tRNAscan-SE file already exists

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tRNAscan-SE file already exists

Seth_m55
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

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Re: tRNAscan-SE file already exists

Carson Holt-2
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 <[hidden email]> 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
_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org