[maker-devel] tRNAscan-SE file already exists

[Carson Holt]

You will need to downgrade. I know 1.3.1 works. I will have to update MAKER for the new tRNAscan.

—Carson

> On Jan 16, 2019, at 9:43 AM, Seth Munholland <munholl at uwindsor.ca> wrote:
> 
> Hi Everyone,
> 
> Just getting my latest Maker install running and I'm running into the following issue when it gets to tRNAscan-SE:
> 
> running  trnascan.
> #--------- command -------------#
> Widget::trnascan:
> /usr/local/bin/tRNAscan-SE -b -q /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_no
> mask.0 > /tmp/maker_5C2HGK/Chr01_94779-3233013.abinit_nomask.0.eukaryotic.trnasc
> an
> #-------------------------------#
> 
> WARNING: -q exists already.
> 
>  (O)verwrite file, (A)ppend to file, or (Q)uit program?
> 
> I have tRNAscan-SE-2.0 installed, which has a -b option for a bed output but needs a file to be specified.  Do I need to roll back to a specific version or would it be easier to skip it and run tRNAscan-SE separately?  Do the outputs get integrated later to adjsut Maker calls or are they stand alone?
> 
> Seth Munholland, Ph.D. Candidate
> Intern, International Society for Computational Biology
> VP, Finance & Extracurricular Affairs, DBGSA
> Department of Biological Sciences
> Rm. 306 Biology Building
> University of Windsor
> 401 Sunset Ave. N9B 3P4
> T: (519) 253-3000 Ext: 4755 <>_______________________________________________
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