<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>One more thing. From the example you gave, is is important to note that the terminal CDS (first or last) can be a single base pair in length (start and end will be the same value). Augustus sometimes does this for example. Do you have non-CDS feature types where this happens, or any internal CDS's where this happens?</div><div><br></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> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, August 5, 2014 at 2:21 PM<br><span style="font-weight:bold">To: </span> Marc Höppner <<a href="mailto:mphoeppner@gmail.com">mphoeppner@gmail.com</a>>, <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: [maker-devel] Maker GFF output with features of 0 length<br></div><div><br></div><div><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>Were you using GFF3 pass-through or correct_est_fusion options? When you rerun do the same features still have lengths of zero (I.e. is it random or is it reproducable)?</div><div><br></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> Marc Höppner <<a href="mailto:mphoeppner@gmail.com">mphoeppner@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, July 30, 2014 at 4:44 AM<br><span style="font-weight:bold">To: </span> <<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 GFF output with features of 0 length<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi,<div><br></div><div>I’ve - more by accident - found that many of the gene builds I have generated with Maker (2.31.3) contain features with identical start and stop positions. </div><div><br></div><div>For example:</div><div><br></div><div><div style="margin: 0px; font-family: Menlo;">scaffold_2927 maker CDS 13013 13013 . + 1 ID=maker-scaffold_2927-augustus-gene-0.8-mRNA-1:cds;Parent=maker-scaffold_2927-augustus-gene-0.8-mRNA-1</div></div><div><br></div><div><br></div><div>This occurs seemingly randomly for all sorts of feature types and I have only seen this when running Maker on full assemblies. Before I start turning every stone, any ideas about possible explanations for this phenomenon? Is this likely some MPI-related communication issue, or NFS problems with synching data? Maker runs fine on our system, but that doesn’t mean that there aren’t any cryptic issues that only on these occasions read their head… Regarding the frequency, out of 450.000 GFF lines, 270 were affected in the case that I looked into the most. So it is pretty rare, but still...</div><div><br></div><div>I am currently using Maker with openmpi-1.7.4 and the file system is mounter of NFS4 and IPoIB. I now switched to Maker 2.31.6, but have no strong reason to suspect that this will make a difference.</div><div><br></div><div>Regards,</div><div><br></div><div>Marc</div><div><br></div><div><br></div></div></div>_______________________________________________
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