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jyhehir / mobster

For more details about Mobster please see
https://jyhehir.github.io/mobster/index.html
GNU General Public License v3.0
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Multithreading `RefAndMEPairFinder` possible? #22

Open SHuang-Broad opened 5 years ago

SHuang-Broad commented 5 years ago

Hi,

according to my two test runs on a WGS 30X bam, below are the time (in minutes) it takes for each stage, all single threaded

PotentialMEIReadFinder:    76    105
BWA MEM:                   27     28
RefAndMEPairFinder:       351    370
Anchorclusterer:            8     10

RefAndMEPairFinder seems to be the stage that takes the longest time. So I'm wondering if it is possible, at least in theory, to make it multithreaded?

Thanks!

jyhehir commented 5 years ago

I had been attempting to run it per chromosome (via a workflow language) and then combine the results at the end. eg first split the bams per chr and then execute. But this is still ongoing.

SHuang-Broad commented 5 years ago

Ha! Funny that I'm trying to do a similar thing. I have built the docker for Mobster and bundled with MOSAIK or BWA (available here and here, all experimental) and am writing WDL for that.

In writing the WDL and testing it, I noticed the runtime above.

Let me know if there's anything I can help with.