<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Note protein/transcript fasts are only created when there are gene models to output to those files (so their absence means there were no gene models for that contig). Most sequences without protein/transcript fasts in your sample are very short and thus don’t contain anything. What is left either have no est2genome results or the est2genome alignments do not have sufficient open reading frame to be turned into a gene model (false merging of regions by trinity can cause this, so make sure you use the jaccard index option when assembling reads with trinity to avoid this).</div><div><br></div><div>You are using only the est2genome=1 option. This will result in a limited set of genes that can be used for training SNAP/Augustus (so not getting results on all contigs is expected). You really won’t get much as far as results until you have one of the ab initio predictors turned on.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, March 11, 2014 at 8:52 AM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Subject: </span> Re: maker output- transcripts.fasta and proteins.fasta files missing<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Alright done. My username is daras<div><br></div><div>Thanks</div><div>Dhivya</div><div><br><div><div>On Mar 10, 2014, at 5:10 PM, Carson Holt wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Input and compressed file of output.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, March 10, 2014 at 2:09 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Subject: </span> Re: maker output- transcripts.fasta and proteins.fasta files missing<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Carson,<div><br></div><div>Do you mean the whole maker output?</div><div><br></div><div>Thanks</div><div>dhivya</div><div><br><div><div>On Mar 10, 2014, at 4:55 PM, Carson Holt wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Could you upload everything here —> <a href="http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi">http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi</a></div><div><br></div><div>Than send us the link generated or your user ID.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, March 10, 2014 at 1:50 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, Daniel Ence <<a href="mailto:dence@genetics.utah.edu">dence@genetics.utah.edu</a>><br><span style="font-weight:bold">Subject: </span> Fwd: maker output- transcripts.fasta and proteins.fasta files missing<br></div><div><br></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Carson and Daniel,<div><br></div><div>I'm sending this across to you separately since maker list is blocking my email due to attachment size.</div><div><br></div><div>As always, thanks for any guidance you can provide.</div><div>Dhivya</div><div><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">March 10, 2014 3:14:03 PM CDT</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>maker output- transcripts.fasta and proteins.fasta files missing</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div><div>Hello,<br><br>I've been running maker with different assembly files, reference files etc and I check the output by:<br><br>1. concatenating the gff files<br>2. concatenating the *transcripts.fasta files<br>3. concatenating the *proteins.fasta files<br><br>I'm noticing that when I ran maker twice with same parameters, the second time around, many of the output subdirectories do not have a *transcripts.fasta or *proteins.fasta file in it.<br>There are 251 subdirectories and only 97 of them have all 3 output files. Maker log looks ok to me, but I've attached it here as well.<br><br>What could be the reason for this?<br><br>Thanks<br>dhivya<br><br></div></blockquote></div></div></div></div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><blockquote type="cite"><div><br><br><br><br></div></blockquote></div><br></div></div></div></span></div></blockquote></div><br></div></div></div></span></div></blockquote></div><br></div></div></div></span></body></html>