MAKER not running properly after installation, help needed

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MAKER not running properly after installation, help needed

Nikolay Alabi

Hello,

 

I am attempting to annotate a garlic mustard genome using maker on a cluster at Queen’s University. I have been following the tutorial on wiki and was attempting to use the practice data to see if the program is running properly and to learn how to train the gene predicting system. Maker is now installed and is working to an extent, however when in use it is not working properly and cannot read/annotate a genome. I suspect two problems that is causing this to occur, first, anytime any maker command is called, it shows that an argument in forks.pm in perl5 is not correct, after trying to fix the problem, I see that the code should be correct, but the error line still occurs. Then every time a maker command Is called another error saying there is an error flow occurring somewhere in perl again. For instance when I command: maker -h, or maker -CTL or anything to do with maker, the error lines occur. Would you advise me to reinstall perl and bioperl? Other than that I believe everything else is properly installed and I do not understand why the program is not running properly. I have even tried using different data genomes, however the same problem occurs of the run never finishing, then retrying, and ultimately failing. Please let me know if there is another possible source of error in the problem.

 

Best regards, Nikolay

 

 


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Re: MAKER not running properly after installation, help needed

Carson Holt-2
Hi Nikolay,

If you can provide the exact error, that would allow me to know more of what you are seeing.  Normally the system perl should be fine (you can check the perl version using 'perl -v' on the command line). 

There was an issue with forks.pm that I believe the authors have fixed by now if you update to the latest version (more info here —> https://groups.google.com/forum/#!msg/maker-devel/2kYQ90TCuXA/FxPaM45YGdoJ ). Also updarte to the current CPAN version of BioPerl if there are doubts about that.

—Caerson

On Oct 31, 2018, at 8:27 AM, Nikolay Alabi <[hidden email]> wrote:

Hello, 
 
I am attempting to annotate a garlic mustard genome using maker on a cluster at Queen’s University. I have been following the tutorial on wiki and was attempting to use the practice data to see if the program is running properly and to learn how to train the gene predicting system. Maker is now installed and is working to an extent, however when in use it is not working properly and cannot read/annotate a genome. I suspect two problems that is causing this to occur, first, anytime any maker command is called, it shows that an argument in forks.pm in perl5 is not correct, after trying to fix the problem, I see that the code should be correct, but the error line still occurs. Then every time a maker command Is called another error saying there is an error flow occurring somewhere in perl again. For instance when I command: maker -h, or maker -CTL or anything to do with maker, the error lines occur. Would you advise me to reinstall perl and bioperl? Other than that I believe everything else is properly installed and I do not understand why the program is not running properly. I have even tried using different data genomes, however the same problem occurs of the run never finishing, then retrying, and ultimately failing. Please let me know if there is another possible source of error in the problem.
 
Best regards, Nikolay
 
 
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