This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Ram Required For Ray-1.4.0

Is there any information on how much RAM is required for Ray to run? I am using Ray-1.4.0 and everytime it crashes after swapping. I am trying to assemble about 30M 100 bp long paired Illumina reads. Is there any way in which RAM usage can be minimized?

Any other suggestions on assembling a Eukaryotic genome?

assembly denovo
• 3,687 views • link
updated by Rob Syme Rob Syme • written by Farhat Farhat

3 answers

There is a -show-memory-usage switch to Ray.

How to assemble a eukaryotic genome is a whole different question that has been discussed elsewhere.

• 0 views • link
written by Martin A Hansen Martin A Hansen

I am aware of that switch. I was wondering if there is a formula or benchmarks that could give expected RAM usage given number of reads, length of reads, coverage etc.

• 0 views • link
written by Farhat Farhat

If I remember correctly, somebody told me that they were using 1T to 1.5T to get a genome assembly in a day (yes, that is 1TB of RAM).

• 0 views • link
written by Pablo Pablo

I can help with some early tests on fungal genomes (which might not be helpful for you) assembled with Ray version: 1.6.0.

Assembled on 8x8 Intel Xeon 2.93 GHz - Nehalem series cores

Genome #1: Estimated genome size ~38MBp. 20 million single-end reads (sorry - oldish data) Assemblies ran in about half an hour.

  • k=47: peak memory usage was 29941MB
  • k=39: peak memory usage was 30211MB
  • k=31: peak memory usage was 19147MB

Genome #2: Estimated genome size ~ 40MBp. 43.5 million paired-end reads (21.8 million pairs)

  • k=27: peak memory usage was 13364MB

I'll try and update later with more memory usage from the second set of reads and some

• 0 views • link
written by Rob Syme Rob Syme

Thanks! That gives some estimates of the RAM involved though I am dealing with an ~1GB genome.

• 0 views • link
written by Farhat Farhat

Log in to answer this question.

More posts like this