Few genes annotated with RNASeq BRAKER3

[bijendrabio]

Hello @KatharinaHoff ,
I am getting significantly fewer annotated genes when using Braker3 with RNASeq. The final number of annotated genes varies between different genomes, ranging from 25K to 30K. However, for other closely related genomes with the same amount of RNASeq data, I am getting around 150K annotated genes. I suspect this discrepancy might be related to the complexity of the specific genomes used for annotation, or it could be due to technical issues. Could you please suggest what might be causing this? Kindly suggest @KatharinaHoff

EXAMPLE
braker.log
bad

Wed Nov 20 21:15:15 2024: Log information is stored in file /projects/tools/BRAKER3/test-run-1/braker.log

#*********

WARNING: Number of reliable training genes is low (481). Recommended are at least 600 genes

#*********

braker.aa

g1.t1
MKKEEEERRRKKKKGKRKKKKEKEKGKRKKKKEKEKGKRKKKKEEERKKEEEERKRKRKK
EEEERRRKKKKGKRKKKKEKEKGKRKKKKEEERKKEEEERKRKRKKEEEERRRKKKKGKR
KKKKEKEKGKRKKKKEEERRRKEKGRRRKKKKKEKGRRRKKKKEKGIFFFFSAPRTTSPP
PYGGGGGGGGGGGGGGGGAE*
g2.t1
MTMEKKRKKKKEEEERRRRRRKKKKKKKRRRKKKKGKRKKEEEERRRKKKKGKRKKKKEK
EKGKRKKKKN*
g3.t1
MTRTKEEERRRRKKKKKKKEEEEEERRRKKKKGKRKKEEEERRRKKKKGKRKKKKEKEKG
KRKKKKEEERRRKEKGRRRKKKKKEKGRRRKRKKEKGIFFLFFLFFVLFYFNYRD*
g13.t1
MRKEEEEEEEEEEEEEEEEEEEEEEEEEEEEGEEEEEEEEKKEEEEGEERIRRGRRRRRR
RRRRRRRRRIRRGRGRGRRRRRRRRRRRRRRRRRRRRRRRRRIRRGRRRRRRRRRRRRRR
RRRRRRIRRGRGRRRRRRRRRRRGEEGGGRRRRRKNKKRKKKEKKKKEKEKEKKNKKRKR
KRKKKKKEQKEKEKEKEEEEEEEEKKKNKKRKKKEEKKKKKEEEEEKNKKRKRKKKKKKE
EEKEKEKEEEEEEEEEEKKKKKKKKKKKKKKKKKKKKKKKKKRKRKKKEKKKKKRRRRRR
RKKKEKKKNKKEKKKKKKNKKRKRKKKEKKKKKKRRRRRRKKKEKKKNKKRKKKEKKKKE
KEKEKEKEKKNKKRKKKEKKKEEEKKEGEEEGEDEEKKRKKKKKKKKKKKKKKKKKKKKK
KKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKEKKKKKRRRRRR
KKKEKKE*
g14.t1
MEGGEVANEQQQHW*
g18.t1
MIAKKEDRLVQDEGGGGEEEEEEEEEEEEEEEEEEEEEEGEEGEEKEKKKKKKKKKKKKK
KKNKKKKKKKKKKKKKKKKKKKKKKKKKKKKKNKNNNNNNNNNKKKKKKKKKKKKKKKKK
KKKKKKKKKKRGGGGGGGGGGGGGGGGGGGGGGGRRRRRRRRRRRRRRRRRRRGGGGGGR
RRRGRRRRRRIRRGRRRRTRRTRRSRRRRRRRRRIRRGRGRRRRRRRRRRRRRRRRRRRN
KAKKK*
g24.t1
MTMIEEKKEKKKEEEEEERRRRRKRKKEEEERRRKKKKGKRKKKKEKKRKKEEEEKGKRK
KKKEEERRRKEKGRRRKKKKRKKEEEEKGKRKKEFFSFFSFFLTTSPPPYGGGGGGGGGG
GGGGGGGV*
g25.t1
MS*
g27.t1
MRMRRGRRRRRRRRRRRRRRRRRRRRRRRRRRRRIRRGRGRRRRRRRRRRRRRRRIRRGR
GRRRRRRRRRRRRRRRRRRRRGRGRRRRRRRRRRRRRRRK*
g28.t1
MRNKEEEEEEEEGEEEEEEEEEEEEEEEGEEEEEEEKKEEEEEEEEKKEEEEEGEERIRR
GRRRRRRRRRRRRRRRRIRRGRGRGRRRRRRRRRRRRRRRRRRRRRRRKRRRIRRGRRRR
RRRRRRRRRRRRRRIRRGRGRRRRRRRRRRRRRRREEGGGRRRRRKNQKRKKKEKKKKEK
EKEKKNKKRKRKRKKKKKEEKEKEKEKEEEEEEEKKKKNKKRKKKEEKKKKEEEEEEEKN
KKRKRKKKKKKEEKEKEKEKEEEERRRRRRRRRRRRRRRRRRRRRIRRGRGRRRRRRRRR
RRRRRRRGEEGGGRRRRRRRRRRRRRRRRRRRRRRRRRRRRRIRRGRGRRRRRRRRRRRR
RRRRIIIRRGRGRRRRIRRRIREEEEEEGEEEEEEEEEKKEEEEEGEEEE*

Kind regards,
B