiajia opened 2 weeks ago
2
Unable to complete an analysis using both protein and rna-seq data

#836 salvatierra8 opened 2 weeks ago
0
get_gc_content.py Error in BRAKER3

#835 georgetarabain opened 4 weeks ago
0
Segfault wiht ghmmp within BRAKER

#834 tshori opened 1 month ago
6
Inclusion of stop_codon in the CDS interval?

#833 gbdias opened 1 month ago
1
Bam files overwriting each other

#832 Tsaranoga opened 1 month ago
2
Failed to execute in braker.pl line 2343

#831 ala98412 opened 1 month ago
3
Using preprocessed (clusteredaligned) PB Iso-Seq data with protein data?

#830 carla-hazelf opened 1 month ago
0
Braker3 optimize_augustus.pl process does not terminate

#829 kataksk closed 6 days ago
3
Issue with filterGenesIn_mRNAname.pl when running BRAKER with singularity

#828 cvargas88 opened 1 month ago
3
Unknown option: threads

#827 Arodiansyah21 closed 1 month ago
4
large differences in the number of genes predicted from different varieties of the same species

#826 ChuanzhengWei opened 1 month ago
7
When running BRAKER3 using Singularity, an error occurred

#825 1039931841 closed 1 month ago
0
fixed pseudo gene removal in evaluation script

#824 LarsGab closed 1 month ago
0
Many gene models do not start with 'M'

#823 caixu0518 closed 1 month ago
1
Higher BUSCO in annotation than assembly?

#822 YingChen94 closed 1 month ago
2
GeneMark-ETP didn't receive enough evidence from the input data

#821 RezwanCAAS opened 1 month ago
4
braker3_lr threads

#820 danielwood1992 opened 1 month ago
13
The ERROR in the file/datapool/home/yangzc/soft/pacbio/BRAKER 3.0.8 / scripts/BRAKER. The details of the pl at line 5414

#819 Somnous1998 opened 1 month ago
0
best_by_compleasm.py unable to find compleasm.py

#818 SAMtoBAM opened 1 month ago
1
How to fix the --busco_lineage argument issue in braker3?

#817 RezwanCAAS closed 1 month ago
5
errors-optimize_augustus.stderr

#816 enriquepola1996 opened 1 month ago
7
Using OrthoDB proteins and functional annotation

#815 enriquepola1996 opened 2 months ago
2
Orthodb11 as protein hints causes an error in GeneMark-ETP

#814 yifeng-evo closed 2 months ago
2
augustus.hints.gtf has 25k genes more than braker.gtf

#813 smallfishcui opened 2 months ago
1
add transcriptomes to input

#812 YanisChrys closed 2 months ago
2
fails to execute compleasm; error line 4551 in braker.pl

#811 AAHRU-Ablab closed 2 months ago
2
How to use MakeHub output with UCSC Genome Browser

#810 yzliu01 opened 2 months ago
1
Failed to execute /usr/bin/perl /opt/Augustus/scripts/join_aug_pred.pl

#809 M-Asim-Javed closed 2 months ago
3
Docker Braker3 with example data: ERROR in file /opt/BRAKER/scripts/braker.pl at line 1238

#808 yzliu01 opened 2 months ago
2
ERROR in file /opt/BRAKER/scripts/braker.pl at line 10092, Failed to open directory ${workingdir}

#807 yyliang12 closed 1 month ago
2
Unnecessary compleasm failure alert

#806 juliadouglasf opened 2 months ago
2
Braker via Singularity, fails to execute Augustus

#805 emgiles closed 2 months ago
2
Queries on RNA-seq and Isoseq data in braker

#804 lidachuis opened 2 months ago
7
Any suggestions for running an array job for Braker?

#803 lw78943 opened 2 months ago
6
GeneMark-ETP license key for singularity container

#802 pstrope closed 2 months ago
1
Convert gtf to gff3

#801 tanpham15 closed 2 months ago
1
How to keep only the t1?

#800 emmafg closed 2 months ago
3
Queries on Isoseq data in braker

#799 karthickbrlab closed 2 months ago
10
ERROR: in file /opt/BRAKER/scripts/braker.pl at line 4490

#798 Wangray123 closed 2 months ago
2
HISAT alignment, sam, bam, sorted.bam steps

#797 SAMtoBAM opened 2 months ago
1
within set_JAVA_PATH, generalize check for java version and prevent substitutions within awk command

#796 douglasgscofield closed 1 month ago
0
Merging exons to genes

#795 RonOLab opened 2 months ago
3
How to determine genes by scaffold ?

#794 emmafg opened 2 months ago
1
error: No spliced alignments were created by Spaln

#793 karthickbrlab closed 2 months ago
3