Platanus only use single thread

Question

[Corentin]

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

Answer 1

[colindaven]

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.

[Corentin]

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.

[Karyo]

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

[colindaven]

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

[vineet.upadhayay03]

Is it over yet ??