BRAKER crashes if the input sequence is shorter than a certain length.

[GallVp]

Solution

• Document this behaviour
• Possibly validate the input sequence and end the pipeline gracefully before doing any downstream processing.
• Try setting braker_extra_args to --min_contig=10000
• Add a test case to the module: https://github.com/GallVp/nxf-components/blob/main/modules/gallvp/braker3/tests/main.nf.test

[GallVp]

Error 'error, input sequence size is too small' is raised by min_seq_size, see:

https://github.com/gatech-genemark/GeneMark-ETP/blob/81ac83e3894a47997e533d2c7cc345998dc5cbbb/bin/gmes/gmes_petap.pl#L1604

Maybe the fix is to set min_seq_size parameter.

[GallVp]

BRAKER has not exposed the min_seq_size option.

Thus, essentially BRAKER can not be used to annotate any assembly shorter than 100,000 (default value of min_seq_size)

[GallVp]

Added a check for input assemblies. If an assembly is smaller than 1 MB (or 300KB in zipped format), the pipeline errors out before starting the downstream processes

[GallVp]

Completed by https://github.com/PlantandFoodResearch/genepal/releases/tag/0.4.0