<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">MAKER can’t give you those details. All MAKER does is try and identify gene models against the assembly you provide.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Sep 22, 2017, at 1:27 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" class="">eennadi@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello all,<div class="">Please how can I determine the following in maker:</div><div class="">1. The total number of chromosomes</div><div class="">2. The size of my genome</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Thanks</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Fri, Sep 1, 2017 at 10:52 PM, Emmanuel Nnadi <span dir="ltr" class=""><<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto" class="">Ok, thanks. <span class=""><div data-smartmail="gmail_signature" class="">Nnadi Nnaemeka Emmanuel<br class="">Department of Microbiology,<br class="">Faculty of Natural and Applied Science,<br class="">Plateau State University, Bokkos, Plateau State, Nigeria.<br class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/<wbr class="">publications</a><br class=""><br class=""> </div></span></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Sep 1, 2017 10:50 PM, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>> wrote:<br type="attribution" class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="auto" class=""><div class="">It would need to be a new run. You won't be able to use the updated contig names with the old run. <br class=""><br class=""><div class=""><span style="font-size:13pt" class="">--Carson</span></div><div class=""><br class=""></div><div class="">Sent from my iPhone</div></div><div class=""><br class="">On Sep 1, 2017, at 3:41 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:<br class=""><br class=""></div><blockquote type="cite" class=""><div class=""><div dir="ltr" class="">Hi carson<div class="">Thanks for the tip</div><div class=""><span style="font-size:12.800000190734863px" class="">perl -ane 's/1_S7_R1_001_\(paired\)_</span><span style="font-size:12.800000190734863px" class="">trim<wbr class="">med_\(paired\)_//g; print' genome.fasta</span><br class=""></div><div class=""><br class=""></div><div class=""><span style="font-size:12.800000190734863px" class="">It worked well however, when i ran it, it removed </span><span style="font-size:12.800000190734863px" class="">1_S7_R1_001_\(paired\)<wbr class="">_</span><span style="font-size:12.800000190734863px" class="">trimmed_\(paired\)_, </span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class="">I have ran maker with </span><span style="font-size:12.800000190734863px" class="">1_S7_R1_001_\(paired\)_</span><span style="font-size:12.800000190734863px" class="">tr<wbr class="">immed_\(paired\)_, </span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class="">1. How can I effect the change when maker has produced some files from the the old sequence?</span></div><div class=""><br class=""></div><div class=""><span style="font-size:12.800000190734863px" class="">I have spent more than 24 hours running maker and it has produced some folders already.</span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class="">How can I make this change?</span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class="">Thanks</span><br class=""></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><span style="font-size:12.800000190734863px" class=""><br class=""></span></div><div class=""><br class=""></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-3532612113651592299m_1824814724788330975gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Fri, Sep 1, 2017 at 4:54 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">BLAST which is used by MAKER can not handle really long contig names. MAKER tries to get around this by adding a secondary tag to the fasta header when long names are detected. Even then it would be better to change the IDs of your contigs to avoid downstream failures.<div class=""><br class=""></div><div class="">I would recommend removing '1_S7_R1_001_(paired)_trimmed_<wbr class="">(paired)_’ from each contig name.</div><div class=""><br class=""></div><div class="">Example command to do that —> </div><div class="">perl -ane 's/1_S7_R1_001_\(paired\)_trim<wbr class="">med_\(paired\)_//g; print' genome.fasta<span class="m_-3532612113651592299m_1824814724788330975HOEnZb"><font color="#888888" class=""><br class=""><div class=""><br class=""></div><div class="">—Carson</div></font></span><div class=""><div class="m_-3532612113651592299m_1824814724788330975h5"><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Aug 30, 2017, at 3:54 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Carson<div class="">Thanks for your response its been helpful</div><div class=""><br class=""></div><div class="">Please bear with me as I work through this</div><div class=""><br class=""></div><div class="">1. Please how do I generate EST for my novel sequences?</div><div class="">2. I am currently running maker without EST and protein sequences is it wrong? Can it predict properly?</div><div class="">3. One error in the contig just returned this value</div><div class=""><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FastaDB::_cleanIndexAndCompact<wbr class="">(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> at /usr/local/bin/RepeatMasker line 1464.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FastaDB::_cleanIndexAndCompact<wbr class="">(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> at /usr/local/bin/RepeatMasker line 1464.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FastaDB::_cleanIndexAndCompact<wbr class="">(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> at /usr/local/bin/RepeatMasker line 1464.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: RepeatMasker failed</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">--> rank=NA, hostname=emmannaemekas-MacBook<wbr class="">-Pro.local</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Failed while doing repeat masking</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Chunk failed at level:0, tier_type:1</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FAILED CONTIG:1_S7_R1_001_(paired)_tr<wbr class="">immed_(paired)_contig_2</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Chunk failed at level:2, tier_type:0</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">FAILED CONTIG:1_S7_R1_001_(paired)_tr<wbr class="">immed_(paired)_contig_2</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">examining contents of the fasta file and run log</span></div></div><div class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Wed, Aug 30, 2017 at 4:12 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">You can query valid species names using the queryTaxonomyDatabase.pl script that comes with RepeatMasker. Try not to be too specific. In general you should use the genus rather than the species for example (or even use all of RepBase).<div class=""><div class=""><br class=""></div><div class="">Example —></div><div class="">perl …/RepeatMasker/util/queryTaxon<wbr class="">omyDatabase.pl -species “drosophila"</div><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">—Carson</div></font></span><div class=""><div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134h5"><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Aug 30, 2017, at 9:05 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831Apple-interchange-newline"><div class=""><div dir="auto" class="">Hi Carson,<div dir="auto" class=""><br class=""></div><div dir="auto" class=""> Thanks</div><div dir="auto" class="">I was able to start using maker.</div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">However I am working with a plant Genome novel. I had set the repeatmasking to </div><div dir="auto" class="">1. Dcotrep a names from the repbase release but maker returned it back as not known to repeat masker</div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">How can I use specific known genomes for repeat masking</div><div dir="auto" class="">Thanks<br class=""><br class=""><div data-smartmail="gmail_signature" dir="auto" class="">Nnadi Nnaemeka Emmanuel<br class="">Department of Microbiology,<br class="">Faculty of Natural and Applied Science,<br class="">Plateau State University, Bokkos, Plateau State, Nigeria.<br class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a><br class=""><br class=""> </div></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Aug 29, 2017 4:26 PM, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>> wrote:<br type="attribution" class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">MAKER will read the genome= options from the maker_opts.ctl file in your current directory or the maker_opts.ctl you specified on the command line. The error means you have left the value empty. Perhaps you did not save the changes you made or you did not specify the location of the maker_opts.ctl file to use.<div class=""><br class=""></div><div class="">You can check the contents of the file using cat. Example —> cat maker_opts.ctl</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Aug 29, 2017, at 5:11 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Carson,<div class="">Thanks a lot for yesterday. I was able to resolve the issue of running maker and i followed the commands in the tutorial.</div><div class="">I however encountered another problem</div><div class=""><br class=""></div><div class="">when I ran the command <span style="font-family:'Courier New';font-size:11pt" class="">nano -c maker_opts.ctl</span></div><div class=""><span style="font-family:'Courier New';font-size:11pt" class=""><br class=""></span></div><div class=""><span style="font-family:'Courier New';font-size:11pt" class="">It gave the following </span><b style="font-family:Menlo;font-size:11px" class="">1_S7_assembly.fa I specified the name of the genome but when I ran maker in another tab it gave </b></div><div class=""><span style="font-family:'Courier New';font-size:11pt" class=""><br class=""></span></div><div class=""><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">#-----Genome (these are always required)</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">genome=<b class="">1_S7_assembly.fa</b> #genome sequence (fasta file or fasta embeded in GFF3 file)</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">#-----Re-annotation Using MAKER Derived GFF3</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">maker_gff= #MAKER derived GFF3 file</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">#-----EST Evidence (for best results provide a file for at least one)</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">est= #set of ESTs or assembled mRNA-seq in fasta format</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">altest= #EST/cDNA sequence file in fasta format from an alternate organism</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">altest_gff= #aligned ESTs from a closly relate species in GFF3 format</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">#-----Protein Homology Evidence (for best results provide a file for at least one)</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">protein= #protein sequence file in fasta format (i.e. from mutiple oransisms)</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">protein_gff= #aligned protein homology evidence from an external GFF3 file</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">#-----Repeat Masking (leave values blank to skip repeat masking)</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">model_org=all #select a model organism for RepBase masking in RepeatMasker</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">repeat_protein=/Users/emmannae<wbr class="">meka/Desktop/Gpm/maker/data/te<wbr class="">_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">rm_gff= #pre-identified repeat elements from an external GFF3 file</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><b class="">I ran maker command on another tab and it returned the following</b></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">STATUS: Parsing control files...</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: You have failed to provide a value for 'genome' in the control files.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><p style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">
</p><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">--> rank=NA, hostname=emmannamekasMBP</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Questions</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">1. Specifying the genome location, do I need to run maker on the same tab or open another bash tab?</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">2. My genome is novel and do not have proteins, how do I generate protein fast for the de novo sequence and EST?</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Thanks</span></div></div>
</div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Mon, Aug 28, 2017 at 6:47 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Here is a class on how to use MAKER taught a couple of years back —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014" target="_blank" class="">http://weatherby.genetics.u<wbr class="">tah.edu/MAKER/wiki/index.php/M<wbr class="">AKER_Tutorial_for_GMOD_Online_<wbr class="">Training_2014</a><div class=""><br class=""></div><div class="">There is also a linked video as well as an amazon image of the class material where you can run the image in the cloud and follow along.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327h5"><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Aug 28, 2017, at 11:43 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div><br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Carson,<div class="">Thanks a lot </div><div class=""><br class=""></div><div class="">I ran this command maker -h it returned the following</div><div class=""><br class=""></div><div class="">The last thing I wish to ask you, how can I load my genome fine and being annotation?</div><div class=""><br class=""></div><div class="">Thanks</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">emmannamekasMBP:maker emmannaemeka$ maker -h</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">MAKER version 2.31.9</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Usage:</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> maker [options] <maker_opts> <maker_bopts> <maker_exe></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Description:</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> MAKER is a program that produces gene annotations in GFF3 format using</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> evidence such as EST alignments and protein homology. MAKER can be used to</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> produce gene annotations for new genomes as well as update annotations</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> from existing genome databases.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> The three input arguments are control files that specify how MAKER should</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> behave. All options for MAKER should be set in the control files, but a</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> few can also be set on the command line. Command line options provide a</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> convenient machanism to override commonly altered control file values.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> MAKER will automatically search for the control files in the current</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> working directory if they are not specified on the command line.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> Input files listed in the control options files must be in fasta format</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> unless otherwise specified. Please see MAKER documentation to learn more</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> about control file configuration. MAKER will automatically try and</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> locate the user control files in the current working directory if these</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> arguments are not supplied when initializing MAKER.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> It is important to note that MAKER does not try and recalculated data that</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> it has already calculated. For example, if you run an analysis twice on</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> the same dataset you will notice that MAKER does not rerun any of the</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> BLAST analyses, but instead uses the blast analyses stored from the</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> previous run. To force MAKER to rerun all analyses, use the -f flag.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> MAKER also supports parallelization via MPI on computer clusters. Just</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> launch MAKER via mpiexec (i.e. mpiexec -n 40 maker). MPI support must be</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> configured during the MAKER installation process for this to work though</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> </span><br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244webkit-block-placeholder"></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">Options:</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -genome|g <file> Overrides the genome file path in the control files</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -RM_off|R Turns all repeat masking options off.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -datastore/ Forcably turn on/off MAKER's two deep directory</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> nodatastore structure for output. Always on by default.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -old_struct Use the old directory styles (MAKER 2.26 and lower)</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -base <string> Set the base name MAKER uses to save output files.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> MAKER uses the input genome file name by default.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -tries|t <integer> Run contigs up to the specified number of tries.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -cpus|c <integer> Tells how many cpus to use for BLAST analysis.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> Note: this is for BLAST and not for MPI!</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -force|f Forces MAKER to delete old files before running again.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244gmail-Apple-tab-span" style="white-space:pre-wrap"> </span> This will require all blast analyses to be rerun.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -again|a recaculate all annotations and output files even if no</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244gmail-Apple-tab-span" style="white-space:pre-wrap"> </span> settings have changed. Does not delete old analyses.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -quiet|q Regular quiet. Only a handlful of status messages.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -qq Even more quiet. There are no status messages.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -dsindex Quickly generate datastore index file. Note that this</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> will not check if run settings have changed on contigs</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -nolock Turn off file locks. May be usful on some file systems,</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> but can cause race conditions if running in parallel.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -TMP Specify temporary directory to use.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -CTL Generate empty control files in the current directory.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -OPTS Generates just the maker_opts.ctl file.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -BOPTS Generates just the maker_bopts.ctl file.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -EXE Generates just the maker_exe.ctl file.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -MWAS <option> Easy way to control mwas_server for web-based GUI</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> options: STOP</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> START</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> RESTART</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -version Prints the MAKER version.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""> -help|? Prints this usage statement.</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class=""></div></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Mon, Aug 28, 2017 at 6:36 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Path needs to be a list of directories to search (you specified an executable location).<div class=""><br class=""></div><div class="">So not this —> <span style="font-family:Menlo;font-size:11px" class="">/Users/emmannaemeka/Desktop<wbr class="">/Gpm/maker/bin/maker</span></div><div class=""><br class=""></div><div class="">Instead it needs to be this —> <span style="font-family:Menlo;font-size:11px" class="">/Users/emmannaemeka/Desktop<wbr class="">/Gpm/maker/bin</span></div><div class=""><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Aug 28, 2017, at 11:32 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>></div></blockquote><div class=""><div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244h5"><blockquote type="cite" class=""><div class=""> wrote:</div><br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thanks <div class=""><br class=""></div><div class="">I tried to export PATH</div><div class=""><br class=""></div><div class="">running </div><div class="">echo $PATH in the maker directory this returned</div><div class=""><br class=""></div><div class=""><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">/usr/bin:/bin:/usr/sbin:/sbin:<wbr class="">/opt/X11/bin:/Users/emmannaeme<wbr class="">ka/Desktop/Gpm/maker/bin/maker</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class="">1. Does it mean that PATH has been exported?</span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">secondly,</div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">I tried to run</div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">the command maker -h, which maker, maker -CTL</div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">nothing returned.</div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">2. how do i start up maker?</div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">3. Do I need to be in maker directory to start maker?</div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">Thanks</div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><br class=""></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div><div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class=""><span style="font-variant-ligatures:no-common-ligatures" class=""><br class=""></span></div></div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class="">Nnadi Nnaemeka Emmanuel<div class="">Department of Microbiology,</div><div class="">Faculty of Natural and Applied Science,</div><div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div><div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a></div></div></div></div>
<br class=""><div class="gmail_quote">On Mon, Aug 28, 2017 at 4:49 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">After install the executables will be in the …/maker/bin directory. Example (if you did the install in your home directory) —> ~/maker/bin/maker<div class=""><br class=""></div><div class="">You need to add the …/maker/bin directory to your PATH for it to be found just by typing ‘maker'</div><div class=""><br class=""></div><div class="">Explanation of the Linux PATH —> <a href="http://www.linfo.org/path_env_var.html" target="_blank" class="">http://www.linfo.org/path_e<wbr class="">nv_var.html</a></div><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">—Carson</div></font></span><div class=""><div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829h5"><div class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Aug 28, 2017, at 8:07 AM, Ence,daniel <<a href="mailto:d.ence@ufl.edu" target="_blank" class="">d.ence@ufl.edu</a>> wrote:</div><br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401Apple-interchange-newline"><div class="">
<div style="word-wrap:break-word" class="">
Sorry I should have typed “maker -CTL”. If that doesn’t work, what is the result of “which maker”?
<div class="">
<div class=""><br class="">
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<div class="">
<blockquote type="cite" class="">
<div class="">On Aug 28, 2017, at 10:00 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div>
<br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Daniel
<div class="">The reply is </div>
<div class="">
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">emmannamekasMBP:maker emmannaemeka$ MAKER -ctl</span></div>
<div style="margin:0px;font-size:11px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">-bash: MAKER: command not found</span></div>
</div>
</div>
<div class="gmail_extra"><br clear="all" class="">
<div class="">
<div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr" class="">Nnadi Nnaemeka Emmanuel
<div class="">Department of Microbiology,</div>
<div class="">Faculty of Natural and Applied Science,</div>
<div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div>
<div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a></div>
</div>
</div>
</div>
<br class="">
<div class="gmail_quote">On Mon, Aug 28, 2017 at 2:57 PM, Ence,daniel <span dir="ltr" class="">
<<a href="mailto:d.ence@ufl.edu" target="_blank" class="">d.ence@ufl.edu</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Hi, It looks like MAKER installed ok. What is the command that you used to try to run MAKER? Can you show the result of running “MAKER -ctl”?
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class="">Daniel Ence</div>
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<div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401h5">
<div class=""><br class="">
</div>
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<div class="">
<blockquote type="cite" class="">
<div class="">On Aug 28, 2017, at 9:24 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div>
<br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi Ence,
<div class="">Thanks for your reply,</div>
<div class=""><br class="">
</div>
<div class="">This is the step and error received</div>
<div class="">
<pre class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-language-bash m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-pre" style="box-sizing:border-box;font-family:Consolas,Monaco,'Andale Mono','Ubuntu Mono',monospace;font-size:13px;padding:1em;margin-top:0.5em;margin-bottom:0.5em;line-height:1.5;word-break:normal;word-wrap:normal;background-color:rgb(245,242,240);border:1px solid rgb(204,204,204);border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;overflow:auto"><code class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-language-bash" style="box-sizing:border-box;font-family:Consolas,Monaco,'Andale Mono','Ubuntu Mono',monospace;font-size:inherit;padding:0px;border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;background-image:none;word-spacing:normal;word-break:normal;word-wrap:normal;line-height:1.5">emmannamekasMBP:src emmannaemeka$ ./build <span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-function" style="box-sizing:border-box;color:rgb(221,74,104)">install</span>
Installing MAKER<span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-punctuation" style="box-sizing:border-box;color:rgb(153,153,153)">..</span>.
Building MAKER
Skip /Users/emmannaemeka/desktop/Gp<wbr class="">m/maker/src/<span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-punctuation" style="box-sizing:border-box;color:rgb(153,153,153)">..</span>/perl/config-dar<wbr class="">win-thread-multi-2level-5.0180<wbr class="">02 <span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-punctuation" style="box-sizing:border-box;color:rgb(153,153,153)">(</span>unchanged<span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-punctuation" style="box-sizing:border-box;color:rgb(153,153,153)">)</span>
The build status is
<span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" 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STATUS MAKER v2.31.9
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m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)"><wbr class="">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span><span class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-token m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail-operator" style="box-sizing:border-box;color:rgb(166,127,89);background-color:rgba(255,255,255,0.498039)">==</span>
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: DISABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK</code></pre>
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<div class="gmail_extra"><br clear="all" class="">
<div class="">
<div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr" class="">Nnadi Nnaemeka Emmanuel
<div class="">Department of Microbiology,</div>
<div class="">Faculty of Natural and Applied Science,</div>
<div class="">Plateau State University, Bokkos, Plateau State, Nigeria.</div>
<div class="">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a></div>
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<br class="">
<div class="gmail_quote">On Mon, Aug 28, 2017 at 2:00 PM, Ence,daniel <span dir="ltr" class="">
<<a href="mailto:d.ence@ufl.edu" target="_blank" class="">d.ence@ufl.edu</a>></span> wrote:<br class="">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word" class="">Hi Emmanuel, In order for anyone to help you, you need post to the mailing list the command and output (including errors) of the step that didn’t work.
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class="">Daniel Ence</div>
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<div class="">On Aug 27, 2017, at 10:16 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank" class="">eennadi@gmail.com</a>> wrote:</div>
<br class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915m_8353924947327656027Apple-interchange-newline">
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<div class="m_-3532612113651592299m_1824814724788330975m_-398983943636321134m_8444501900503387831m_-6684140088689646327m_1282370664674665244m_3913477412906085829m_4338527200514116401m_500455824137929915h5">
<div dir="auto" class="">Hello all,
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">I downloaded Maker and tried to install it. I succeeded in installing all prerequisites however running maker ./build install, it showed that maker installed.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">However trying to run maker it wouldn't run.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Please how do I install maker to run on local computer?</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Thanks<br class="">
<br class="">
<div data-smartmail="gmail_signature" dir="auto" class="">Nnadi Nnaemeka Emmanuel<br class="">
Department of Microbiology,<br class="">
Faculty of Natural and Applied Science,<br class="">
Plateau State University, Bokkos, Plateau State, Nigeria.<br class="">
Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank" class="">https://www.researchgate.net/<wbr class="">profile/Emmanuel_Nnadi/publica<wbr class="">tions</a><br class="">
<br class="">
</div>
</div>
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</div>
</div>
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