[mira_talk] memory usage

  • From: Dimitar Kenanov <dimitar@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 30 Oct 2012 17:16:48 +0800

Hi Bastien,
i was reading the manual about memory usage and saw that i can use my swap for up to 20% of the needed total memory.

I have 25M PE Illumina reads. So if MIRA is using about 1.5 Gb RAM per 1M reads i need roughly 25*3=75GB RAM. Well i dont have so much :) but i have 64 and i specially made a swap of 32GB RAM. So i would need additional ~ 11GB RAM from the swap which is less then 20% of the total needed.

Do you think i can try MIRA under that circumstances?

And one more technical question i think. Surely there is connection between the length of the reads and the RAM needed. For example the above estimation is for reads which are 100bp (from previous communication). But my reads after the trimming are 64bp. How does this relate to the memory consumption?

Thank you for your time and help.

Last but not least. I already used MIRA 3.9.5 for EST denovo and it was even able to resume from the previous 3.9.4 version without a hitch. It finished correctly also. I am happy :) cos MIRA is my favorite assembler so far. Thank you for the really good work!

Best regards
Dimitar
--
Dimitar Kenanov
Bioinformatician
Tel:+65 6778 6822 (ext 114)
Fax:+65 6778 2962
email: Dimitar@xxxxxxxxxxxxxx


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