Question: meet "not enough memory" problem during SOAPdenovo assembly
1
gravatar for Yingzi Zhang
7 weeks ago by
Yingzi Zhang30
Beijing
Yingzi Zhang30 wrote:

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 • 205 views
ADD COMMENTlink modified 7 weeks ago by b.nota4.6k • written 7 weeks ago by Yingzi Zhang30

Hello,

could you please provide the command you use?

fin swimmer

ADD REPLYlink written 7 weeks ago by finswimmer4.5k

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

ADD REPLYlink written 7 weeks ago by b.nota4.6k

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

ADD REPLYlink written 7 weeks ago by Yingzi Zhang30

yes, it's:

SOAPdenovo-127mer all -s ./config_file -K 29 -p 20 -R -o graph_prefix 1 > ass.log 2 > ass.err
ADD REPLYlink modified 7 weeks ago by genomax54k • written 7 weeks ago by Yingzi Zhang30

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

Thank you!

ADD REPLYlink written 7 weeks ago by genomax54k

copy that. thank you

ADD REPLYlink written 7 weeks ago by Yingzi Zhang30
2
gravatar for b.nota
7 weeks ago by
b.nota4.6k
Netherlands
b.nota4.6k wrote:

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.

ADD COMMENTlink written 7 weeks ago by b.nota4.6k

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

ADD REPLYlink written 7 weeks ago by Yingzi Zhang30

Hello Yingzi,

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted.

Upvote|Bookmark|Accept

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by finswimmer4.5k
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