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<p class="MsoNormal">Emmanuel,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Look for anything that will help calculate basic assembly metrics, such as N50, NG50, L50, etc.; these almost always give overall assembly size, and total scaffolds/contigs. For instance I’ve used this:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><a href="http://korflab.ucdavis.edu/datasets/Assemblathon/Assemblathon2/Basic_metrics/assemblathon_stats.pl">http://korflab.ucdavis.edu/datasets/Assemblathon/Assemblathon2/Basic_metrics/assemblathon_stats.pl</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(it requires FALite, which is here: <a href="http://korflab.ucdavis.edu/Unix_and_Perl/FAlite.pm">
http://korflab.ucdavis.edu/Unix_and_Perl/FAlite.pm</a> )<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The Broad also has GAEMR (<a href="http://software.broadinstitute.org/software/gaemr/">http://software.broadinstitute.org/software/gaemr/</a> ), but I haven’t tested it myself (I’ve heard it’s a bit finicky).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Also, see this: <a href="https://www.biostars.org/p/237591/">
https://www.biostars.org/p/237591/</a> , which has a few more options.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">chris<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">maker-devel <maker-devel-bounces@yandell-lab.org> on behalf of Carson Holt <carsonhh@gmail.com><br>
<b>Date: </b>Friday, September 22, 2017 at 3:09 PM<br>
<b>To: </b>Emmanuel Nnadi <eennadi@gmail.com><br>
<b>Cc: </b>"maker-devel@yandell-lab.org" <maker-devel@yandell-lab.org><br>
<b>Subject: </b>Re: [maker-devel] Maker not installing<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">MAKER can’t give you those details. All MAKER does is try and identify gene models against the assembly you provide.
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">—Carson<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On Sep 22, 2017, at 1:27 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello all, <o:p></o:p></p>
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<p class="MsoNormal">Please how can I determine the following in maker:<o:p></o:p></p>
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<p class="MsoNormal">1. The total number of chromosomes<o:p></o:p></p>
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<p class="MsoNormal">2. The size of my genome<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks<o:p></o:p></p>
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<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<div>
<p class="MsoNormal">Nnadi Nnaemeka Emmanuel <o:p></o:p></p>
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<p class="MsoNormal">Department of Microbiology,<o:p></o:p></p>
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<p class="MsoNormal">Faculty of Natural and Applied Science,<o:p></o:p></p>
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<p class="MsoNormal">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></p>
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<div>
<p class="MsoNormal">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Fri, Sep 1, 2017 at 10:52 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
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<p class="MsoNormal">Ok, thanks. <o:p></o:p></p>
<div>
<p class="MsoNormal">Nnadi Nnaemeka Emmanuel<br>
Department of Microbiology,<br>
Faculty of Natural and Applied Science,<br>
Plateau State University, Bokkos, Plateau State, Nigeria.<br>
Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><br>
<br>
<o:p></o:p></p>
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<div>
<div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Sep 1, 2017 10:50 PM, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">It would need to be a new run. You won't be able to use the updated contig names with the old run. <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:13.0pt">--Carson</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Sent from my iPhone<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
On Sep 1, 2017, at 3:41 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<div>
<p class="MsoNormal">Hi carson <o:p></o:p></p>
<div>
<p class="MsoNormal">Thanks for the tip<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">perl -ane 's/1_S7_R1_001_\(paired\)_trimmed_\(paired\)_//g; print' genome.fasta</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">It worked well however, when i ran it, it removed 1_S7_R1_001_\(paired\)_trimmed_\(paired\)_, </span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">I have ran maker with 1_S7_R1_001_\(paired\)_trimmed_\(paired\)_, </span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">1. How can I effect the change when maker has produced some files from the the old sequence?</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">I have spent more than 24 hours running maker and it has produced some folders already.</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">How can I make this change?</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.5pt">Thanks</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal">Nnadi Nnaemeka Emmanuel <o:p></o:p></p>
<div>
<p class="MsoNormal">Department of Microbiology,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Faculty of Natural and Applied Science,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Fri, Sep 1, 2017 at 4:54 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
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<p class="MsoNormal">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. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">I would recommend removing '1_S7_R1_001_(paired)_trimmed_(paired)_’ from each contig name.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Example command to do that —> <o:p></o:p></p>
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<p class="MsoNormal">perl -ane 's/1_S7_R1_001_\(paired\)_trimmed_\(paired\)_//g; print' genome.fasta<span class="m-3532612113651592299m1824814724788330975hoenzb"><span style="color:#888888"><o:p></o:p></span></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal"><span style="color:#888888">—Carson<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On Aug 30, 2017, at 3:54 PM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Hi Carson <o:p></o:p></p>
<div>
<p class="MsoNormal">Thanks for your response its been helpful<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Please bear with me as I work through this<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">1. Please how do I generate EST for my novel sequences?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">2. I am currently running maker without EST and protein sequences is it wrong? Can it predict properly?<o:p></o:p></p>
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<p class="MsoNormal">3. One error in the contig just returned this value<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">FastaDB::_cleanIndexAndCompact(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> at /usr/local/bin/RepeatMasker line 1464.<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">FastaDB::_cleanIndexAndCompact(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> at /usr/local/bin/RepeatMasker line 1464.<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">FastaDB::_cleanIndexAndCompact(): Fasta file contains a sequence identifier which is too long ( max id length = 50 )<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> at /usr/local/bin/RepeatMasker line 1464.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">ERROR: RepeatMasker failed<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">--> rank=NA, hostname=emmannaemekas-MacBook-Pro.local<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">ERROR: Failed while doing repeat masking<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">ERROR: Chunk failed at level:0, tier_type:1<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">FAILED CONTIG:1_S7_R1_001_(paired)_trimmed_(paired)_contig_2<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">ERROR: Chunk failed at level:2, tier_type:0<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">FAILED CONTIG:1_S7_R1_001_(paired)_trimmed_(paired)_contig_2<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">examining contents of the fasta file and run log<o:p></o:p></span></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<div>
<p class="MsoNormal">Nnadi Nnaemeka Emmanuel <o:p></o:p></p>
<div>
<p class="MsoNormal">Department of Microbiology,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Faculty of Natural and Applied Science,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></p>
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<p class="MsoNormal">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Wed, Aug 30, 2017 at 4:12 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">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).
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Example —><o:p></o:p></p>
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<p class="MsoNormal">perl …/RepeatMasker/util/queryTaxonomyDatabase.pl -species “drosophila"<o:p></o:p></p>
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<p class="MsoNormal"><span style="color:#888888"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:#888888">—Carson<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Aug 30, 2017, at 9:05 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi Carson, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> Thanks<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">I was able to start using maker.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">However I am working with a plant Genome novel. I had set the repeatmasking to <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">1. Dcotrep a names from the repbase release but maker returned it back as not known to repeat masker<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">How can I use specific known genomes for repeat masking<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Thanks<o:p></o:p></p>
<div>
<p class="MsoNormal">Nnadi Nnaemeka Emmanuel<br>
Department of Microbiology,<br>
Faculty of Natural and Applied Science,<br>
Plateau State University, Bokkos, Plateau State, Nigeria.<br>
Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><br>
<br>
<o:p></o:p></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Aug 29, 2017 4:26 PM, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal">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. <o:p>
</o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">You can check the contents of the file using cat. Example —> cat maker_opts.ctl<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">—Carson<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Aug 29, 2017, at 5:11 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi Carson, <o:p></o:p></p>
<div>
<p class="MsoNormal">Thanks a lot for yesterday. I was able to resolve the issue of running maker and i followed the commands in the tutorial.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">I however encountered another problem<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">when I ran the command <span style="font-family:"Courier New",serif">nano -c maker_opts.ctl</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Courier New",serif">It gave the following </span><b><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">1_S7_assembly.fa I specified the name of the genome but when I ran maker in another tab it gave </span></b><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">#-----Genome (these are always required)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">genome=<b>1_S7_assembly.fa</b> #genome sequence (fasta file or fasta embeded in GFF3 file)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">#-----Re-annotation Using MAKER Derived GFF3<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">maker_gff= #MAKER derived GFF3 file<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">#-----EST Evidence (for best results provide a file for at least one)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">est= #set of ESTs or assembled mRNA-seq in fasta format<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">altest= #EST/cDNA sequence file in fasta format from an alternate organism<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">altest_gff= #aligned ESTs from a closly relate species in GFF3 format<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">#-----Protein Homology Evidence (for best results provide a file for at least one)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">protein= #protein sequence file in fasta format (i.e. from mutiple oransisms)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">protein_gff= #aligned protein homology evidence from an external GFF3 file<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">#-----Repeat Masking (leave values blank to skip repeat masking)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">model_org=all #select a model organism for RepBase masking in RepeatMasker<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">rmlib= #provide an organism specific repeat library in fasta format for RepeatMasker<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">repeat_protein=/Users/emmannaemeka/Desktop/Gpm/maker/data/te_proteins.fasta #provide a fasta file of transposable element proteins for RepeatRunner<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">rm_gff= #pre-identified repeat elements from an external GFF3 file<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><b><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">I ran maker command on another tab and it returned the following</span></b><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">STATUS: Parsing control files...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">ERROR: You have failed to provide a value for 'genome' in the control files.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">--> rank=NA, hostname=emmannamekasMBP<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">Questions<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">1. Specifying the genome location, do I need to run maker on the same tab or open another bash tab?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">2. My genome is novel and do not have proteins, how do I generate protein fast for the de novo sequence and EST?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">Thanks<o:p></o:p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal">Nnadi Nnaemeka Emmanuel <o:p></o:p></p>
<div>
<p class="MsoNormal">Department of Microbiology,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Faculty of Natural and Applied Science,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><o:p></o:p></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Mon, Aug 28, 2017 at 6:47 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal">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">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014</a>
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">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.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Carson<o:p></o:p></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Aug 28, 2017, at 11:43 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi Carson, <o:p></o:p></p>
<div>
<p class="MsoNormal">Thanks a lot <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I ran this command maker -h it returned the following<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">The last thing I wish to ask you, how can I load my genome fine and being annotation?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">emmannamekasMBP:maker emmannaemeka$ maker -h<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">MAKER version 2.31.9<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">Usage:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> maker [options] <maker_opts> <maker_bopts> <maker_exe><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">Description:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> MAKER is a program that produces gene annotations in GFF3 format using<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> evidence such as EST alignments and protein homology. MAKER can be used to<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> produce gene annotations for new genomes as well as update annotations<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> from existing genome databases.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> The three input arguments are control files that specify how MAKER should<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> behave. All options for MAKER should be set in the control files, but a<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> few can also be set on the command line. Command line options provide a<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> convenient machanism to override commonly altered control file values.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> MAKER will automatically search for the control files in the current<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> working directory if they are not specified on the command line.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> Input files listed in the control options files must be in fasta format<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> unless otherwise specified. Please see MAKER documentation to learn more<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> about control file configuration. MAKER will automatically try and<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> locate the user control files in the current working directory if these<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> arguments are not supplied when initializing MAKER.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> It is important to note that MAKER does not try and recalculated data that<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> it has already calculated. For example, if you run an analysis twice on<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> the same dataset you will notice that MAKER does not rerun any of the<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> BLAST analyses, but instead uses the blast analyses stored from the<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> previous run. To force MAKER to rerun all analyses, use the -f flag.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> MAKER also supports parallelization via MPI on computer clusters. Just<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> launch MAKER via mpiexec (i.e. mpiexec -n 40 maker). MPI support must be<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> configured during the MAKER installation process for this to work though<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">Options:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -genome|g <file> Overrides the genome file path in the control files<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -RM_off|R Turns all repeat masking options off.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -datastore/ Forcably turn on/off MAKER's two deep directory<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> nodatastore structure for output. Always on by default.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -old_struct Use the old directory styles (MAKER 2.26 and lower)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -base <string> Set the base name MAKER uses to save output files.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> MAKER uses the input genome file name by default.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -tries|t <integer> Run contigs up to the specified number of tries.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -cpus|c <integer> Tells how many cpus to use for BLAST analysis.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> Note: this is for BLAST and not for MPI!<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -force|f Forces MAKER to delete old files before running again.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">This will require all blast analyses to be rerun.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -again|a recaculate all annotations and output files even if no<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">settings have changed. Does not delete old analyses.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -quiet|q Regular quiet. Only a handlful of status messages.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -qq Even more quiet. There are no status messages.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -dsindex Quickly generate datastore index file. Note that this<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> will not check if run settings have changed on contigs<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -nolock Turn off file locks. May be usful on some file systems,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> but can cause race conditions if running in parallel.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -TMP Specify temporary directory to use.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -CTL Generate empty control files in the current directory.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -OPTS Generates just the maker_opts.ctl file.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -BOPTS Generates just the maker_bopts.ctl file.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -EXE Generates just the maker_exe.ctl file.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -MWAS <option> Easy way to control mwas_server for web-based GUI<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> options: STOP<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> START<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> RESTART<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -version Prints the MAKER version.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"> -help|? Prints this usage statement.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal">Nnadi Nnaemeka Emmanuel <o:p></o:p></p>
<div>
<p class="MsoNormal">Department of Microbiology,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Faculty of Natural and Applied Science,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><o:p></o:p></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Mon, Aug 28, 2017 at 6:36 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal">Path needs to be a list of directories to search (you specified an executable location).
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">So not this —> <span style="font-size:8.5pt;font-family:"Menlo",sans-serif">/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Instead it needs to be this —> <span style="font-size:8.5pt;font-family:"Menlo",sans-serif">/Users/emmannaemeka/Desktop/Gpm/maker/bin</span><o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">—Carson<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Aug 28, 2017, at 11:32 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>><o:p></o:p></p>
</div>
</blockquote>
<div>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Thanks <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">I tried to export PATH<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">running <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">echo $PATH in the maker directory this returned<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/Users/emmannaemeka/Desktop/Gpm/maker/bin/maker<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">1. Does it mean that PATH has been exported?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">secondly,<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">I tried to run<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">the command maker -h, which maker, maker -CTL<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">nothing returned.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">2. how do i start up maker?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">3. Do I need to be in maker directory to start maker?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">Thanks<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif"><br>
<br>
<o:p></o:p></span></p>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal">Nnadi Nnaemeka Emmanuel <o:p></o:p></p>
<div>
<p class="MsoNormal">Department of Microbiology,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Faculty of Natural and Applied Science,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><o:p></o:p></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Mon, Aug 28, 2017 at 4:49 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal">After install the executables will be in the …/maker/bin directory. Example (if you did the install in your home directory) —> ~/maker/bin/maker
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">You need to add the …/maker/bin directory to your PATH for it to be found just by typing ‘maker'<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Explanation of the Linux PATH —> <a href="http://www.linfo.org/path_env_var.html" target="_blank">http://www.linfo.org/path_env_var.html</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:#888888"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="color:#888888">—Carson<o:p></o:p></span></p>
</div>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Aug 28, 2017, at 8:07 AM, Ence,daniel <<a href="mailto:d.ence@ufl.edu" target="_blank">d.ence@ufl.edu</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Sorry I should have typed “maker -CTL”. If that doesn’t work, what is the result of “which maker”?
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Aug 28, 2017, at 10:00 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Daniel <o:p></o:p></p>
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<p class="MsoNormal">The reply is <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">emmannamekasMBP:maker emmannaemeka$ MAKER -ctl<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:8.5pt;font-family:"Menlo",sans-serif">-bash: MAKER: command not found<o:p></o:p></span></p>
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<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<p class="MsoNormal">Nnadi Nnaemeka Emmanuel <o:p></o:p></p>
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<p class="MsoNormal">Department of Microbiology,<o:p></o:p></p>
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<p class="MsoNormal">Faculty of Natural and Applied Science,<o:p></o:p></p>
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<p class="MsoNormal">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></p>
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<p class="MsoNormal">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Aug 28, 2017 at 2:57 PM, Ence,daniel <<a href="mailto:d.ence@ufl.edu" target="_blank">d.ence@ufl.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">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”?
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks,<o:p></o:p></p>
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<p class="MsoNormal">Daniel Ence<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Aug 28, 2017, at 9:24 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Ence, <o:p></o:p></p>
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<p class="MsoNormal">Thanks for your reply,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">This is the step and error received<o:p></o:p></p>
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<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in;box-sizing:border-box;word-wrap:normal;border-top-left-radius:4px;border-top-right-radius:4px;border-bottom-right-radius:4px;border-bottom-left-radius:4px;overflow:auto"><code><span style="font-family:"Consolas",sans-serif">emmannamekasMBP:src emmannaemeka$ ./build </span></code><span class="m-3532612113651592299m1824814724788330975m-398983943636321134m8444501900503387831m-6684140088689646327m1282370664674665244m3913477412906085829m4338527200514116401m500455824137929915gmail-token"><span style="font-family:"Consolas",sans-serif;color:#DD4A68">install</span></span><code><span style="font-family:"Consolas",sans-serif"><o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">Installing MAKER</span></code><span class="m-3532612113651592299m1824814724788330975m-398983943636321134m8444501900503387831m-6684140088689646327m1282370664674665244m3913477412906085829m4338527200514116401m500455824137929915gmail-token"><span style="font-family:"Consolas",sans-serif;color:#999999">..</span></span><code><span style="font-family:"Consolas",sans-serif">.<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">Building MAKER<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">Skip /Users/emmannaemeka/desktop/Gpm/maker/src/</span></code><span class="m-3532612113651592299m1824814724788330975m-398983943636321134m8444501900503387831m-6684140088689646327m1282370664674665244m3913477412906085829m4338527200514116401m500455824137929915gmail-token"><span style="font-family:"Consolas",sans-serif;color:#999999">..</span></span><code><span style="font-family:"Consolas",sans-serif">/perl/config-darwin-thread-multi-2level-5.018002 </span></code><span class="m-3532612113651592299m1824814724788330975m-398983943636321134m8444501900503387831m-6684140088689646327m1282370664674665244m3913477412906085829m4338527200514116401m500455824137929915gmail-token"><span style="font-family:"Consolas",sans-serif;color:#999999">(</span></span><code><span style="font-family:"Consolas",sans-serif">unchanged</span></code><span class="m-3532612113651592299m1824814724788330975m-398983943636321134m8444501900503387831m-6684140088689646327m1282370664674665244m3913477412906085829m4338527200514116401m500455824137929915gmail-token"><span style="font-family:"Consolas",sans-serif;color:#999999">)</span></span><code><span style="font-family:"Consolas",sans-serif"><o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif"><o:p> </o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">The build status is<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif"><o:p> </o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><span class="m-3532612113651592299m1824814724788330975m-398983943636321134m8444501900503387831m-6684140088689646327m1282370664674665244m3913477412906085829m4338527200514116401m500455824137929915gmail-token"><span style="font-family:"Consolas",sans-serif;color:#A67F59">=============================================================================</span></span><code><span style="font-family:"Consolas",sans-serif"><o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">STATUS MAKER v2.31.9<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><span class="m-3532612113651592299m1824814724788330975m-398983943636321134m8444501900503387831m-6684140088689646327m1282370664674665244m3913477412906085829m4338527200514116401m500455824137929915gmail-token"><span style="font-family:"Consolas",sans-serif;color:#A67F59">==============================================================================</span></span><code><span style="font-family:"Consolas",sans-serif"><o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">PERL Dependencies: VERIFIED<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">External Programs: VERIFIED<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">External C Libraries: VERIFIED<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">MPI SUPPORT: DISABLED<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">MWAS Web Interface: DISABLED<o:p></o:p></span></code></pre>
<pre style="mso-margin-top-alt:6.0pt;margin-right:0in;margin-bottom:6.0pt;margin-left:0in;background:#F5F2F0;border:none;padding:0in"><code><span style="font-family:"Consolas",sans-serif">MAKER PACKAGE: CONFIGURATION OK</span></code><span style="font-family:"Consolas",sans-serif"><o:p></o:p></span></pre>
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<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<p class="MsoNormal">Nnadi Nnaemeka Emmanuel <o:p></o:p></p>
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<p class="MsoNormal">Department of Microbiology,<o:p></o:p></p>
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<p class="MsoNormal">Faculty of Natural and Applied Science,<o:p></o:p></p>
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<p class="MsoNormal">Plateau State University, Bokkos, Plateau State, Nigeria.<o:p></o:p></p>
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<p class="MsoNormal">Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Aug 28, 2017 at 2:00 PM, Ence,daniel <<a href="mailto:d.ence@ufl.edu" target="_blank">d.ence@ufl.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">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.
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thanks,<o:p></o:p></p>
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<p class="MsoNormal">Daniel Ence<o:p></o:p></p>
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<p class="MsoNormal">On Aug 27, 2017, at 10:16 AM, Emmanuel Nnadi <<a href="mailto:eennadi@gmail.com" target="_blank">eennadi@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello all, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I downloaded Maker and tried to install it. I succeeded in installing all prerequisites however running maker ./build install, it showed that maker installed.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">However trying to run maker it wouldn't run.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Please how do I install maker to run on local computer?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Thanks<o:p></o:p></p>
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<p class="MsoNormal">Nnadi Nnaemeka Emmanuel<br>
Department of Microbiology,<br>
Faculty of Natural and Applied Science,<br>
Plateau State University, Bokkos, Plateau State, Nigeria.<br>
Publications: <a href="https://www.researchgate.net/profile/Emmanuel_Nnadi/publications" target="_blank">https://www.researchgate.net/profile/Emmanuel_Nnadi/publications</a><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><o:p></o:p></p>
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<p class="MsoNormal">_______________________________________________<br>
maker-devel mailing list<br>
<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a><br>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a><o:p></o:p></p>
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