Issue with BRAKER and AUGUSTUS

Discussions about BRAKER, the automated joint usage of GeneMark and AUGUSTUS.

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Issue with BRAKER and AUGUSTUS

Post by yzhang » Tue Feb 21, 2017 7:11 pm


I can't make BRAKER1 working, because of a bad "design" in AUGUSTUS (in my opiniion).

In simple, I had pushed my BRAKER1 job to pass the GeneMark part. But it couldn't continue with augustus, because when augustus knows I am annotating a new species, it would try to write the AUGUSTUS installation directory for the parameter files.

I have AUGUSTUS installed in a distributed system, and since a few people will use it, I installed it system wide, meaning everyone can use "module load" method to call AUGUSTUS, but only the "root" or system adim (when sudo-ed as root) can write inthe installation directory.

So I can't make AUGUSTUS to run.

I am wondering whether you could really make the use of the "workingdir" option? Could you have the parameter files for a new species to be written in the "workingdir"? This seems easy, since you just need to change "AUGUSTUS_CONFIG_PATH" in script to "workingdir", and reference to workingdir ever since.


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Re: Issue with BRAKER and AUGUSTUS

Post by katharina » Tue Jul 25, 2017 8:59 am

Hi Ying,

the current BRAKER release does not have this problem, anymore. It now works to specify a non-root AUGUSTUS_CONFIG_PATH.

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Re: Issue with BRAKER and AUGUSTUS

Post by torriwilson » Tue Jul 07, 2020 11:07 am

i am also facing same issue. Still didn,t get proper solution.
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