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Hi Lucy,
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<div class="">What were your settings for the second training run? Did you leave protein2genome=1? </div>
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<div class="">~Daniel</div>
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<div class="">On Mar 6, 2017, at 9:40 AM, <a href="mailto:lucys-world@mailbox.org" class="">
lucys-world@mailbox.org</a> wrote:</div>
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<p class="">Dear maker-devel group,<br class="">
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<p class="">I have some issues with my maker ab initio gene prediction (for a new mammal genome) when creating an HMM via SNAP.<br class="">
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<p class="">after two maker runs I wanted to create a new HMM for the third maker run, but the command
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<p style="padding-left: 30px;" class=""><em class="">fathom genome.ann genoma.dna -gene-stats</em><br class="">
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<p style="" class="">resulted in 0 genes.<br class="">
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<p style="" class="">What have I done so far:<br class="">
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<li class="">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 class="">
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<li class="">I was able to create an HMM based on all merged *.gff But these were not many:<br class="">
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<li class="">out of 27.032 Scafolds (Sequences) only 280 were used for the HMM; here the gene-stats:<br class="">
</li><li class="">280 sequences<br class="">
0.458676 avg GC fraction (min=0.338014 max=0.708052)<br class="">
7445 genes (plus=3192 minus=4253)<br class="">
1621 (0.217730) single-exon<br class="">
5824 (0.782270) multi-exon<br class="">
168.412018 mean exon (min=1 max=5224)<br class="">
1464.349243 mean intron (min=30 max=41197)<br class="">
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<li class="">For the second maker run I then used this HMM and again the BUSCO+SwissPort.fasta reference file.<br class="">
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<li class="">the gene-stats for the output of the second maker run are:<br class="">
</li><li class="">282 sequences<br class="">
0.473125 avg GC fraction (min=0.338014 max=0.725131)<br class="">
0 genes (plus=0 minus=0)<br class="">
0 (-nan) single-exon<br class="">
0 (-nan) multi-exon<br class="">
-nan mean exon (min=2147483647 max=0)<br class="">
-nan mean intron (min=2147483647 max=0)<br class="">
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<p class="">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 class="">
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<p class="">Thank you for your time and help<br class="">
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<p class="">kind regards<br class="">
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<p class="">Lucy<br class="">
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