[maker-devel] Ab initio gene prediction; 0 genes when creating HMM via SNAP

[Carson Holt]

It looks like you have no genes to train with. So you did something wrong on your second run. Either no gene predictor was running or you provided no evidence for the predictor, so you produced no models.

—Carson


> On Mar 6, 2017, at 7:40 AM, lucys-world at mailbox.org wrote:
> 
> Dear maker-devel group,
> 
> 
> 
> I have some issues with my maker ab initio gene prediction (for a new mammal genome) when creating an HMM via SNAP.
> 
> after two maker runs I wanted to create a new HMM for the third maker run, but the command 
> 
> 
> 
> fathom genome.ann genoma.dna -gene-stats
> 
> 
> 
> resulted in 0 genes.
> 
> 
> 
> What have I done so far:
> 
> for the first training run I only used BUSCO and Swiss-Port data bank as references (Since no EST are available for my species). Additionally I set protein2genome =1
> 
> 
> I was able to create an HMM based on all merged *.gff But these were not many:
> out of 27.032 Scafolds (Sequences) only 280 were used for the HMM; here the gene-stats:
> 280 sequences
> 0.458676 avg GC fraction (min=0.338014 max=0.708052)
> 7445 genes (plus=3192 minus=4253)
> 1621 (0.217730) single-exon
> 5824 (0.782270) multi-exon
> 168.412018 mean exon (min=1 max=5224)
> 1464.349243 mean intron (min=30 max=41197)
> 
> 
> For the second maker run I then used this HMM and again the BUSCO+SwissPort.fasta reference file.
> the gene-stats for the output of the second maker run are:
> 282 sequences
> 0.473125 avg GC fraction (min=0.338014 max=0.725131)
> 0 genes (plus=0 minus=0)
> 0 (-nan) single-exon
> 0 (-nan) multi-exon
> -nan mean exon (min=2147483647 max=0)
> -nan mean intron (min=2147483647 max=0)
> 
> 
> Would you recommend to rerun everything, e.g. with an additional Augustus gene prediction (species=human), or EST from related species? (If so how close related?)
> 
> 
> 
> Thank you for your time and help
> 
> kind regards
> 
> Lucy
> 
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