panEDTA timing out on large genomes

[joannarifkin]

Hi Shujun,

I'm trying to wrap up some work on the Hesperis matronalis genome and am having a problem with panEDTA - it keeps timing out. I've cranked up the RAM to a terabyte and it still just runs out the 2 week job - this is the latest set of error logs.

I just started a new job to run only the H. matronalis genome so I can incorporate it into panEDTA later - all the other genomes so far have annotated fine, it just gets stuck on this big one. But is there something I'm missing here?

Thank you!

Joanna

panEDTA-7128863-4294967294.log
panEDTA_error-7128863-4294967294.log

[oushujun]

Yeah I noticed the exceptional time it may take for this step in the new version. i am still adjusting it to balance speed and accuracy. You may want to request for longer walltime for large genomes for now. Sorry for the incovenience.

Shujun

[joannarifkin]

Thanks! Do you think I can run the new version of panEDTA on all my old EDTA runs? I know the old version isn't as sensitive as the new one, but it did finish, and our results were interesting. Or will I run into the same problem when it reannotates? Cheers, Joanna

…

On Tue, May 14, 2024 at 12:26 PM Shujun Ou ***@***.***> wrote: Yeah I noticed the exceptional time it may take for this step in the new version. i am still adjusting it to balance speed and accuracy. You may want to request for longer walltime for large genomes for now. Sorry for the incovenience. Shujun — Reply to this email directly, view it on GitHub <#463 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPL6CTZBRJR5FSJFZGOLY3ZCI3J5AVCNFSM6AAAAABHPPUBPWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMJQGY2DONZTGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Joanna Rifkin PhD they/them Computational biologist