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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks for the info, Carson. We are running v2.31.9, and were able to get MWAS running, with some work. That is the current Maker version right?
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Jodi<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Carson Holt [mailto:carsonhh@gmail.com]
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<b>Sent:</b> Thursday, October 19, 2017 10:33 AM<br>
<b>To:</b> Humann, Jodi Lynn <jhumann@wsu.edu><br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] fix nucleotides option on MWAS<o:p></o:p></span></p>
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<p class="MsoNormal">Hi Jodi,<o:p></o:p></p>
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<p class="MsoNormal">I didn’t even know anyone else even had an MWAS server running (I’ve actually pulled all of the Build options for MWAS out of current releases). But you should be able to add the fix_nucleotide option to the command run by MWAS by editing
the mwas_server script (…/maker/MWAS/bin/mwas_server).<o:p></o:p></p>
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<p class="MsoNormal">Somewhere inside the script there will be a line like this —><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:Courier"> $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";</span><o:p></o:p></p>
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<p class="MsoNormal">You can add -fix_nucleotides to that command so it always runs. fix_nucleotides is as command line flag. It’s basically a warning for the user to let them know something is weird (i.e. it is possible they mixed up transcript/protein sequence
files). And then it allows the user to tell MAKER they did not mix files up, rather the data is supposed to look that way and they are ok with MAKER altering the sequence by replacing the letters or dashes seen with N’s.<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">Carson<o:p></o:p></p>
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<p class="MsoNormal">On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <<a href="mailto:jhumann@wsu.edu">jhumann@wsu.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Hello,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I was wondering if there was any way to enable the ‘–fix_nucleotides’ option on the MWAS version we are running locally on our server? I have a genome sequence with a degenerate
nucleotide and get the following error:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Arial",sans-serif;color:#333333;background:white">ERROR: The nucleotide sequence file '/local/www/maker/data/users/1/NZ_CP006580.1_EcP101.fasta' appears to contain protein sequence or unrecognized
characters. Note the following nucleotides may be valid but are unsupported [RYKMSWBDHV] Please check/fix the file before continuing, or set -fix_nucleotides on the command line to fix this automatically. Invalid Character: 'K' --> rank=NA, hostname=compute2</span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">The error message says the option can be used on the command line. Is that set on the actual command to run Maker (when using the command line version), or is it something
that can be set in one of the control files? Any input would be greatly appreciated. I know I can fix my input file, but would prefer to just enable the option if I can.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Jodi<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Jodi Humann, Ph.D.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Main Bioinformatics Lab Project Coordinator<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Department of Horticulture<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Washington State University<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">PO Box 646414<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Pullman, WA 99164-6414<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">509-335-3206<o:p></o:p></span></p>
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<p class="MsoNormal"><a href="mailto:jhumann@wsu.edu"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#954F72">jhumann@wsu.edu</span></a><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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