Question: SPAdes: <jemalloc>: Error in malloc(): out of memory
0
gravatar for Paul
12 months ago by
Paul50
India
Paul50 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 12 months ago by h.mon14k • written 12 months ago by Paul50
1

Try it on a machine with more memory.

ADD REPLYlink written 12 months ago by Devon Ryan79k

How much more?? around 32 GB RAM?

ADD REPLYlink written 12 months ago by Paul50
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 12 months ago • written 12 months ago by Devon Ryan79k

+1 for ¯\ _ (ツ)_/¯

ADD REPLYlink written 6 months ago by Vijay Lakhujani2.1k
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 12 months ago • written 12 months ago by Buffo1.1k

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

ADD REPLYlink written 12 months ago by st.ph.n2.2k
3
gravatar for h.mon
12 months ago by
h.mon14k
Brazil
h.mon14k 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 12 months ago • written 12 months ago by h.mon14k

Installing the latest version solved the issue... Thanks

ADD REPLYlink written 12 months ago by Paul50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2070 users visited in the last hour