formating the gff file
Posted: Thu Nov 19, 2015 2:58 pm
Originally posted in the old forum by Clement on 16.10.2014 - 19:19
Hi all,
I'm using Augustus for gene prediction in a new species. Both the genome and the hint file are home-made.
When running autoAugTrain.pl, i get the following error message :
ERROR: training.gb is empty. Possible reasons:
a) features in a provided training gene structure gff file were not compliant with the autoAug.pl pipeline (for instructions read at e.g.
http://bioinf.uni-greifswald.de/webaugu ... #structure)
The link seems to be invalid now, so I'm hoping to get help in this forum. This is how my gff file looks like :
pilon_round_18_contig_2558 exonerate CDS 345798 345888 . - . ID=gene_1
pilon_round_18_contig_2558 exonerate CDS 344999 345193 . - . ID=gene_1
pilon_round_18_contig_3684 exonerate CDS 684414 685064 . - . ID=gene_2
pilon_round_18_contig_3684 exonerate CDS 683996 684190 . - . ID=gene_2
Do you see any obvious problem with the formating ?
Best,
Clement
Hi all,
I'm using Augustus for gene prediction in a new species. Both the genome and the hint file are home-made.
When running autoAugTrain.pl, i get the following error message :
ERROR: training.gb is empty. Possible reasons:
a) features in a provided training gene structure gff file were not compliant with the autoAug.pl pipeline (for instructions read at e.g.
http://bioinf.uni-greifswald.de/webaugu ... #structure)
The link seems to be invalid now, so I'm hoping to get help in this forum. This is how my gff file looks like :
pilon_round_18_contig_2558 exonerate CDS 345798 345888 . - . ID=gene_1
pilon_round_18_contig_2558 exonerate CDS 344999 345193 . - . ID=gene_1
pilon_round_18_contig_3684 exonerate CDS 684414 685064 . - . ID=gene_2
pilon_round_18_contig_3684 exonerate CDS 683996 684190 . - . ID=gene_2
Do you see any obvious problem with the formating ?
Best,
Clement