<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style></head><body lang=EN-IN link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>Hi,<o:p></o:p></span></p><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output.<o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this.<o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'><img width=1330 height=327 style='width:13.8541in;height:3.4062in' id="Picture_x0020_3" src="cid:image003.png@01D5212F.A4C374B0" alt="https://groups.google.com/group/snap-user/attach/7e794dc33147c/Auto%20Generated%20Inline%20Image%201?part=0.1&view=1&authuser=0"></span><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'><o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error.<o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'><o:p> </o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>**********Command Used*****************<o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>> maker2zff genome.all.gff<o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>> fathom -validate geneome.ann genome.dna > snap_validate.output.txt<o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>Can anyone please help me to solve this problem...<o:p></o:p></span></p></div><div><p class=MsoNormal style='background:white'><span style='font-size:10.0pt;font-family:"Arial",sans-serif;color:#222222'>Thanks in advance. <o:p></o:p></span></p></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><o:p> </o:p></p></div></body></html>