Failed to execute: /opt/Augustus/bin//etraining Could not locate command line parameters file:

[tallnuttrbgv]

I am running braker3 version 3.0.8 with prothints from orthoDB as described in docs, but Augustus fails and I get no final output. log attached.

command:

singularity exec -B ${PWD}:${PWD} /g/data/nm31/bin/braker3.sif braker.pl --gff3 --genome=/g/data/dy44/r21_genome_paralogs/genomes/hedy_masked.fasta --prot_seq=/g/data/dy44/r21_genome_paralogs/prothint/seed_proteins.faa --threads=48

It seems braker3 cannot find an augustus config file. Is this a problem with the installation?

From gbFilterEtraining.stdout, the stderr file was empty:

Could not locate command line parameters file: /home/554/ta0341/.augustus/parameters/aug_cmdln_parameters.json.

braker.log gbFilterEtraining.stdout.txt

[tallnuttrbgv]

Files /dirs obtained when braker3 ended:

GeneMark-EP GeneMark-EP.stdout GeneMark-ES GeneMark-ES.stdout Spaln braker.log cmd.log diamond downsample_traingenes.log ensure_min_n_training_genes.stdout errors evidence.gff filterGenemark.stdout gbFilterEtraining.stdout gc_content.out gene_stat.yaml genemark_evidence.gff genemark_hintsfile.gff genome.fa genome_header.map good_genes.lst hintsfile.gff nuc.fasta proteins.fa prothint.gff prothint_augustus.gff seed_proteins.faa species top_chains.gff train.f.gb train.gb what-to-cite.txt

[tallnuttrbgv]

N.B. I have another genome, with RNAseq data and it is giving exactly the same error:

Could not locate command line parameters file: /home/554/ta0341/.augustus/parameters/aug_cmdln_parameters.json.

[tallnuttrbgv]

I can confirm that there is no directory:

/home/554/ta0341/.augustus/parameters/

These exist: cgp extrinsic model profile species

[tallnuttrbgv]

Possibly solved by copying the config from the sif: https://github.com/Gaius-Augustus/BRAKER/issues/609

This should be added to the install instructions.

[tallnuttrbgv]

Getting another error..

Could not locate command line parameters file: /home/554/ta0341/.augustus/parameters/aug_cmdln_parameters.json.

so also need to copy the parameters dir?

[tallnuttrbgv]

There is no '/opt/Augustus/parameters' to copy so dead end.

Can you please fix the singularity image? I think it may have worked for you because you had also run braker3 on the same system without singularity and the correct Augustus file existed.

[tallnuttrbgv]

Tried copying config to ~/.augustus and it then cannot find ./augustus/parameters. If I copy config contents to ~/.augustus, species, parameters, etc. (this is where it is looking) when braker3 is run, it deletes them all then gives this message:

WARNING: in file /opt/BRAKER/scripts/braker.pl at line 1933 AUGUSTUS_CONFIG_PATH/species (in this case /opt/Augustus/config//species) is not writeable. BRAKER will try to copy the AUGUSTUS config directory to a writeable location. chmod: cannot access '/home/554/ta0341/.augustus/species': No such file or directory ERROR in file /opt/BRAKER/scripts/braker.pl at line 2044 Failed to execute chmod u+w /home/554/ta0341/.augustus/species!

[tallnuttrbgv]

Ok. Finally, this worked for me, just set the Augustus config path (in bash profile) to always be the current dir (so also works on PBS job node).

export AUGUSTUS_CONFIG_PATH=./