Question: System Error in SPADES during fungal denovo-genome assembly?
1
gravatar for jigarnt
4.3 years ago by
jigarnt30
Canada
jigarnt30 wrote:

Hi All,

I am trying to perform a denovo assembly of my Fungal genome in SPADES. After running for a while, I am getting unexpected error. Can SPADES be incapable of handling bigger genomes (30mb)?

This the error I am getting:

== Error == system call for: "['/Users/lindakohn/Desktop/Tools/SPAdes-3.7.1-Darwin/bin/spades', '/Users/Desktop/European_denovo/K77/configs/config.info']" finished abnormally, err code: -9

assembly software error • 3.6k views
ADD COMMENTlink modified 2.5 years ago by 7640228220 • written 4.3 years ago by jigarnt30
1

How much memory are you using for this job?
E.coli genome requires a peak of ~9GB of RAM so a 30 mb genome will require a proportionately larger amount (default RAM size is 250G, if available).

ADD REPLYlink written 4.3 years ago by genomax85k

I have a memory of 64GB RAM.

Is that the reason?

ADD REPLYlink written 4.3 years ago by jigarnt30
1

I have a feeling that you may not have enough RAM available.

ADD REPLYlink written 4.3 years ago by genomax85k
0
gravatar for ant_genome
4.2 years ago by
ant_genome0
ant_genome0 wrote:

I also get the same problem, however, my RAM is almost 500G, it seem not the problem of RAM, maybe it could not work on large genome.

ADD COMMENTlink written 4.2 years ago by ant_genome0
0
gravatar for Govardhan Anande
4.2 years ago by
Australia
Govardhan Anande130 wrote:

This is not problem with RAM, SPAdes is bacterial genome assembler. So far it assembled 5.3 Mb of genome successfully.

If you want to assemble bigger genome, you can try MaSuRCA or SOAPdenovo.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Govardhan Anande130
0
gravatar for 764022822
2.5 years ago by
7640228220
7640228220 wrote:

Dear all, I have tried to perform a denovo assembly of Virome in metaspades.I got the error code:9?

This is the error == Error == system call for: "['/home/user167/software/SPAdes-3.11.1-Linux/bin/spades', '/home/user167/zhoulong/hongbingduzu/K21/configs/config.info', '/home/user167/zhoulong/hongbingduzu/K21/configs/mda_mode.info', '/home/user167/zhoulong/hongbingduzu/K21/configs/meta_mode.info']" finished abnormally, err code: -9

ADD COMMENTlink written 2.5 years ago by 7640228220
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