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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Out of Memory Issue #1167

Open magcurly opened 1 year ago

magcurly commented 1 year ago

Description of bug

I am trying to run meta-spades on a virome sample. I found that after showing the mimalloc: warning: unable to allocate from region: size 4194304, the virtual memory started to explode to a very large amount. Besides, the actual usage of RAM seemed to be just one third of the virtual memory usage. I looked up solutions in issue lists and I found one of the solution which is changing the system parameter vm.max_map_count. It's unlikely to do such setting when using HPC, since it's impossible to get a root access from the administrator. I wonder if you can make some improvements in RAM usage other than changing system parameters or requiring root access. Besides, it would be better if it's possible to set a length threshold on contigs then it may be able to lower the usage of RAM since short fragments are all removed from the assembly.

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes v3.15.5

Operating System

CentOS 7

Python Version

python 3.10.12

Method of SPAdes installation

mamba

No errors reported in spades.log

mdMoinuddinSheam commented 11 months ago

Did you manage to fix that

anbadilla commented 6 months ago

I'm experiencing the same issue as you -did you resolve it?

tiagobrc commented 3 months ago

I have those warnings too, but so far it is still running.