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zhaoyanswill / RAPSearch2

Reduced Alphabet based Protein similarity Search
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How much memory is enough while aligning 3Million reads againt NR database #7

Open rohitasinha opened 10 years ago

rohitasinha commented 10 years ago

How much memory does RAPsearch2 needs to finish alignment of 3Million reads. I allowed 10GB but it failed (using 4 threads) . I think papers suggests max memory required is 4GB

Thanks Rohita

zhaoyanswill commented 10 years ago

Because more and more computers are equipped with larger memory than two years ago, so we added some new features in the updated versions which may consume more memory. On the other hand, memory usage will increase when there are too many hits between queries and references as well. You may consider to use '-s' parameter (e.g., '-s 40' or large number for your 20GB database) while indexing the reference to split database in smaller pieces.

Let me know if you have any questions! Thanks!

Sincerely, Y. Z.

On 08/01/2014 02:01 PM, rohitasinha wrote:

How much memory does RAPsearch2 needs to finish alignment of 3Million reads. I allowed 10GB but it failed (using 4 threads) . I think papers suggests max memory required is 4GB

Thanks Rohita

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/7.