assembly restart clarification

[bfoster-lbl]

Hi,
I have a general question regarding megahit assembler. Since it assembles kmers one after another, I was wondering if it is possible to restart a killed assembly and have it run to completion. I ask this because our cluster can have a wallclock limit at which point it will terminate the running job. It would be a nice feature to be able to restart it from where it left off.

Thanks,
bfoster

[voutcn]

Hi bofster,
Thanks for your feedback. Your suggestion make sense to me. It is not a tough job, but I am tied up with other tasks at this stage. I will probably add the this feature to MEGAHIT in one to two weeks.
Dinghua

[bfoster-lbl]

Thanks ... that would be really great.

On Sun, Jan 18, 2015 at 12:46 AM, Dinghua Li notifications@github.com
wrote:

Hi bofster,
Thanks for your feedback. Your suggestion make sense to me. It is not a
tough job, but I am tied up with other tasks at this stage. I will probably
add the this feature to MEGAHIT in one to two weeks.
Dinghua

—
Reply to this email directly or view it on GitHub
#12 (comment).

[voutcn]

bofster,

Please check out the commit 0d6e306 on the branch dev-continue-mode. To continue a interrupted run, please run MEGAHIT with option --continue -o OUTPUT_DIR. I've done several tests on a small dataset with the continue mode. See whether it works for you. I look forward to your feedback.

Cheers,
Dinghua

[bfoster-lbl]

It looks like it is working for me on small datasets too. I will test it on larger sets. This is a great feature!
Would it be possible to be able to specify --continue on the first run also? Maybe disregard the --continue flag if it is a first run? If it were allowed on first run, the user would not have to change the command line at all for resubmission after failure.

[voutcn]

Please try this commit e248ce0
Using --continue on the first run will raise a warning message but switch to the normal mode after then.

[bfoster-lbl]

It looks good to me. -continue mode works on initial run and restarting failures. Thanks!
I did notice it prints 8 messages.(I was using 8 threads)

Cannot find ./megahit_out/opts.txt
Please check whether the output directory is correctly set by "-o"
Now switching to normal mode.
Cannot find ./megahit_out/opts.txt
Please check whether the output directory is correctly set by "-o"
Now switching to normal mode.
Cannot find ./megahit_out/opts.txt
Please check whether the output directory is correctly set by "-o"
Now switching to normal mode.
Cannot find ./megahit_out/opts.txt
....

[voutcn]

Fixed. b97ae36
And fix a bug when using both --continue and --input-cmd. 3f4c93b
The branch of continue mode has been merged to master branch.

[bfoster-lbl]

I downloaded and tried MEGAHIT v0.2.0 master branch. Great release!