[OMA] If my jobs stop (SGE) will the results be conserved (AllvsAll) in the cache folder ?

Question

[pourbiostars]

Hi,

I would like to know if the jobs are stopped because they're overruning the SGE server where i'm working on limit time, the results generated are conserved and not overwrited ?

To be more precise: If I re-run the same job, will OMA take in count that some results are still here, and will continue to the next step ? I assume that from the sentence seen in the tutorial:

http://omabrowser.org/standalone/#usage

" Adding/Updating new genomes

It is possible to add new genomes without recomputing the all-against-all phase for pre-existing genomes. To do so, simply add the new fasta databases in the DB/ directory and re-run OMA. Likewise, it is possible to update a genome by deleting the old genome from the DB/ directory, and adding a new file. Important: to avoid clashes with previously computed results, the updated genome must use a different filename than any previously computed result."

But I want to be sure !

Thanks a lot !

Answer 1

[Christophe Dessimoz]

The work chunks that have finished computing will be reused—it does not matter what job scheduler you used or if you even used one in the first place. These are the gzipped files in the Cache/AllAll folder.

However, if the SGE run was interrupted, there might be some chunks that are incomplete and thus will appear as "in-progress" to the new run but really aren't been worked on any longer. This also happens if a single job dies prematurely for whatever reason. If you have no instance of OMA running, these are the uncompressed files in Cache/AllAll.

So the trick is to make sure to delete these incomplete files before restarting a new run.

Answer 2

[pourbiostars]

It works great ! Thanks a lot !