[maker-devel] Troubleshooting Maker failure

[Carson Holt]

What I really need is the captured STDERR from the failed run.

—Carson

> On Sep 10, 2021, at 9:19 AM, Kevin Kocot <kmkocot at ua.edu> wrote:
> 
> Hi Carson and all,
>  
> I ran Maker 3.01.03 on a chromosome-level mollusc genome assembly using some evidence I previously generated with Funannotate and BRAKER2, but Maker is not completing successfully. Every scaffold in the datastore_index.log file has both STARTED and FAILED statuses. I can't figure out where the problem lies, though. Running ./Build status indicates all the dependencies are there (I’m not using MPI). The run.log files just ends with "DIED RANK 0" and "DIED COUNT 3." Is there a way to tell which (if any) of the dependencies is misbehaving here (they all seem to run fine independently) or if my evidence .gff3 files are not correctly formatted?
>  
> I’ve uploaded a zipped sample output folder as well as my config files and the datastore.log file here: http://genomes.ua.edu/Kocot/2021-09-10_Maker/ <http://genomes.ua.edu/Kocot/2021-09-10_Maker/>
>  
> Any guidance on what might be the issue would be greatly appreciated.
>  
> Thanks!
> Kevin
>  
> Kevin M. Kocot
> he/him/his
> Associate Professor & Curator of Invertebrates
> Department of Biological Sciences & Alabama Museum of Natural History
> The University of Alabama <https://www.ua.edu/> 
> 307 Mary Harmon Bryant Hall
> Box 870344
> Tuscaloosa, AL 35487
> phone 205-348-4052 <tel:205-348-4052> | fax 205-348-4039 
> kmkocot at ua.edu <mailto:kmkocot at ua.edu> | www.kocotlab.com <http://www.kocotlab.com/>
> https://uasystem.zoom.us/j/3755490727 <https://uasystem.zoom.us/j/3755490727>
>  
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