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meet "not enough memory" problem during SOAPdenovo assembly

Hey guys, I am doing de novo assembly. The data is downloaded from NCBI and they are DNA-seq short paired-end reads, 100bp x 2, about 120G in total. I use SOAPdenovo to assembly them. The k-mer value was set 29. After 10 hours, the server reported like this:

Ran out of memory while applying 13290854152bytes
There may be errors as follows:
1) Not enough memory.
2) The ARRAY may be overrode.
3) The wild pointers.

It was done on a server with 768G RAM and 50T internal storage. I don't know why it ran out of memory while applying 13G data, could anyone explain a little bit? There was no other tasks during the assembly.

Thank you.

assembly genome

Hello,

could you please provide the command you use?

fin swimmer

Not enough memory is probably referring to RAM, not internal storage. How much RAM does the server has?

yes... I misunderstood the concepts. sorry for the mistake. The server's RAM is 768G, with a 50T internal storage.

yes... I misunderstood the concepts. sorry for the mistake. The server's RAM is 768G, with a 50T internal storage.

yes, it's:

SOAPdenovo-127mer all -s ./config_file -K 29 -p 20 -R -o graph_prefix 1 > ass.log 2 > ass.err

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
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Thank you!

1 answer

Did you use the latest version? There was a bug giving the same error in previous versions, see here, they seem to have fixed it in newer versions.

yes, i changed to the latest version and it worked. thank you very much!

Hello Yingzi,

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