[maker-devel] fix nucleotides option on MWAS

[Carson Holt]

Yes. That is the current version.

—Carson

> On Oct 19, 2017, at 12:45 PM, Humann, Jodi Lynn <jhumann at wsu.edu> wrote:
> 
> 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?
>  
> Jodi
>  
> From: Carson Holt [mailto:carsonhh at gmail.com <mailto:carsonhh at gmail.com>] 
> Sent: Thursday, October 19, 2017 10:33 AM
> To: Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>>
> Cc: maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] fix nucleotides option on MWAS
>  
> Hi Jodi,
>  
> 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).
>  
> Somewhere inside the script there will be a line like this —>
>  $command = "$FindBin::RealBin/../../bin/maker -qq -base $job_id";
>  
> 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.
>  
> Thanks,
> Carson
>  
>  
> On Oct 18, 2017, at 2:38 PM, Humann, Jodi Lynn <jhumann at wsu.edu <mailto:jhumann at wsu.edu>> wrote:
>  
> Hello,
>  
> 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:
>  
> 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
>  
> 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.
>  
> Thanks,
> Jodi
>  
> Jodi Humann, Ph.D.
> Main Bioinformatics Lab Project Coordinator
> Department of Horticulture
> Washington State University
> PO Box 646414
> Pullman, WA 99164-6414
> 509-335-3206
> jhumann at wsu.edu <mailto:jhumann at wsu.edu>
>  
>  
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