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

[lucys-world at mailbox.org]

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:
o out of 27.032 Scafolds (Sequences) only 280 were used for the HMM; here the gene-stats:
o 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.
o the gene-stats for the output of the second maker run are:
o 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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