<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>Yes.</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> "shaohua.fan" <<a href="mailto:lengjingmao@gmail.com">lengjingmao@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, 25 March, 2013 10:07 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> <<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 terminated strangely<br></div><div><br></div><div dir="ltr">Hi Carson, <div><br></div><div style="">Do you mean standard output from maker? If yes, I need to upload the file to our ftp server, since it is quite big around 1.1 Gb. </div><div style=""><br></div><div style="">Shaohua</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2013/3/25 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span><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>Could you send your captured standard error. That would contain messages that highlight the specific cause.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></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> "shaohua.fan" <<a href="mailto:lengjingmao@gmail.com" target="_blank">lengjingmao@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, 25 March, 2013 9:49 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] maker terminated strangely<br></div><div><div class="h5"><div><br></div><div dir="ltr">Hi Maker developers, <div><br></div><div>I met a problem when I was using Maker version 2.27 beta version that the pipeline terminated in the middle of the process without any error message. </div><div><br></div><div><br></div><div>The genome I am working with is a Eukaryotic genome which is consisted by around 6000 scaffolds. I combined de novo (Augustus and SNAP) and evidence based (protein from a closely related species and transcriptome from the same species) for the gene prediction (the genome is already repeat masked). The MPI (mpich2 version 1.5) enabled maker was run on a cluster by using SGE. I checked with the administrator of our cluster, there is no limitation of SGE job. </div><div><br></div><div>The maker was run by using mpiexec -n 48 /home/shafan/maker/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl</div><div><br></div><div>I attached my maker_opt.ctl, please let me know if you need any information for this problem. </div><div><br></div><div>Thanks a lot!</div><div><br></div><div>Shaohua </div></div></div></div>
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