[maker-devel] tradeoff between run time & file number

[Rebecca Harris]

Hi -

I'm running maker on a dataset of >400,000 scaffolds with MPI -n 64. I've
gone through it once - and used the clean_up option because otherwise maker
exceeds the clusters file_quote. However, now I'm retraining SNAP and it is
taking a very long time - probably because it has to go through BLAST
again. Is there anyway of getting around this? I expect I may have to train
SNAP and rerun maker multiple times and it is taking about 3 weeks to get
through my dataset. Is there a way to prune down my original dataset based
on maker's output?

Thanks,
Rebecca
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