Question: bwa mem failed to allocate memory
1
gravatar for cmo
6.0 years ago by
cmo60
United States
cmo60 wrote:

I am aligning a modest number of short reads (10.5 M) to a large genome (~4 Gb) with bwa mem .  I expect a high error rate and expect many multiply mapping reads, so I relax some of the parameters as follows:

bwa mem  -t 32 -k 15  -r 1.25  -c 100000000  -B 1  -O 0  -E 1  -L 500  -T 12

I keep getting errors related to memory allocation

[M::process] read 4529482 sequences (320000032 bp)...
[M::process] read 3965734 sequences (279216556 bp)...
[mem_chain2aln] Failed to allocate 22528 bytes at bwamem.c line 715: Cannot allocate memory
[mem_chain2aln] Failed to allocate 22528 bytes at bwamem.c line 715: Cannot allocate memory
[mem_chain2aln] Failed to allocate 22528 bytes at bwamem.c line 715: Cannot allocate memory
[mem_chain2aln] Failed to allocate 22528 bytes at bwamem.c line 715: Cannot allocate memory

 

This process is running on a 16-core node (32 with hyperthreading) with 128 GB memory and ~1 TB disk space.

How can it be running out of memory?

 

bwa memory allocate bwa-mem • 4.8k views
ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by cmo60

Are you the only one using that node and how much memory did you request (if this is applicable for your cluster)?

ADD REPLYlink written 6.0 years ago by Devon Ryan98k

Good point Devon.  Yes, i allocated the whole node, so it is all mine.

ADD REPLYlink written 6.0 years ago by cmo60

Hi, did you this error get fixed? I'm working on a project at the moment and I'm having the same issues.

ADD REPLYlink written 4.2 years ago by dyogoborst0
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