bwa mem failed to allocate memory
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7.0 years ago
cmo ▴ 90

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 • 5.4k views
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Are you the only one using that node and how much memory did you request (if this is applicable for your cluster)?

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

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

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