[maker-devel] [EXTERNAL] Re: Troubleshooting Maker failure

[Carson Holt]

Hi Kevin,

The files are already being skipped because of previous failures. Can you increase the try count (-t on the command line) to something like 6, and send me the STDERR after it generates a new failure.

—Carson 

Sent from my iPhone

> On Sep 20, 2021, at 4:56 AM, Kevin Kocot <kmkocot at ua.edu> wrote:
> 
> 
> Thanks Carson! I've uploaded that file here:
> http://genomes.ua.edu/Kocot/2021-09-10_Maker/round1_run_maker_try2.log
> 
> 
> From: Carson Holt
> Sent: Tuesday, September 14, 2021 9:51 PM
> To: Kevin Kocot
> Cc: maker-devel at yandell-lab.org
> Subject: [EXTERNAL] Re: [maker-devel] Troubleshooting Maker failure
> 
> 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/
>>  
>> 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 
>> 307 Mary Harmon Bryant Hall
>> Box 870344
>> Tuscaloosa, AL 35487
>> phone 205-348-4052 | fax 205-348-4039 
>> kmkocot at ua.edu | www.kocotlab.com
>> https://uasystem.zoom.us/j/3755490727
>> 
>>  
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at yandell-lab.org
>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
> 
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