8000 resume job ? · Issue #6 · lbcb-sci/ra · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

resume job ? #6

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
ptranvan opened this issue Oct 19, 2019 · 3 comments
Open

resume job ? #6

ptranvan opened this issue Oct 19, 2019 · 3 comments

Comments

@ptranvan
Copy link

Hi,

My job failed due to cluster limit.
Is it possible to resume a job ?

I was at this stage :

[M::main] Version: 2.14-r892-dirty
[M::main] CMD: ra/vendor/minimap2/minimap2 -t 53 -x ava-ont Tpa_nanopore.fastq Tpa_nanopore.fastq
[M::main] Real time: 269685.254 sec; CPU: 11681533.570 sec; Peak RSS: 57.985 GB
[Ra::run] preconstruction stage
[rala::Graph::initialize] loaded sequences
@rvaser
Copy link
rvaser commented Oct 19, 2019

Hello,
the answer is maybe. If the working directory is still there, you could modify the script so that it skips overlap step and uses the old directory. Comment out lines https://github.com/lbcb-sci/ra/blob/master/scripts/ra.py#L53-L68, add the full path to the old working directory here https://github.com/lbcb-sci/ra/blob/master/scripts/ra.py#L25, and run cmake again.

Best regards,
Robert

@ptranvan
Copy link
Author

Thanks for your answer. Yes I still have the old directory.

Before it stops, the step [rala::Graph::initialize] loaded sequences stucked for almost 3 days and the file preconstruction.fasta was empty.

Is it normal ? I have 80X nanopore data and my genome size is 1.2G

@rvaser
Copy link
rvaser commented Oct 19, 2019

Yeah, I had a problem in parsing gzipped files and did not have time to update the old repository. However, this is resolved in our upgraded assembler: https://github.com/lbcb-sci/raven. For both Ra and Raven, you will need RAM equal to the size of sequences plus some epsilon.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@rvaser @ptranvan
0