augustus: ERROR

Hello!

I have a problem with genome annotation of Argopecten irradians. I launched Augustus on my data:

augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --stop=off --stop=off --cds=on --singlestrand=false /data/dnb07/galaxy_db/files/c/a/d/dataset_cad6702a-19f0-48b2-b3e4-ad8bde8a6cd4.dat --UTR=off --genemodel=complete --softmasking=0 --species=Argopecten_irridians | tee ‘/data/jwd/main/050/787/50787823/outputs/galaxy_dataset_751f08c3-3b9e-4f7e-9dd8-c274f5689e25.dat’ | python /opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/bgruening/augustus/28433faa6e42/augustus/extract_features.py --protein /data/jwd/main/050/787/50787823/outputs/galaxy_dataset_4d9ff515-7a7a-4fab-b875-b96e8d6ce149.dat --codingseq /data/jwd/main/050/787/50787823/outputs/galaxy_dataset_22dde9b1-47eb-41a6-a202-dbabb5600e31.dat

But it finished with the error:

Could not find the config file /usr/local/tools/_conda/envs/__augustus@3.4.0/config/species/Argopecten_irridians/Argopecten_irridians_parameters.cfg.
Looking for Argopecten_irridians_parameters.cfg in the configuration directory instead … not found.

augustus: ERROR
Species-specific configuration files not found in /usr/local/tools/_conda/envs/__augustus@3.4.0/config/species/. Type “augustus --species=help” to see available species.

It looks like the file Argopecten_irridians_parameters.cfg is absent. Could you help me?

Hi @Denis_Grouzdev

There probably isn’t a trainingset available. I have a technical guess about why, but let’s ask @gallardoalba (the tool author who added it in this commit).

Alternatives include creating one with: augustus_training/3.4.0+galaxy1

Tutorials: search?query=augustus