<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">Could you send me these two files. I put the full path below based on your STDERR report. Also this log was from the original run having the issue, and not a new repeated attempt at that one, correct?</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">First file —></div><div><font face="Calibri,sans-serif">/gulo/glob/saneash/acrasis_makerv2.28/run1/re-run0/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130708_datastore/71/F8/AR_HYBRID_130113_TINTIN_EF2ON_C1/theVoid.AR_HYBRID_130113_TINTIN_EF2ON_C1/AR_HYBRID_130113_TINTIN_EF2ON_C1.abinit_masked.0.run0%2Ehmm.snap</font></div><div><font face="Calibri,sans-serif"><br></font></div><div><font face="Calibri,sans-serif"><br></font></div><div><font face="Calibri,sans-serif">Second file —></font></div><div><span style="font-family: Calibri, sans-serif;">/gulo/glob/saneash/acrasis_makerv2.28/run1/re-run0/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130708.maker.output/AR_Hybrid_X2k_Y33_Z200_redundant_remove_130708_datastore/71/F8/AR_HYBRID_130113_TINTIN_EF2ON_C1/</span><span style="font-family: Calibri, sans-serif;">AR_HYBRID_130113_TINTIN_EF2ON_C1.gff</span></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">Thanks,</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;">Carson</div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><br></div><span id="OLK_SRC_BODY_SECTION" style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><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> Sanea Sheikh <<a href="mailto:saneasheikh@gmail.com">saneasheikh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, January 16, 2014 at 3:52 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>>, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Subject: </span> Fwd: [maker-devel] Problem with re-annotation<br></div><div><br></div><div dir="ltr"><div class="gmail_default" style="font-family:tahoma,sans-serif">Hello Carson<br></div><div class="gmail_quote"><div dir="ltr"><div style="font-family:tahoma,sans-serif">Here it is.</div><span class="HOEnZb"><font color="#888888"><div style="font-family:tahoma,sans-serif">
Sanea</div></font></span><div><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">
On Tue, Jan 14, 2014 at 1:39 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Hi Sanea,</div><div><br></div><div>There are no snap calls in your results. It’s as if SNAP never even ran. Did you capture STDERR from your second run? If so can you send it to me. I just want to see if it even shows SNAP as having run in the progress reports. </div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none"><span style="font-weight:bold">From: </span> Sanea Sheikh <<a href="mailto:saneasheikh@gmail.com" target="_blank">saneasheikh@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, January 13, 2014 at 2:17 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Problem with re-annotation<br></div><div><div><br></div><div dir="ltr"><div style="font-family:tahoma,sans-serif">Hello</div><div style="font-family:tahoma,sans-serif"><br>I am using Maker to annotate a genome for which I only have EST data and some protein data. I ran Maker once using this EST and protein data (est2genome=1, protein2genome=1). I had the Maker output. I combined all the GFF files for all the contigs. I used the combined GFF file to train SNAP which gave me a .hmm file. Now I modified the Maker opts control file. I provided the hmm file in snap_hmm. I set est2genome=0 and protein2genome=0. I ran Maker again assuming that now I have trained the gene predictor and I would have better annotations. But now the output file that I get does not have Maker annotation. I have attached the control files and the output file for the re-run so you can have a look and let me know what I am doing wrong in order to re-annotate the genome using the output from the previous run. </div><div style="font-family:tahoma,sans-serif"><br>Sanea</div></div></div>
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