Question: SPAdes running out of ram !!!!
gravatar for elbarchef
11 months ago by
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/']" 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 • 462 views
ADD COMMENTlink modified 11 months ago by colindaven2.2k • written 11 months ago by elbarchef10

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 11 months ago by ATpoint35k
gravatar for jared.andrews07
11 months ago by
St. Louis, MO
jared.andrews075.5k 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 11 months ago by jared.andrews075.5k
gravatar for colindaven
11 months ago by
Hannover Medical School
colindaven2.2k 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 11 months ago by colindaven2.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 899 users visited in the last hour