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Published 20 hours ago • verified publisher icon oushujun

TIR-Learner is slow with many contigs

Open mergi-2674 opened this issue 2 years ago • 3 comments

I would like to appreciate for the best pipeline you developed so far! However, I was running EDTA on the plant genome which has a size of 3GB and EDTA was running for a week on a pc with 380GB of RAM and 32 threads. It didn't gave me the final result ans stacked on TIR step. How long does it takes to finish the analysis?

Best Mergi

Screenshot from 2022-10-19 11-41-36

mergi-2674 avatar Oct 19 '22 09:10 mergi-2674

Yeah the TIR step will be slow if you have a very fragmented genome. TIR-Learner will get slow down for thousands of contigs. You may want to remove the small contigs and rerun or keep waiting... Alternatively, you can concatenate the small contigs into Chr0 which will much speed up the run.

Shujun

oushujun avatar Oct 21 '22 21:10 oushujun

Hi Shujun Thank you for replay. I have a genome with thousands of contigs and that is why the TIR step takes more longer. I wanted to concatenate the small contigs into chr0 but i don't know how. Could you help me with this please?

Best, Mergi

mergi-2674 avatar Oct 23 '22 15:10 mergi-2674

Hi Mergi,

You may search around and make your own. For example, you can start from here: https://www.biostars.org/p/379245/

Best, Shujun

oushujun avatar Oct 24 '22 03:10 oushujun