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Platanus only use single thread

Hi,

I am currently trying to assemble a heterozygous plant genome (estimated size 1 Gbp).

I wanted to try "Platanus" (http://platanus.bio.titech.ac.jp/), I launched the "Platanus assemble" command with 80 threads, but now, at the "connecting kmers..." step it only uses one. It has run for several days now,

Does seomeone else had the same issue ?

Regards, Corentin

assembly platanus performance
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updated by vineet.upadhayay03 • vineet.upadhayay03 • written by Corentin Corentin

1 answer

You need to have a lot of patience for genome assembly. Most tools have steps where only one thread is used, ie. for initial IO or steps which have not yet been parallelized.

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written by colindaven colindaven

Yes, that what I expected. But I was just thinking that the de Bruijn graph construction would be parallelized, maybe it is not implemented yet.

• 1 views • link
written by Corentin Corentin

Thank you for the comment. I am experiencing the same problem... But how much patience? one day? more than three days?

• 0 views • link
written by Karyo • Karyo

Depends on your genome and amount of data. Some programs take weeks. Just keep checking the tool is reading and writing data, eg with the tools htop, glances, gotop, ls -lrth etc

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written by colindaven colindaven

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