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dzerbino / velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829
https://europepmc.org/article/pmc/2336801
GNU General Public License v2.0
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rerunning velvetg #40

Closed Koorvo closed 6 years ago

Koorvo commented 6 years ago

Hello and sorry if that question looks stupid, I'm newbie not only with velvet.

I have searched for that in biostar and other forums.

My problem is about rerun velvet jobs, specially velvetg. For example I ran this command which demands a lot of RAM:

velvetg dir_27 -read_trkg yes -ins_length 240 1>dir_27.log 2>dir_27.err

To run that I need 700GB of RAM so I have to use HPC resources froma server, and obviusly I have to reserve time.

My question is, can I recover a job of velvetg which stop cause to timeout? because when I rerun the command it just overwrite the previous output.

Thank you

dzerbino commented 6 years ago

Hello @Koorvo ,

Sincere apologies for the delay in answering. No, Velvet has no timepointing functionalities so interrupted jobs needs to be started again.

Cheers,

Daniel