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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can't find compleasm_to_hints.py

#889 SolayMane opened 1 day ago
0
Few annotated genes resulting from Braker3 with RNASeq

#888 bijendrabio opened 1 day ago
0
Issue occurred when ProtHint running in the iterative mode

#887 tianchuw-TinaWu opened 2 days ago
1
Does anyone try to apply InGenAnnot adding UTR function after Braker annotation

#886 Abieskawa opened 2 days ago
0
Suggestions of input datasets I used for braker2/3

#885 hungweichen0327 opened 1 week ago
0
503: SyntaxWarning: invalid escape sequence '\.'

#884 Georicl opened 1 week ago
3
Issues about the codes provided in paper navigating eukaryotic genome annotation pipeline

#883 Abieskawa closed 2 weeks ago
3
best_by_compleasm.py ERROR (GeneMark trancript too long)

#882 jolbi opened 2 weeks ago
15
fix for using other openjdk java (e.g. Zulu from Azul)

#881 schloegl closed 3 weeks ago
0
Error while running BRAKER3

#880 InesGaLu opened 3 weeks ago
8
Questions regarding tsebra

#879 bauerlev opened 1 month ago
0
Extreme difference in accuracy between chromosomes

#878 GijsBerkenbosch closed 1 month ago
1
GeneMark error on the names in the genome file

#877 pelotbdr opened 1 month ago
0
--busco_lineage helps with busco scores but not with protein number

#876 aureliendejode opened 1 month ago
4
[GeneMark-ES.stderr] uninitialized value $name in concatenation (.) or string at gmes_petap.pl

#875 wym0072003 opened 1 month ago
0
Failed to execute: /opt/Augustus/bin//etraining Could not locate command line parameters file:

#874 tallnuttrbgv closed 1 month ago
8
fix_in_frame_stop_codon_genes.py crashes on line 701

#873 rainmanv84 opened 1 month ago
1
regarding softmasking

#872 vbhardwaj3010 opened 1 month ago
0
BRAKER gft score

#871 vbhardwaj3010 opened 1 month ago
0
Provide stringtie output directly to braker3

#870 allind opened 1 month ago
1
Error with Singularity image

#869 lucaskbobadilla opened 1 month ago
3
Hisat mapping

#868 aureliendejode opened 1 month ago
0
Internal UTR features were found after decorating UTR by stringtie2utr.py

#867 xo2003 opened 1 month ago
1
How can I specify the number of CPU cores to use when running AUGUSTUS for ab initio gene prediction?

#866 Vijithkumar2020 opened 1 month ago
0
More proteins than transcripts in BRAKER annotation results

#865 xeniaroda closed 1 month ago
2
Failed to execute: tsebra.py

#864 GLking123 opened 1 month ago
0
Using Iso-seq data for Braker annotation

#863 Upendra19993 opened 2 months ago
10
Does BRAKER3 support the annotation of chromosomes larger than 2 million base pairs?

#862 octpalacios opened 2 months ago
1
error, output file is empty data/ep.gff

#861 gladjabo opened 2 months ago
1
Very comprehensive assessment！

#860 ZhangPY-bioinformatics opened 2 months ago
2
Exon models look good, but gene models are far too large

#859 jtoy7 opened 2 months ago
3
Braker 1 and Braker 2

#858 RacheliHadjez closed 1 month ago
6
Can not find file: genome_gmst.gtf.

#857 sunnycqcn closed 2 months ago
5
Failed to execute /usr/bin//etraining

#856 gladjabo opened 2 months ago
1
can't download long reads singularity image

#855 sqwwww closed 1 month ago
1
Missing information about Solanum lycopersicum RNAseq used in Braker3 paper?

#854 JBerthelier closed 3 months ago
2
Reproducibility issue

#853 JBerthelier closed 3 months ago
4
Failed to execute: /opt/Augustus/bin//augustus ExonModel: Couldn't open file *_exon_probs.pbl

#852 kwiyounghan closed 1 month ago
2
GeneMark-ETP didn't receive enough evidence from the input data, in this case

#851 xuyinnnan opened 3 months ago
1
Genemark ETP issue with fungus option: failed to execute... gmes_petap.pl

#850 ngreatens opened 3 months ago
0
Public RNAseq as evidence for BRAKER?

#849 V-JJ closed 3 months ago
2
No output results from AUGUSTUS

#848 JMUwenjian opened 4 months ago
0
using compute_accuracies.sh

#847 JBerthelier closed 2 months ago
4
Continue BRAKER due to timeout

#846 m4558 opened 4 months ago
0
Failed to create directory Augustus!

#845 RezwanCAAS opened 4 months ago
0
Adding training genes?

#844 Artifice120 opened 4 months ago
2
Braker failing on some chromosomes but not others

#843 amsession opened 4 months ago
0
Very satisfying annotations ... Except for one species

#842 vpymerel opened 5 months ago
3
Continue a failed run?

#841 Artifice120 opened 5 months ago
2
The environment variable AUGUSTUS_CONFIG_PATH

#840 Adolfocp94 opened 5 months ago
0