Re: MAKER and tRNAscan

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Re: MAKER and tRNAscan

李青 Li, Qing
Hi Nazila,
The right one to contact is Carson and Maker developer group (cced).
best,
Qing 

On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila <[hidden email]> wrote:
Dear Maker group
My name is Nazila, I am a Ph.D. student at Miami University. I'm working on Phrynosoma platyrhinos genome annotation and I'm trying to use MAKER. So as a requirement I'm trying to use tRNAscan. First I used the latest version (2.0) and I got the first -q file but I faced a warning like this:

WARNING: -q exists already.

 (O)verwrite file, (A)ppend to file, or (Q)uit program? 

And I tried overwrite and append but it just froze and didn't work anymore.
So I tried to use an older version (1.3.1) but this one is hard to make it work too. I'm getting an error:

Can't locate object method "new" via package "tRNAscanSE::Constants" (perhaps you forgot to load "tRNAscanSE::Constants"?) at /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57.

Would you please help me with it? Which version should I use? And how could I solve the problem for that version?
Looking forward for your reply;
Thanks,
Nazila

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Re: MAKER and tRNAscan

Carson Hinton Holt
Use version 1.3.1 (last stable version for 1.X series), we haven’t updated maker to handle tRNAscan version 2 options and output yet.

All version here —> http://trna.ucsc.edu/software/

—Carson


On May 22, 2019, at 10:18 AM, 李青 Li, Qing <[hidden email]> wrote:

Hi Nazila,
The right one to contact is Carson and Maker developer group (cced).
best,
Qing 

On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila <[hidden email]> wrote:
Dear Maker group
My name is Nazila, I am a Ph.D. student at Miami University. I'm working on Phrynosoma platyrhinos genome annotation and I'm trying to use MAKER. So as a requirement I'm trying to use tRNAscan. First I used the latest version (2.0) and I got the first -q file but I faced a warning like this:

WARNING: -q exists already.

 (O)verwrite file, (A)ppend to file, or (Q)uit program? 

And I tried overwrite and append but it just froze and didn't work anymore.
So I tried to use an older version (1.3.1) but this one is hard to make it work too. I'm getting an error:

Can't locate object method "new" via package "tRNAscanSE::Constants" (perhaps you forgot to load "tRNAscanSE::Constants"?) at /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57.

Would you please help me with it? Which version should I use? And how could I solve the problem for that version?
Looking forward for your reply;
Thanks,
Nazila


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