Updated AftrRAD Parallel Version Draft with Bug Fix Related To Demultiplexed Data

[Mike Sovic]

Hi All,

It seems I introduced a bug in the draft parallel version of AftrRAD that I posted recently.  This bug appears when running the script on data that are already demultiplexed.  Attached is an updated version that will hopefully fix the problem.  Thanks to Bartosz Ulaszewski for bringing this issue to our attention!

                   Mike 

[Bartosz Ulaszewski]

Dear Mike,
After some serious test of the data the script works well. I have one tip, if you use multithreds try to check what the optimal number of cores. From my experaince if you use to much, the Parallel::ForkManager is working abruptly, it can even work when u kill the process from the console. From the Parallel::ForkManager documentation and my experience :) it is a bad idea to run the parallel work in more that one terminal window. The optimal number of cores in my case was '4' wen i tried to run the data on 8, 12 or 16 it was working much slower, probably due to memory limitations.

[Mike Sovic]

Hi Bartosz,

Thanks very much for the feedback!  I don't think we've ever tried running the parallel version simultaneously in multiple windows, so it's good to know this may be a problem.  Not sure that this is exactly related, but based on some recent e-mail conversations we've had with another user who has a very large demultiplexed dataset, we're working on making a few edits that will help reduce RAM requirements, and it's possible these may apply to any memory limitations you've seen too.  I'll hopefully have more details on this in another post soon.

                  Mike