<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="">Hi Jodi,<div class=""><br class=""></div><div class="">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).</div><div class=""><br class=""></div><div class="">Somewhere inside the script there will be a line like this —></div><div class=""><font face="Courier" class=""> $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";</font></div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <<a href="mailto:jhumann@wsu.edu" class="">jhumann@wsu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hello,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 13.5pt; font-family: Arial, sans-serif; color: rgb(51, 51, 51); background-color: white; background-position: initial initial; background-repeat: initial initial;" class="">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><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Jodi<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Jodi Humann, Ph.D.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Main Bioinformatics Lab Project Coordinator<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Department of Horticulture<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Washington State University<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">PO Box 646414<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Pullman, WA 99164-6414<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">509-335-3206<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="mailto:jhumann@wsu.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">jhumann@wsu.edu</a><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">maker-devel mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:maker-devel@box290.bluehost.com" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">maker-devel@box290.bluehost.com</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a></div></blockquote></div><br class=""></div></body></html>