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Old 10-21-2013, 05:15 AM   #1
rjoyons
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Location: Manchester

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Default Hardware requirements for metavelvet

Hi everyone,

I just received my very first set of shotgun-metagenomic sequencing results. They are illumina pair ended reads produced using the 2x250bp method. I have 26.5 million reads.

My question is about the memory requirements of metavelvet.. In the manual (http://metavelvet.dna.bio.keio.ac.jp/) it says the program requires "At least 12Gb of RAM (more is no luxury)" But they go onto use a computer with 48Gb of RAM to produce their example data in table 1 and the "required memory" for each assembly in table 1 is up to 72Gb.

I'm finding this quite confusing! What happens when the memory requirement exceeds the amount of RAM on the workstation? Will the program crash or start making temporary files on the hard drive? Can you really use a computer with only 12Gb of RAM?

Any advice would be greatly appreciated!!

Ryan

(originally posted in metagenomics forum but I have moved it to here as it is probably more appropriate!)
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Old 04-15-2014, 09:23 PM   #2
af1a
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Location: Yokohama, Japan

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Default

Hi Ryan,

As my undestanding, higher kmer size, more memory required.
Anyway, if the memory requirements exceed the available RAM, the assembly process will stop and give an error message.

Best regards,
Afia
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