too many genes

[mictadlo]

Hi,
I used the following commands for Augustus. However, Augustus predicted 270.000 genes. How is it possible to reduce the count?

#bam2augustus
bam2hints –intronsonly --in=${r1} --out=${r1}.intron-hints.gff

bam2wig $r1 > ${r1}.wig

cat ${r1}.wig | wig2hints.pl --width=10 --margin=10 --minthresh=2 --minscore=4 --prune=0.1 --src=W --type=ep --radius=4.5 --pri=4 --strand="." > ${r1}.ep-hints.gff

cat ${r1}.intron-hints.gff ${r1}.ep-hints.gff > ${r1}.hints.gff 

#Augustus
cat extrinsic.cfg
[SOURCES]
M RM E W

exonpart    1   .992    M 1 1e+100 RM 1 1    E 1 1   W 1 1.005
intron      1   .34     M 1 1e+100 RM 1 1    E 1 1e5 W 1 1
CDSpart     1   1 0.985 M 1 1e+100 RM 1 1    E 1 1   W 1 1
UTRpart     1   1 0.985 M 1 1e+100 RM 1 1    E 1 1   W 1 1
nonexonpart 1   1       M 1 1e+100 RM 1 1.01 E 1 1   W 1 1

#augustus
augustus ${asm} --noInFrameStop=false --genemodel=complete --species=coyote_tobacco --gff3=on --UTR=on --extrinsicCfgFile=$3 --alternatives-from-sampling=false --alternatives-from-evidence=true --uniqueGeneId=true --hintsfile=${hints} --allow_hinted_splicesites=atac > ${2}/${output}.gff3

Thank you in advance,

Michal

[apredeus]

Perhaps you need to softmask the genome? I've had a similar experience when my genome wasn't masked.