format of .gb .gff

[ziejan]

Hi, I want to annotate a Verticillium Genome via command line. I installed augustus and all neccesary stuff to get it work and tested with the example data -> worked.

My Verticillium Genome is also working via web interface (at least one contig step by step) (good results so far). Now I want to annotate via command line. Because there is no verticillium dataset available offline I tried to create one by myself by using the autoAugTrain.pl script. Again, this works for me with the example data. But with the Verticillium dahliae data I downloaded from ncbi I can't get it done. I tried with: autoAugTrain.pl --species=Verticillium_dahliae --genome=/home/test/Verticillium.fa --trainingset=/home/test/Verticillium.gff (Program aborted Inappropriate ioctl for device) and with autoAugTrain.pl --species=Verticillium_dahliae --trainingset=/home/test/Verticillium.gb (appears to be in corrupt Genbank format. 'ORIGIN' missing and appears to be in corrupt Genbank format. '//' missing) but both commands output that I have the wrong format. Any clue of how to convert the ncbi .gff or ncbi .gb file format into a Augustus-working format?

I do recognize that there are differences between the example format and my format but I have no clue what changes I have to take exactly...

[kimnegrette3]

Hi! I have the same problem. I want to train augustus using a .gbff file I downloaded from ncbi https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/611/645/GCF_000611645.1_mono_v1/GCF_000611645.1_mono_v1_genomic.gbff.gz But randomSplit.pl fails with "size 100 is greater than the number of genes in file Monoraphidium_neglectum_genomic.gbff. Aborting." The file of course has more than 100 genes, but it seems that the format is not quite well. Did you make it work? I would really appreciate any help here. Thanks!

Kimberly.

[ziejan]

@kimnegrette3 No, I didn't make it work. I just used the training set for Verticillium longisporum and I got some good results as it is quite close to our verticillium dahliae...