Mario Stanke

You could alternatively use the C version in `Augustus/auxprogs/bam2wig`.

It reports 0 annotated genes in the reference annotation that you input. The nan comes from a division by 0. Compare your input .gb file with one in the examples...

I just tried with the current version of Augustus the following and it worked: ``` cd Augustus/docs/tutorial/data msa2prfl.pl --prefix_from_seqnames --max_entropy=0.75 --blockscorefile=PF00225_seed.blocks.txt PF00225_seed.txt > PF00225_seed.prfl fastBlockSearch --cutoff=1.1 chr4.103M.fa PF00225_seed.prfl ``` I...

@LarsGab It looks like this exception is thrown in Profile::parse_stream. Can you please take this up?

Thanks, Andrew. That may explain why the problem came up recently and I couldn't reproduce it before upgrading my computer. Thanks for the code. Lars, I reproduced the problem on...

What does `ls -la /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species` return (only the line from the directory `.`)?

OK. You already have a directory with that name. Maybe that is it. Can you ``` rm -r /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species/for_bad_genes_removing mkdir /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species/for_bad_genes_removing rmdir /ds3512/home/panyp/genome_assess/augustus-3.3.3/config//species/for_bad_genes_removing ``` as the same user as and...

Please have a look at the input files to the last command, `train.gb` and `onlytrain.gb` manually. For example, they could be empty or have too few genes (LOCUS) for a...

Another idea may be that your input training gene set contains too few UTRs. You could try to diagnose (eliminate this possibility) with `--noutr`.

I suspect that we have had alignments in MAF format as input that used a "-" to separate the species name from the sequence name. I don't remember any such...