<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>Hi Jennifer,</div><div><br></div><div>The contig you ran with was only 52 bp in length and contained only repetitive sequence. Exonerate only runs if there are BLAST results that need polishing, which there weren't.</div><div>The Snig2_XXXXXXX.maker.proteins.fasta and Snig2_XXXXXXX.maker.transcripts.fasta were not produced because there were no proteins or transcripts to report.</div><div><br></div><div>In general running on sequence shorter than 10,000 bp isn't useful. This is because programs like SNAP and Augustus need sequence flanking the actual gene to make their calls, and with intron/exon structure you are unlikely to fully capture a gene (end to end) at random in under 10kb for many eukaryotic organisms.</div><div><br></div><div>If you are trying to use raw reads, you will need to assemble them first before running MAKER. Let us know specifically what you are trying to do, and we can give you pointers on how to proceed.</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> Jennifer Liberto <<a href="mailto:jrliberto@yahoo.com">jrliberto@yahoo.com</a>><br><span style="font-weight:bold">Reply-To: </span> Jennifer Liberto <<a href="mailto:jrliberto@yahoo.com">jrliberto@yahoo.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 6 June, 2012 2:22 PM<br><span style="font-weight:bold">To: </span> "<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>" <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] MAKER output concerns<br></div><div><br></div><div><div><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><!--[if gte mso 9]><xml>
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<![endif]--><!--StartFragment--><div class="MsoNormal">To whom this may concern,</div><div class="MsoNormal"><o:p> </o:p></div><div class="MsoNormal">I am brand new to MAKER and I am concerned about the output
files that I am receiving. My
partner and I were able to run the dpp test with no errors, all the files and
directories were accounted for.
However, when we tried to run it on our own small dataset of 5 genes,
and a surfperch genome, we were missing 2 files in the output of every contig:</div><div class="MsoNormal"><o:p> </o:p></div><div class="MsoNormal">Snig2_XXXXXXX.maker.proteins.fasta</div><div class="MsoNormal">Snig2_XXXXXXX.maker.transcripts.fasta</div><div class="MsoNormal"><o:p> </o:p></div><div class="MsoNormal">When I look at the run log for each of the contigs, I see that
blastx, blastn, tblastx, augustus, snap, and repeatrunner were called but not
exonerate; I have attached a sample run log with this post. Also, our gff files
contain only short 52 bp repeat sequences (I have attached one of these here as
well in a .txt format) and looks nothing like the gff file we received in out
dpp test. If you could give any
pointers or hints as to why we are not receiving the two files, why exonerate
is not being called, and why our gff files contain only uniformly small repeat
sequences, the help would be greatly appreciated. </div><div class="MsoNormal"><o:p> </o:p></div><div class="MsoNormal">Thank you for your time,</div><div class="MsoNormal">Jennifer Liberto</div><!--EndFragment--></div></div></div></div>_______________________________________________
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