time to run ReferenceOpt.sh

[Russell P]

I'm running bash ReferenceOpt.sh 1 9 1 9 PE 40 on a subset of 15 individuals (file sizes ranging from 300 to 700 Mb). It seems to be taking a very long time for any progress. It's been sitting at K1 is 1 K2 is 2 c is 0.08 for over an hour...and it's using all 40 CPUs. I'm watching the processes using 'top' and it ran perl and mawk and now it's running cd-hit-est. I've attached the cd-hit-est log file.

Since I have a limited allotment of time on the computer, I didn't want to waste it if things aren't running properly.

How long should I expect it to take to run to completion? A few hours...or a few days? Am I going about this correctly?

Thanks!!

Russell

[Russell P]

And the kopt.log file attached here.

[Jon Puritz]

Hi Russel,

This is really difficult for me to estimate for you.  I would suggest though, not starting either cutoff value at 1, as this will drastically increase your run time.

Jon

Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

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