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Is there a protocol for "adjust metarpars" after WebAUGUSTUS has problems with accuracy?

Open SchwarzEM opened this issue 1 year ago • 1 comments

I have used WebAUGUSTUS to generate AUGUSTUS species-specific parameters for a parasitic nematode genome with high accuracy (1e-04 error rate) and contiguity (chromosomal single scaffolds). Two other genomes of this quality were very easy to get decently high accuracy for AUGUSTUS (>= 0.80) using the BRAKER2 pipeline, but this particular genome for unclear reasons had repeatedly bad accuracy and gene predictions in BRAKER2, so I instead tried training AUGUSTUS with either cDNA or protein via WebAUGUSTUS. My problems with this particular genome continued: the accuracy of protein-based AUGUSTUS parameters was mediocre (around 0.50) but not horrible; for cDNA-based parameters, the accuracy was quite awful (around 0.18!).

In both cases, I got the following error messages:

0 WARNING: optimization did not improve accuracy!
1 WARNING: Optimizing didn't improve the accuracy, maybe need to adjust XXX_metarpars!

Which I would be happy to do, except ... how? How exactly do I go about adjusting the meta parameters? Is there a protocol for doing this? I would very much like to find one.

SchwarzEM avatar Jan 13 '23 16:01 SchwarzEM