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</head><body><div class="io-ox-signature"><p>Dear maker-devel group,<br></p><p><br></p><p>I have some issues with my maker ab initio gene prediction (for a new mammal genome) when creating an HMM via SNAP.<br></p><p>after two maker runs I wanted to create a new HMM for the third maker run, but the command <br></p><p><br></p><p style="padding-left: 30px;"><em>fathom genome.ann genoma.dna -gene-stats</em><br></p><p style=""><br></p><p style="">resulted in 0 genes.<br></p><p style=""><br></p><p style="">What have I done so far:<br></p><ul><li>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<br></li></ul><p><br></p><ul><li>I was able to create an HMM based on all merged *.gff But these were not many:<br><ul><li>out of 27.032 Scafolds (Sequences) only 280 were used for the HMM; here the gene-stats:<br></li><li>280 sequences<br>0.458676 avg GC fraction (min=0.338014 max=0.708052)<br>7445 genes (plus=3192 minus=4253)<br>1621 (0.217730) single-exon<br>5824 (0.782270) multi-exon<br>168.412018 mean exon (min=1 max=5224)<br>1464.349243 mean intron (min=30 max=41197)<br></li></ul></li></ul><p><br></p><ul><li>For the second maker run I then used this HMM and again the BUSCO+SwissPort.fasta reference file.<br><ul><li>the gene-stats for the output of the second maker run are:<br></li><li>282 sequences<br>0.473125 avg GC fraction (min=0.338014 max=0.725131)<br>0 genes (plus=0 minus=0)<br>0 (-nan) single-exon<br>0 (-nan) multi-exon<br>-nan mean exon (min=2147483647 max=0)<br>-nan mean intron (min=2147483647 max=0)<br></li></ul></li></ul><p><br></p><p>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?)<br></p><p><br></p><p>Thank you for your time and help<br></p><p>kind regards<br></p><p>Lucy<br></p></div></body></html>