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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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RepeatModeler2.0 bug fix question #108

Closed johnssproul closed 3 years ago

johnssproul commented 3 years ago

I ran several analyses with RepeatModeler2.0 but I notice that the version history of v2.0.1 references a rare bug related to RepeatScout that was present in 2.0. Does that bug cause a the run to crash? I am wondering if there is an easy way to know if that bug affected my past runs.

jebrosen commented 3 years ago

This one?

RepeatScout in some rare cases will generate models for very long-period satellites. This can cause Refiner to go crazy creating tons of off-diagonal alignments. This version filters out these rare cases.

If I remember correctly this problem did lead to an out-of-memory error that caused the entire run to fail, so if you had a successful run it's unlikely this bug affected you.

johnssproul commented 3 years ago

Yes, that’s the one. Good to know it is likely that bug would have crashed the run. Thanks for the follow up!

On Nov 20, 2020, at 1:46 PM, Jeb Rosen notifications@github.com wrote:

This one?

RepeatScout in some rare cases will generate models for very long-period satellites. This can cause Refiner to go crazy creating tons of off-diagonal alignments. This version filters out these rare cases.

If I remember correctly this problem did lead to an out-of-memory error that caused the entire run to fail, so if you had a successful run it's unlikely this bug affected you.

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