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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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Failed to execute /usr/bin//etraining #856

Open gladjabo opened 2 months ago

gladjabo commented 2 months ago

Dear I met with such errors when I run Braker3. ERROR in file /opt/BRAKER/scripts/braker.pl at line 6172 Failed to execute: /usr/bin//etraining --species=Carberry2 --AUGUSTUS_CONFIG_PATH=/home/AAFC-AAC/jiab/miniforge3/pkgs/augustus-3.4.0-pl5262h5a9fe7b_2/config /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/train.f.gb 1> /isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/gbFilterEtraining.stdout 2>/isilon/projects/J-001961_4DWheat/Genome_assembly/Genome/Carberry/braker/errors/gbFilterEtraining.stderr INFO: Cleaning up image...

and I also check the gbFilterEtraining.stderr, it shows like this GBProcessor::getGeneList(): Could not read the following line in Genbank file. caacaa ggtaaacaca ccacacatgg tgtgacatga tgcacaacaa Maximum line length is 39998.

Encountered error after reading 278400 annotations. terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)

Could you please check what's problem with that? thanks

Best Bosen

KatharinaHoff commented 2 months ago

Can you send us the file train.f.gb and the species parameter folder (e.g. as tar.gz or zip archive)? You can send a share link to katharina.hoff@uni-greifswald.de .