Question: SPAdes: <jemalloc>: Error in malloc(): out of memory
0
gravatar for Paul
3.0 years ago by
Paul80
India
Paul80 wrote:

I am working on De-novo assembly of a bacterial genome. While running SPAdes I get this following error.

*********
<jemalloc>: Error in malloc(): out of memory
== Error ==  system call for: "['/root/SPAdes-3.5.0-Linux/bin/hammer',
'/root/spades_AM1_output/corrected/configs/config.info']" finished
abnormally, err code: -6
********

But I am using a system with the following configuration

Thread 16
Memory 16GB
Disk Space 500GB

Please let me what can I do to rectify this error?

ADD COMMENTlink modified 3.0 years ago by h.mon29k • written 3.0 years ago by Paul80
1

Try it on a machine with more memory.

ADD REPLYlink written 3.0 years ago by Devon Ryan95k

How much more?? around 32 GB RAM?

ADD REPLYlink written 3.0 years ago by Paul80
3

¯\ _ (ツ)_/¯ Enough that you don't run out. Alternatively, you could try a different assembler, perhaps something else will be more memory efficient.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Devon Ryan95k

+1 for ¯\ _ (ツ)_/¯

ADD REPLYlink written 2.5 years ago by lakhujanivijay5.0k
1

It depends basically of: How much reads do you have? How long is your genome expected to be? and, in the case of spades, which and how many kmers are you using?, spades_manual you may try: -k 21,33 --careful --only-assembler

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Buffo1.8k

Can you show the command you used, that gave you the error?

ADD REPLYlink written 3.0 years ago by st.ph.n2.5k
3
gravatar for h.mon
3.0 years ago by
h.mon29k
Brazil
h.mon29k wrote:

This is not an answer to your question, but it is very important anyway:

Are you running SPAdes as root? I see it was installed on the /root/ folder, which is really bad practice. By default, the /root/ folder permissions are rwx------ root root, which means only the root user could access this folder. You either changed the /root/ folder default permissions (bad), or you are running SPAdes as root (worst). The only thing you need to do as root are system-wide administrative tasks - do not run everyday stuff as root.

Install SPAdes on your HOME folder:

mkdir -p ~/SPAdes-3.5.0/
cd ~/SPAdes-3.5.0/
[continue with install ...]

Finally, why using such an old version?

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by h.mon29k

Installing the latest version solved the issue... Thanks

ADD REPLYlink written 3.0 years ago by Paul80
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