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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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out of memory ? #87

Closed xiaoyezao closed 5 years ago

xiaoyezao commented 5 years ago

Hi, I am running wtdbg2 on a 24-core node:

-- total memory 132009044.0 kB -- available 130766524.0 kB -- 24 cores -- Starting program: /BIGDATA1/wbgcas_tfeng_1/app/wtdbg2//wtdbg2 -x sq -t 0 -i *.gz

after the stage "scanning kmers", the program exits reporting:

[Tue Mar 19 21:06:42 2019] - high frequency kmer depth is set to 3970 -- Out of memory, try to allocate 107374182400 bytes, old size 256, old addr 0x226bc50 in encap_list -- mem_share.h:219 --

however, the suggested memory " 107374182400 bytes " does not exceed the node memory.

what's going wrong here?

ruanjue commented 5 years ago

Program try to alloc addtional 100G RAM.