Speed up maker annotation on long scaffolds

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Speed up maker annotation on long scaffolds

Yiyuan Li
Dear Maker support,
I have a quick question about annotating chromosome-level scaffolds. I have a new genome assembly from Hi-C data. The top 4 scaffolds are chromosome-level, which are ~100-170M bp long. I tried to use Maker MPI but it runs slow. Each scaffold has been running for weeks. I was wondering if you may have any suggestions on how to make the annotation process faster?

Thank you!

YY
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Re: Speed up maker annotation on long scaffolds

Carson Holt-2
You might not have MPI setup correctly. MPI spread across 10 machines (20 cores each) can annotate an entire maize chromosome in ~20 minutes.

A few tests.

#this command should print all the hosts you are running MPI on and how many cores on each host. If you don’t see multiple hosts you are not spreading across machines.
mpiexec hostname | sort | uniq -c

#this will let you know if maker is running MPI correctly (should print help message only once)
mpiexec maker -h

—Carson



> On Oct 16, 2018, at 10:49 PM, Yiyuan Li <[hidden email]> wrote:
>
> Dear Maker support,
> I have a quick question about annotating chromosome-level scaffolds. I have a new genome assembly from Hi-C data. The top 4 scaffolds are chromosome-level, which are ~100-170M bp long. I tried to use Maker MPI but it runs slow. Each scaffold has been running for weeks. I was wondering if you may have any suggestions on how to make the annotation process faster?
>
> Thank you!
>
> YY
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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