<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto">Just make the desired path be your working directory then use -base to specify a name for the maker.output directory.<div><br></div><div>—Carson<br><br><div dir="ltr">Sent from my iPhone</div><div dir="ltr"><br><blockquote type="cite">On Oct 1, 2019, at 11:15 PM, Emmanuel Nnadi <eennadi@gmail.com> wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Hi Carson<div>Thanks for your email</div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">I tried to use the -base option to make maker output into a new directory </span><span style="font-family:-webkit-standard;font-size:medium">/mnt/data/emmanuel/Makersupport/mucuna</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">The log report is found below </span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">The 'base' option is an ID used in generating names for</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">multiple files and directories. It is not a directory path.</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span style="font-variant-ligatures:no-common-ligatures">You must remove all '/' characters from '/mnt/data/emmanuel/Makersupport/mucuna'</span></p>
<p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p></div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">Thanks</p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><br></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)">Emmanuel</p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><br></p><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Nnadi Nnaemeka Emmanuel,Ph.D<div>Department of Microbiology,</div><div>Faculty of Natural and Applied Science,</div><div>Plateau State University, Bokkos, Plateau State, Nigeria.</div><div>+2348068124819</div><div>Publications: </div><div> <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div></div></div><br></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Oct 1, 2019 at 5:34 PM Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div style="word-wrap:break-word;line-break:after-white-space"><br><div><br><blockquote type="cite"><div>On Oct 1, 2019, at 7:59 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:</div><br><div><div dir="ltr"><div dir="ltr"><div dir="ltr">Hi Carson<div><span style="font-family:-webkit-standard;font-size:inherit">I want marker to output into a directory /mnt/data/emmanuel/Makersupport. Please how can I make that?</span></div></div></div></div></div></blockquote><div><br></div><div><br></div><div><br></div><div>From the usage statement —></div><div><br></div><div> -base <string> Set the base name MAKER uses to save output files.<br> MAKER uses the input genome file name by default.</div><div><br></div><div><br></div><br><blockquote type="cite"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"></span></p><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Also,</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(252,50,32)"><span style="font-variant-ligatures:no-common-ligatures">I added </span><span style="font-variant-ligatures:no-common-ligatures">RepBaseRepeatMaskerEdition-20170127.tar into the directory </span><span style="font-variant-ligatures:no-common-ligatures">/home/emmanuel/maker/exe/RepeatMasker</span></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></div><div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">used tar xvf </span><span style="font-variant-ligatures:no-common-ligatures;color:rgb(252,50,32)">RepBaseRepeatMaskerEdition-20170127.tar to unpack it. In my </span><span style="font-variant-ligatures:no-common-ligatures">/home/emmanuel/maker/exe/RepeatMasker/Libraries I have RMRBSeqs.embl but running maker it tells me it repbase is not installed.</span></div></div></div></div></div></div></blockquote><div><br></div><div><br></div><div>After uncaring RepBase you have to run the ./configure script with rmblast installed and it will create the needed blast indexes and libraries</div><div><br></div><div><div>RepeatMasker.lib</div><div>RepeatMaskerLib.embl</div><div>RepeatMasker.lib.nhr</div><div>RepeatMasker.lib.nin</div><div>RepeatMasker.lib.nsq</div><div>RepeatMasker.lib.xnd</div><div>RepeatMasker.lib.xni</div><div>RepeatMasker.lib.xns</div><div>RepeatMasker.lib.xnt</div><div>RepeatPeps.lib</div><div>RepeatPeps.lib.phr</div><div>RepeatPeps.lib.pin</div><div>RepeatPeps.lib.psq</div><div>RepeatPeps.lib.xpd</div><div>RepeatPeps.lib.xpi</div><div>RepeatPeps.lib.xps</div><div>RepeatPeps.lib.xpt</div></div><div><br></div><div><br></div><div>—Carson</div><div><br></div></div></div></blockquote></div>
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