Running out of time in MAKER

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Running out of time in MAKER

Christian Ayala
Good afternoon,

I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run?

Thanks for your help.

Best regards,

Christian Ayala-Ortiz

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Re: Running out of time in MAKER

Ence,daniel
Hi Christian, 

If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. 

Hopefully this is helps, 
Daniel Ence


Daniel Ence
Postdoctoral Associate 
School of Forest Resources and Conservation
University of Florida

On Apr 30, 2019, at 2:42 PM, Christian Ayala <[hidden email]> wrote:

Good afternoon,

I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run?

Thanks for your help.

Best regards,

Christian Ayala-Ortiz
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Re: Running out of time in MAKER

Mark Yandell

Hey Dan,

 

How’s life? What are you up to these days?

 

--mark

 

From: maker-devel <[hidden email]> on behalf of "Ence,daniel" <[hidden email]>
Date: Monday, May 13, 2019 at 7:21 AM
To: Christian Ayala <[hidden email]>
Cc: "[hidden email]" <[hidden email]>
Subject: Re: [maker-devel] Running out of time in MAKER

 

Hi Christian, 

 

If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. 

 

Hopefully this is helps, 

Daniel Ence

 

 

Daniel Ence

Postdoctoral Associate 

School of Forest Resources and Conservation

University of Florida



On Apr 30, 2019, at 2:42 PM, Christian Ayala <[hidden email]> wrote:

 

Good afternoon,

 

I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run?

 

Thanks for your help.

 

Best regards,

 

Christian Ayala-Ortiz

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maker-devel mailing list
[hidden email]
https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e=

 


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