BRAKER3 fails with ‘Genemark’ error

[kamran.azim]

Failed to execute: /usr/bin/perl /opt/ETP/bin/gmetp.pl --cfg /data/jwd08/main/098/601/98601025/working/braker/GeneMark-ETP/etp_config.yaml --workdir /data/jwd08/main/098/601/98601025/working/braker/GeneMark-ETP --bam /data/jwd08/main/098/601/98601025/working/braker/GeneMark-ETP/etp_data/ --cores 6 --softmask  1>/data/jwd08/main/098/601/98601025/working/braker/errors/GeneMark-ETP.stdout 2>/data/jwd08/main/098/601/98601025/working/braker/errors/GeneMark-ETP.stderr
The most common problem is that GeneMark-ETP didn't receive enough evidence from the input data, in this case, see errors/GeneMark-ETP.stderr!

[wm75]

Please see this prior Q&A:

BRAKER3 fails with 'Genemark not installed' error

[image]: When running BRAKER3 for genome annotation on Galaxy Europe, the job fails with: Error: "Genemark is not installed properly on this Galaxy server." Upload genome (FASTA) and protein-seq data. Run BRAKER3 with default parameters. Job crashes during execution. Expected vs. Actual Behavior: Expected: Successful annotation. Actual: Tool dependency error (Genemark missing). Troubleshooting Attempted: Checked Galaxy Europe documentation. Re-ran with different input data → same error. Question: Is Genemark intentionally unavailable on Galaxy Europe? Are there workarounds (e.g., alternative tools)?