Comments (2)
Hi Bios4Biol,
Sorry to hear that. Admittedly Cupressus is phylogenetically far from most of our training and testing genomes. The existing trained models may simply not perform well in this case.
Thanks for letting us know, that's something that we can work on in the future, however prompt improvements in available models are unlikely.
If you have better annotations available (preferable, and either for this or perhaps a few closely related species), or simply want to try from the pseudolabels (riskier starting from a low Busco score), fine tuning the plant models is likely to help.
https://github.com/weberlab-hhu/Helixer/blob/main/docs/fine_tuning.md
from helixer.
Oh, and fine tuning is only recommended if you're determined feeling adventurous. It's experimental.
from helixer.
Related Issues (20)
- Name the genes in order HOT 1
- Issues with Gymnosperms HOT 2
- Online Version HOT 8
- Fail early and clearly on fasta files with duplicate IDs
- Some tensorflow warning/error messages when running Helixer via Singularity HOT 3
- results from web tool not sent HOT 2
- boolean index did not match indexed array along dimension 0 HOT 2
- gff3 specification HOT 1
- nohup not helping in Helixer.py, run is stopped when connection is lost HOT 5
- Helixer and the protein related domain HOT 1
- ModuleNotFoundError: No module named 'tensorflow.keras' HOT 2
- How does helixer evaluate performance when predicting genomes? HOT 1
- sqlite3.DataError: string or blob too big HOT 2
- OSError: [Errno 9] Bad file descriptor HOT 1
- When I run python Helixer.py, met: "ImportError: cannot import name 'where' from 'certifi' (unknown location" HOT 1
- Question: How to find more smaller genes HOT 2
- hypothetical all-eukaryote model HOT 3
- Micro exons with single bases or two
- error message = 'No space left on device"
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from helixer.