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System Error in SPADES during fungal denovo-genome assembly?

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
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updated by Yanpeng Chen • Yanpeng Chen • written by jigarnt • jigarnt

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).

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written by GenoMax GenoMax

I have a memory of 64GB RAM.

Is that the reason?

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written by jigarnt • jigarnt

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

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written by GenoMax GenoMax

3 answers

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.

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written by ant_genome • ant_genome

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.

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written by Govardhan Anande Govardhan Anande

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

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written by Yanpeng Chen • Yanpeng Chen

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