Question: SPAdes running out of ram !!!!
1
gravatar for elbarchef
4 months ago by
elbarchef10
elbarchef10 wrote:

Hello guys,

  1. i install ubuntu next to windows to use SPAdes which works just under linux but when i run this software it returns this error -> == Error == system call for: "['/usr/lib/spades/bin/spades', '/home/spades_test/K55/configs/config.info']" finished abnormally, err code: -11
  2. when I contacted support Spades, they sent me this mail, but I still can't solve the problem: Memory limit (in Gb): 3 So, you're likely running out of RAM. I doubt you could do any useful assembly having such low amount of RAM.
  3. when i tap free -h i have this result! image
assembly • 274 views
ADD COMMENTlink modified 4 months ago by colindaven1.8k • written 4 months ago by elbarchef10
1

It of course depends on multiple factors how much RAM the tool needs but if you google around you find posts from people reporting the same issues even on bigger HPC nodes with dozens or hundreds of GB RAM. A laptop is certainly not suitable to do genomic assemblies. Either check if your institution provides access to a computing cluster, or check if Galaxy can offer what you need. If both fails, you probably need to check cloud services such as AWS to perform your analysis.

ADD REPLYlink written 4 months ago by ATpoint25k
4
gravatar for jared.andrews07
4 months ago by
jared.andrews073.9k
St. Louis, MO
jared.andrews073.9k wrote:

Well, they told you the issue - your computer doesn't have enough memory to run the software on your data. 4 GB of memory is very little for bioinformatics analysis. Adding more to your PC or using a PC/computing cluster with more is likely going to be necessary.

ADD COMMENTlink written 4 months ago by jared.andrews073.9k
2
gravatar for colindaven
4 months ago by
colindaven1.8k
Hannover Medical School
colindaven1.8k wrote:

One alternative is to use Spades on one of the usegalaxy servers. It's free and they have compute clusters with plenty of RAM.

ADD COMMENTlink written 4 months ago by colindaven1.8k
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