System Error in SPADES during fungal denovo-genome assembly?

Question

[jigarnt]

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

[GenoMax]

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).

[jigarnt]

I have a memory of 64GB RAM.

Is that the reason?

[GenoMax]

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

Answer 1

[ant_genome]

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.

Answer 2

[Govardhan Anande]

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.

Answer 3

[Yanpeng Chen]

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