Skip to content

setup for large genome assembly #848

@ersgupta

Description

@ersgupta

I am using canu 1.7 for assembling a genome of ~1.4gb size with ~70X pacbio data.
canu -p canu -d canu-pacbio useGrid=false maxThreads=60 maxMemory=500 genomeSize=1.4g -pacbio-raw file1 ....

I have the following queries:

  1. What would be the expected runtime? I have few nodes with 1tb RAM and >100 cores (ofcourse there are other users also). For now I run on single node specifying the options above.
  2. How much disk space can I expect it to occupy?
  3. I have not run this using the grid option, as I am not sure how much load this would put on the headnode, I use PBS. Any advise for this?
  4. Are there any other recommended parameters which I should change for my setup?

Thanks :)

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions