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Old 04-04-2013, 11:59 AM   #1
yzzhang
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Location: florida

Join Date: Jan 2013
Posts: 67
Default augustus utr training error

Hi, all.
I tried to train AUGUSTUS for my genome. I am using version 2.7beta to predict my genome using one repeatmasked genome (240 Mb), one cdna data set (~12000 transcripts) and cegma output (446 genes) as traingeneset. I ran the autoAug.pl. The first steps worked well, but for the 6th step "Training AUGUSTUS with UTR ", the command
Code:
perl /home/zhang/software/augustus.2.7/config/../scripts/makeUtrTrainingSet.pl stops.and.starts.gff 
/home/zhang/software/augustus.2.7/scripts/autoAug/seq/genome_clean.fa /home/zhang/software/augustus.2.7/scripts/autoAug/cdna/cdna.psl utr
gave the print log
Code:
404 hints were filtered because of gene overlap.17383 hints would be compatible if the hints with gene-overlap wouldn't be filtered. Finished!
But I checked the utr.gb and utr.gff file and found both were empty, so the next steps could not run correctly. It is impossible that no transcript have utr, because I did tblastn augustus predicted proteins against those transcripts and found many transcripts have utrs and these transcripts truly start not with the start codon "ATG, TTG or GTG".
Did someone faced this problem? How to fix it, many thanks for your help.
Best Wishes,
yunz
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